Daily Papers

In the conventional cellular system, devices are not allowed to communicate directly with each other in the licensed cellular bandwidth and all communications take place through the base stations. The users requirements has led the technology to become fast and faster. Multimedia rich data exchange, fast service, high quality voice calls, newer and more demanding applications, information at fingertips, everything requires technology and communication between devices. A constant need to increase network capacity for meeting the users growing demands has led to the growth of cellular communication networks from the first generation(1G) to the fifth generation(5G). There will be crores of connected devices in the coming future . A large number of connections are going to be heterogeneous, demanding lesser delays, higher data rates, superior throughput and enhanced system capacity. The available spectrum resources are limited and has to be flexibly used by mobile network operators to cope with the rising demands. An emerging facilitator of the upcoming high data rate demanding next-generation networks are device-to-device(D2D) communication. This paper has developed a model that establishes Device-to-Device (D2D) communication between two end-users without involving the eNB (evolved Node B). We have sharded the UEs and CUs based on the criteria of DISTANCE. To do so, we used the K-means clustering method.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

We introduce **EvoGraph**, a framework that enables software systems to evolve their own source code, build pipelines, documentation, and tickets. EvoGraph represents every artefact in a typed directed graph, applies learned mutation operators driven by specialized small language models (SLMs), and selects survivors with a multi-objective fitness. On three benchmarks, EvoGraph fixes 83% of known security vulnerabilities, translates COBOL to Java with 93% functional equivalence (test verified), and maintains documentation freshness within two minutes. Experiments show a 40% latency reduction and a sevenfold drop in feature lead time compared with strong baselines. We extend our approach to **evoGraph**, leveraging language-specific SLMs for modernizing .NET, Lisp, CGI, ColdFusion, legacy Python, and C codebases, achieving 82-96% semantic equivalence across languages while reducing computational costs by 90% compared to large language models. EvoGraph's design responds to empirical failure modes in legacy modernization, such as implicit contracts, performance preservation, and integration evolution. Our results suggest a practical path toward Software 3.0, where systems adapt continuously yet remain under measurable control.

Recent advances in LLM-guided evolutionary computation, particularly AlphaEvolve (Novikov et al., 2025; Georgiev et al., 2025), have demonstrated remarkable success in discovering novel mathematical constructions and solving challenging optimization problems. However, the high-level descriptions in published work leave many implementation details unspecified, hindering reproducibility and further research. In this report we present GigaEvo, an extensible open-source framework that enables researchers to study and experiment with hybrid LLM-evolution approaches inspired by AlphaEvolve. Our system provides modular implementations of key components: MAP-Elites quality-diversity algorithms, asynchronous DAG-based evaluation pipelines, LLM-driven mutation operators with insight generation and bidirectional lineage tracking, and flexible multi-island evolutionary strategies. In order to assess reproducibility and validate our implementation we evaluate GigaEvo on challenging problems from the AlphaEvolve paper: Heilbronn triangle placement, circle packing in squares, and high-dimensional kissing numbers. The framework emphasizes modularity, concurrency, and ease of experimentation, enabling rapid prototyping through declarative configuration. We provide detailed descriptions of system architecture, implementation decisions, and experimental methodology to support further research in LLM driven evolutionary methods. The GigaEvo framework and all experimental code are available at https://github.com/AIRI-Institute/gigaevo-core.

The effort devoted to hand-crafting neural network image classifiers has motivated the use of architecture search to discover them automatically. Although evolutionary algorithms have been repeatedly applied to neural network topologies, the image classifiers thus discovered have remained inferior to human-crafted ones. Here, we evolve an image classifier---AmoebaNet-A---that surpasses hand-designs for the first time. To do this, we modify the tournament selection evolutionary algorithm by introducing an age property to favor the younger genotypes. Matching size, AmoebaNet-A has comparable accuracy to current state-of-the-art ImageNet models discovered with more complex architecture-search methods. Scaled to larger size, AmoebaNet-A sets a new state-of-the-art 83.9% / 96.6% top-5 ImageNet accuracy. In a controlled comparison against a well known reinforcement learning algorithm, we give evidence that evolution can obtain results faster with the same hardware, especially at the earlier stages of the search. This is relevant when fewer compute resources are available. Evolution is, thus, a simple method to effectively discover high-quality architectures.

Evolution, the engine behind the survival and growth of life on Earth, operates through the population-based process of reproduction. Inspired by this principle, this paper formally defines a newly emerging problem -- the population-based evolution of large language models (LLMs) -- and introduces a novel framework. Starting with a population of parent LLMs, our framework enables the population to evolve through four key operations: (i) crossover, merging the weights of different parents to create offspring LLMs, (ii) mutation, introducing small, random changes to model weights to foster diversity, (iii) selection, prioritizing high-performing models, and (iv) succession, transferring the learned experience from parent to offspring LLMs. With only 200 samples per new task, the LLM population evolves rapidly to adapt to the task at hand, without any gradients. Experiments on 12 datasets show that our framework consistently outperforms existing multi-LLM merging and adaptation methods, achieving accuracy gains of up to 54.8% over the best LLM in the initial population. Moreover, our framework allows for the evolution of LLMs across multiple new tasks simultaneously, scaling effectively with populations of up to 40 LLMs, and even zero-shot generalization to unseen held-out tasks. We have open-sourced the code on GitHub and released the weights of 10 parent LLMs, fine-tuned from gemma-2-2b-it, on HuggingFace$, enabling reproduction of our proposed framework using just a single 4090 GPU with 24GB memory, without any performance degradation.

We introduce EvoGit, a decentralized multi-agent framework for collaborative software development driven by autonomous code evolution. EvoGit deploys a population of independent coding agents, each proposing edits to a shared codebase without centralized coordination, explicit message passing, or shared memory. Instead, all coordination emerges through a Git-based phylogenetic graph that tracks the full version lineage and enables agents to asynchronously read from and write to the evolving code repository. This graph-based structure supports fine-grained branching, implicit concurrency, and scalable agent interaction while preserving a consistent historical record. Human involvement is minimal but strategic: users define high-level goals, periodically review the graph, and provide lightweight feedback to promote promising directions or prune unproductive ones. Experiments demonstrate EvoGit's ability to autonomously produce functional and modular software artifacts across two real-world tasks: (1) building a web application from scratch using modern frameworks, and (2) constructing a meta-level system that evolves its own language-model-guided solver for the bin-packing optimization problem. Our results underscore EvoGit's potential to establish a new paradigm for decentralized, automated, and continual software development. EvoGit is open-sourced at https://github.com/BillHuang2001/evogit.

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at https://github.com/IBM/EvolveGCN.

Multi-turn-to-single-turn (M2S) compresses iterative red-teaming into one structured prompt, but prior work relied on a handful of manually written templates. We present X-Teaming Evolutionary M2S, an automated framework that discovers and optimizes M2S templates through language-model-guided evolution. The system pairs smart sampling from 12 sources with an LLM-as-judge inspired by StrongREJECT and records fully auditable logs. Maintaining selection pressure by setting the success threshold to theta = 0.70, we obtain five evolutionary generations, two new template families, and 44.8% overall success (103/230) on GPT-4.1. A balanced cross-model panel of 2,500 trials (judge fixed) shows that structural gains transfer but vary by target; two models score zero at the same threshold. We also find a positive coupling between prompt length and score, motivating length-aware judging. Our results demonstrate that structure-level search is a reproducible route to stronger single-turn probes and underscore the importance of threshold calibration and cross-model evaluation. Code, configurations, and artifacts are available at https://github.com/hyunjun1121/M2S-x-teaming.

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -- or codes -- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

Machine learning research has advanced in multiple aspects, including model structures and learning methods. The effort to automate such research, known as AutoML, has also made significant progress. However, this progress has largely focused on the architecture of neural networks, where it has relied on sophisticated expert-designed layers as building blocks---or similarly restrictive search spaces. Our goal is to show that AutoML can go further: it is possible today to automatically discover complete machine learning algorithms just using basic mathematical operations as building blocks. We demonstrate this by introducing a novel framework that significantly reduces human bias through a generic search space. Despite the vastness of this space, evolutionary search can still discover two-layer neural networks trained by backpropagation. These simple neural networks can then be surpassed by evolving directly on tasks of interest, e.g. CIFAR-10 variants, where modern techniques emerge in the top algorithms, such as bilinear interactions, normalized gradients, and weight averaging. Moreover, evolution adapts algorithms to different task types: e.g., dropout-like techniques appear when little data is available. We believe these preliminary successes in discovering machine learning algorithms from scratch indicate a promising new direction for the field.

Recent advancements in generation models have showcased remarkable capabilities in generating fantastic content. However, most of them are trained on proprietary high-quality data, and some models withhold their parameters and only provide accessible application programming interfaces (APIs), limiting their benefits for downstream tasks. To explore the feasibility of training a text-to-image generation model comparable to advanced models using publicly available resources, we introduce EvolveDirector. This framework interacts with advanced models through their public APIs to obtain text-image data pairs to train a base model. Our experiments with extensive data indicate that the model trained on generated data of the advanced model can approximate its generation capability. However, it requires large-scale samples of 10 million or more. This incurs significant expenses in time, computational resources, and especially the costs associated with calling fee-based APIs. To address this problem, we leverage pre-trained large vision-language models (VLMs) to guide the evolution of the base model. VLM continuously evaluates the base model during training and dynamically updates and refines the training dataset by the discrimination, expansion, deletion, and mutation operations. Experimental results show that this paradigm significantly reduces the required data volume. Furthermore, when approaching multiple advanced models, EvolveDirector can select the best samples generated by them to learn powerful and balanced abilities. The final trained model Edgen is demonstrated to outperform these advanced models. The code and model weights are available at https://github.com/showlab/EvolveDirector.

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Thought" (EoT) technique further enhances GE by enabling LLMs to reflect on and learn from the outcomes of previous mutations. This results in a self-sustaining feedback loop that augments decision-making in model evolution. GE maintains genetic diversity, crucial for evolutionary algorithms, by leveraging LLMs' capability to generate diverse responses from expertly crafted prompts and modulate model temperature. This not only accelerates the evolution process but also injects expert like creativity and insight into the process. Our application of GE in evolving the ExquisiteNetV2 model demonstrates its efficacy: the LLM-driven GE autonomously produced variants with improved accuracy, increasing from 92.52% to 93.34%, without compromising model compactness. This underscores the potential of LLMs to accelerate the traditional model design pipeline, enabling models to autonomously evolve and enhance their own designs.

Recent advances in multimodal large language models (MLLMs) have shown impressive reasoning capabilities. However, further enhancing existing MLLMs necessitates high-quality vision-language datasets with carefully curated task complexities, which are both costly and challenging to scale. Although recent self-improving models that iteratively refine themselves offer a feasible solution, they still suffer from two core challenges: (i) most existing methods augment visual or textual data separately, resulting in discrepancies in data complexity (e.g., over-simplified diagrams paired with redundant textual descriptions); and (ii) the evolution of data and models is also separated, leading to scenarios where models are exposed to tasks with mismatched difficulty levels. To address these issues, we propose C2-Evo, an automatic, closed-loop self-improving framework that jointly evolves both training data and model capabilities. Specifically, given a base dataset and a base model, C2-Evo enhances them by a cross-modal data evolution loop and a data-model evolution loop. The former loop expands the base dataset by generating complex multimodal problems that combine structured textual sub-problems with iteratively specified geometric diagrams, while the latter loop adaptively selects the generated problems based on the performance of the base model, to conduct supervised fine-tuning and reinforcement learning alternately. Consequently, our method continuously refines its model and training data, and consistently obtains considerable performance gains across multiple mathematical reasoning benchmarks. Our code, models, and datasets will be released.

The complete connectome of the Drosophila larva brain offers a unique opportunity to investigate whether biologically evolved circuits can support artificial intelligence. We convert this wiring diagram into a Biological Processing Unit (BPU), a fixed recurrent network derived directly from synaptic connectivity. Despite its modest size 3,000 neurons and 65,000 weights between them), the unmodified BPU achieves 98% accuracy on MNIST and 58% on CIFAR-10, surpassing size-matched MLPs. Scaling the BPU via structured connectome expansions further improves CIFAR-10 performance, while modality-specific ablations reveal the uneven contributions of different sensory subsystems. On the ChessBench dataset, a lightweight GNN-BPU model trained on only 10,000 games achieves 60% move accuracy, nearly 10x better than any size transformer. Moreover, CNN-BPU models with ~2M parameters outperform parameter-matched Transformers, and with a depth-6 minimax search at inference, reach 91.7% accuracy, exceeding even a 9M-parameter Transformer baseline. These results demonstrate the potential of biofidelic neural architectures to support complex cognitive tasks and motivate scaling to larger and more intelligent connectomes in future work.

Large Transformer models are capable of implementing a plethora of so-called in-context learning algorithms. These include gradient descent, classification, sequence completion, transformation, and improvement. In this work, we investigate whether large language models (LLMs), which never explicitly encountered the task of black-box optimization, are in principle capable of implementing evolutionary optimization algorithms. While previous works have solely focused on language-based task specification, we move forward and focus on the zero-shot application of LLMs to black-box optimization. We introduce a novel prompting strategy, consisting of least-to-most sorting of discretized population members and querying the LLM to propose an improvement to the mean statistic, i.e. perform a type of black-box recombination operation. Empirically, we find that our setup allows the user to obtain an LLM-based evolution strategy, which we call `EvoLLM', that robustly outperforms baseline algorithms such as random search and Gaussian Hill Climbing on synthetic BBOB functions as well as small neuroevolution tasks. Hence, LLMs can act as `plug-in' in-context recombination operators. We provide several comparative studies of the LLM's model size, prompt strategy, and context construction. Finally, we show that one can flexibly improve EvoLLM's performance by providing teacher algorithm information via instruction fine-tuning on previously collected teacher optimization trajectories.

In this work, we introduce CodeEvolve, an open-source evolutionary coding agent that unites Large Language Models (LLMs) with genetic algorithms to solve complex computational problems. Our framework adapts powerful evolutionary concepts to the LLM domain, building upon recent methods for generalized scientific discovery. CodeEvolve employs an island-based genetic algorithm to maintain population diversity and increase throughput, introduces a novel inspiration-based crossover mechanism that leverages the LLMs context window to combine features from successful solutions, and implements meta-prompting strategies for dynamic exploration of the solution space. We conduct a rigorous evaluation of CodeEvolve on a subset of the mathematical benchmarks used to evaluate Google DeepMind's closed-source AlphaEvolve. Our findings show that our method surpasses AlphaEvolve's performance on several challenging problems. To foster collaboration and accelerate progress, we release our complete framework as an open-source repository.

Given the recent impressive accomplishments of language models (LMs) for code generation, we explore the use of LMs as adaptive mutation and crossover operators for an evolutionary neural architecture search (NAS) algorithm. While NAS still proves too difficult a task for LMs to succeed at solely through prompting, we find that the combination of evolutionary prompt engineering with soft prompt-tuning, a method we term EvoPrompting, consistently finds diverse and high performing models. We first demonstrate that EvoPrompting is effective on the computationally efficient MNIST-1D dataset, where EvoPrompting produces convolutional architecture variants that outperform both those designed by human experts and naive few-shot prompting in terms of accuracy and model size. We then apply our method to searching for graph neural networks on the CLRS Algorithmic Reasoning Benchmark, where EvoPrompting is able to design novel architectures that outperform current state-of-the-art models on 21 out of 30 algorithmic reasoning tasks while maintaining similar model size. EvoPrompting is successful at designing accurate and efficient neural network architectures across a variety of machine learning tasks, while also being general enough for easy adaptation to other tasks beyond neural network design.

Advances in Large Language Models (LLMs) have enabled a new class of self-evolving agents that autonomously improve through interaction with the environment, demonstrating strong capabilities. However, self-evolution also introduces novel risks overlooked by current safety research. In this work, we study the case where an agent's self-evolution deviates in unintended ways, leading to undesirable or even harmful outcomes. We refer to this as Misevolution. To provide a systematic investigation, we evaluate misevolution along four key evolutionary pathways: model, memory, tool, and workflow. Our empirical findings reveal that misevolution is a widespread risk, affecting agents built even on top-tier LLMs (e.g., Gemini-2.5-Pro). Different emergent risks are observed in the self-evolutionary process, such as the degradation of safety alignment after memory accumulation, or the unintended introduction of vulnerabilities in tool creation and reuse. To our knowledge, this is the first study to systematically conceptualize misevolution and provide empirical evidence of its occurrence, highlighting an urgent need for new safety paradigms for self-evolving agents. Finally, we discuss potential mitigation strategies to inspire further research on building safer and more trustworthy self-evolving agents. Our code and data are available at https://github.com/ShaoShuai0605/Misevolution . Warning: this paper includes examples that may be offensive or harmful in nature.

Noise is a ubiquitous feature of the physical world. As a result, the first prerequisite of life is fault tolerance: maintaining integrity of state despite external bombardment. Recent experimental advances have revealed that biological systems achieve fault tolerance by implementing mathematically intricate error-correcting codes and by organizing in a modular fashion that physically separates functionally distinct subsystems. These elaborate structures represent a vanishing volume in the massive genetic configuration space. How is it possible that the primitive process of evolution, by which all biological systems evolved, achieved such unusual results? In this work, through experiments in Boolean networks, we show that the simultaneous presence of error correction and modularity in biological systems is no coincidence. Rather, it is a typical co-occurrence in noisy dynamic systems undergoing evolution. From this, we deduce the principle of error correction enhanced evolvability: systems possessing error-correcting codes are more effectively improved by evolution than those without.

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Recent advancements in prompt engineering strategies, such as Chain-of-Thought (CoT) and Self-Discover, have demonstrated significant potential in improving the reasoning abilities of Large Language Models (LLMs). However, these state-of-the-art (SOTA) prompting strategies rely on single or fixed set of static seed reasoning modules like "think step by step" or "break down this problem" intended to simulate human approach to problem-solving. This constraint limits the flexibility of models in tackling diverse problems effectively. In this paper, we introduce Auto-Evolve, a novel framework that enables LLMs to self-create dynamic reasoning modules and downstream action plan, resulting in significant improvements over current SOTA methods. We evaluate Auto-Evolve on the challenging BigBench-Hard (BBH) dataset with Claude 2.0, Claude 3 Sonnet, Mistral Large, and GPT 4, where it consistently outperforms the SOTA prompt strategies. Auto-Evolve outperforms CoT by up to 10.4% and on an average by 7% across these four models. Our framework introduces two innovations: a) Auto-Evolve dynamically generates reasoning modules for each task while aligning with human reasoning paradigm, thus eliminating the need for predefined templates. b) We introduce an iterative refinement component, that incrementally refines instruction guidance for LLMs and helps boost performance by average 2.8% compared to doing it in a single step.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models nucleotide evolution on phylogenetic trees using multispecies whole-genome alignments. Our approach integrates an alignment into the loss function during training but does not require it for making predictions, thereby enhancing the model's applicability. We applied this framework to train PhyloGPN, a model that excels at predicting functionally disruptive variants from a single sequence alone and demonstrates strong transfer learning capabilities.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Most graph neural network models learn embeddings of nodes in static attributed graphs for predictive analysis. Recent attempts have been made to learn temporal proximity of the nodes. We find that real dynamic attributed graphs exhibit complex co-evolution of node attributes and graph structure. Learning node embeddings for forecasting change of node attributes and birth and death of links over time remains an open problem. In this work, we present a novel framework called CoEvoGNN for modeling dynamic attributed graph sequence. It preserves the impact of earlier graphs on the current graph by embedding generation through the sequence. It has a temporal self-attention mechanism to model long-range dependencies in the evolution. Moreover, CoEvoGNN optimizes model parameters jointly on two dynamic tasks, attribute inference and link prediction over time. So the model can capture the co-evolutionary patterns of attribute change and link formation. This framework can adapt to any graph neural algorithms so we implemented and investigated three methods based on it: CoEvoGCN, CoEvoGAT, and CoEvoSAGE. Experiments demonstrate the framework (and its methods) outperform strong baselines on predicting an entire unseen graph snapshot of personal attributes and interpersonal links in dynamic social graphs and financial graphs.

Population-based search has recently emerged as a possible alternative to Reinforcement Learning (RL) for black-box neural architecture search (NAS). It performs well in practice even though it is not theoretically well understood. In particular, whereas traditional population-based search methods such as evolutionary algorithms (EAs) draw much power from crossover operations, it is difficult to take advantage of them in NAS. The main obstacle is believed to be the permutation problem: The mapping between genotype and phenotype in traditional graph representations is many-to-one, leading to a disruptive effect of standard crossover. This paper presents the first theoretical analysis of the behaviors of mutation, crossover and RL in black-box NAS, and proposes a new crossover operator based on the shortest edit path (SEP) in graph space. The SEP crossover is shown theoretically to overcome the permutation problem, and as a result, have a better expected improvement compared to mutation, standard crossover and RL. Further, it empirically outperform these other methods on state-of-the-art NAS benchmarks. The SEP crossover therefore allows taking full advantage of population-based search in NAS, and the underlying theory can serve as a foundation for deeper understanding of black-box NAS methods in general.

Despite exceptional capabilities in knowledge-intensive tasks, Large Language Models (LLMs) face a critical gap in understanding how they internalize new knowledge, particularly how to structurally embed acquired knowledge in their neural computations. We address this issue through the lens of knowledge circuit evolution, identifying computational subgraphs that facilitate knowledge storage and processing. Our systematic analysis of circuit evolution throughout continual pre-training reveals several key findings: (1) the acquisition of new knowledge is influenced by its relevance to pre-existing knowledge; (2) the evolution of knowledge circuits exhibits a distinct phase shift from formation to optimization; (3) the evolution of knowledge circuits follows a deep-to-shallow pattern. These insights not only advance our theoretical understanding of the mechanisms of new knowledge acquisition in LLMs, but also provide potential implications for improving continual pre-training strategies to enhance model performance. Code and data will be available at https://github.com/zjunlp/DynamicKnowledgeCircuits.

Network Architecture Search and specifically Regularized Evolution is a common way to refine the structure of a deep learning model.However, little is known about how models empirically evolve over time which has design implications for designing caching policies, refining the search algorithm for particular applications, and other important use cases.In this work, we algorithmically analyze and quantitatively characterize the patterns of model evolution for a set of models from the Candle project and the Nasbench-201 search space.We show how the evolution of the model structure is influenced by the regularized evolution algorithm. We describe how evolutionary patterns appear in distributed settings and opportunities for caching and improved scheduling. Lastly, we describe the conditions that affect when particular model architectures rise and fall in popularity based on their frequency of acting as a donor in a sliding window.

The NeuroEvolution of Augmenting Topologies (NEAT) algorithm has received considerable recognition in the field of neuroevolution. Its effectiveness is derived from initiating with simple networks and incrementally evolving both their topologies and weights. Although its capability across various challenges is evident, the algorithm's computational efficiency remains an impediment, limiting its scalability potential. In response, this paper introduces a tensorization method for the NEAT algorithm, enabling the transformation of its diverse network topologies and associated operations into uniformly shaped tensors for computation. This advancement facilitates the execution of the NEAT algorithm in a parallelized manner across the entire population. Furthermore, we develop TensorNEAT, a library that implements the tensorized NEAT algorithm and its variants, such as CPPN and HyperNEAT. Building upon JAX, TensorNEAT promotes efficient parallel computations via automated function vectorization and hardware acceleration. Moreover, the TensorNEAT library supports various benchmark environments including Gym, Brax, and gymnax. Through evaluations across a spectrum of robotics control environments in Brax, TensorNEAT achieves up to 500x speedups compared to the existing implementations such as NEAT-Python. Source codes are available at: https://github.com/EMI-Group/tensorneat.

Developing Large Language Model (LLM) agents that exhibit human-like behavior, encompassing not only individual heterogeneity rooted in unique user profiles but also adaptive response to socially connected neighbors, is a significant research challenge. Social media platforms, with their diverse user data and explicit social structures, provide an ideal testbed for such investigations. This paper introduces EvoBot, an Evolving LLM-based social Bot that significantly enhances human-like generative capabilities through a novel adversarial learning framework. EvoBot is initialized by Supervised Fine-Tuning (SFT) on representative data from social media and then iteratively refines its generation of sophisticated, human-like content via Direct Preference Optimization (DPO). This refinement is guided by feedback from a co-adapting Detector which concurrently improves its ability to distinguish EvoBot from humans, thereby creating an increasingly challenging learning environment for EvoBot. Experiments demonstrate that EvoBot generates content aligned with diverse user profiles, increasingly bypassing the co-adapting Detector through human-like expression. Moreover, it exhibits strong social responsiveness, more accurately modeling real-world opinion dynamics and information spread in multi-agent simulations. The framework also yields a more robust Detector, underscoring its broader utility for both advanced agent development and related detection tasks. The code is available at https://github.com/kfq20/EvoBot.

Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. Results In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

Agents based on Large Language Models (LLMs) are increasingly permeating various domains of human production and life, highlighting the importance of aligning them with human values. The current alignment of AI systems primarily focuses on passively aligning LLMs through human intervention. However, agents possess characteristics like receiving environmental feedback and self-evolution, rendering the LLM alignment methods inadequate. In response, we propose an evolutionary framework for agent evolution and alignment, named EvolutionaryAgent, which transforms agent alignment into a process of evolution and selection under the principle of survival of the fittest. In an environment where social norms continuously evolve, agents better adapted to the current social norms will have a higher probability of survival and proliferation, while those inadequately aligned dwindle over time. Experimental results assessing the agents from multiple perspectives in aligning with social norms demonstrate that EvolutionaryAgent can align progressively better with the evolving social norms while maintaining its proficiency in general tasks. Effectiveness tests conducted on various open and closed-source LLMs as the foundation for agents also prove the applicability of our approach.

Large Language Models (LLMs) for formal theorem proving have shown significant promise, yet they often lack generalizability and are fragile to even minor transformations of problem statements. To address this limitation, we introduce a novel data augmentation pipeline designed to enhance model robustness from two perspectives: symmetry and difficulty. From the symmetry perspective, we propose two complementary methods: EvolAST, an Abstract Syntax Tree (AST) based approach that targets syntactic symmetry to generate semantically equivalent problem variants, and EvolDomain, which leverages LLMs to address semantic symmetry by translating theorems across mathematical domains. From the difficulty perspective, we propose EvolDifficulty, which uses carefully designed evolutionary instructions to guide LLMs in generating new theorems with a wider range of difficulty. We then use the evolved data to train EvolProver, a 7B-parameter non-reasoning theorem prover. EvolProver establishes a new state-of-the-art (SOTA) on FormalMATH-Lite with a 53.8% pass@32 rate, surpassing all models of comparable size, including reasoning-based models. It also sets new SOTA records for non-reasoning models on MiniF2F-Test (69.8% pass@32), Ineq-Comp-Seed (52.2% pass@32), and Ineq-Comp-Transformed (34.0% pass@32). Ablation studies further confirm our data augmentation pipeline's effectiveness across multiple benchmarks.

Large language models hold promise as scientific assistants, yet existing agents either rely solely on algorithm evolution or on deep research in isolation, both of which face critical limitations. Pure algorithm evolution, as in AlphaEvolve, depends only on the internal knowledge of LLMs and quickly plateaus in complex domains, while pure deep research proposes ideas without validation, resulting in unrealistic or unimplementable solutions. We present DeepEvolve, an agent that integrates deep research with algorithm evolution, uniting external knowledge retrieval, cross-file code editing, and systematic debugging under a feedback-driven iterative loop. Each iteration not only proposes new hypotheses but also refines, implements, and tests them, avoiding both shallow improvements and unproductive over-refinements. Across nine benchmarks in chemistry, mathematics, biology, materials, and patents, DeepEvolve consistently improves the initial algorithm, producing executable new algorithms with sustained gains. By bridging the gap between unguided evolution and research without grounding, DeepEvolve provides a reliable framework for advancing scientific algorithm discovery. Our code is available at https://github.com/liugangcode/deepevolve.

We introduce Biomaker CA: a Biome Maker project using Cellular Automata (CA). In Biomaker CA, morphogenesis is a first class citizen and small seeds need to grow into plant-like organisms to survive in a nutrient starved environment and eventually reproduce with variation so that a biome survives for long timelines. We simulate complex biomes by means of CA rules in 2D grids and parallelize all of its computation on GPUs through the Python JAX framework. We show how this project allows for several different kinds of environments and laws of 'physics', alongside different model architectures and mutation strategies. We further analyze some configurations to show how plant agents can grow, survive, reproduce, and evolve, forming stable and unstable biomes. We then demonstrate how one can meta-evolve models to survive in a harsh environment either through end-to-end meta-evolution or by a more surgical and efficient approach, called Petri dish meta-evolution. Finally, we show how to perform interactive evolution, where the user decides how to evolve a plant model interactively and then deploys it in a larger environment. We open source Biomaker CA at: https://tinyurl.com/2x8yu34s .

Model merging is a powerful technique for integrating the specialized knowledge of multiple machine learning models into a single model. However, existing methods require manually partitioning model parameters into fixed groups for merging, which restricts the exploration of potential combinations and limits performance. To overcome these limitations, we propose Model Merging of Natural Niches (M2N2), an evolutionary algorithm with three key features: (1) dynamic adjustment of merging boundaries to progressively explore a broader range of parameter combinations; (2) a diversity preservation mechanism inspired by the competition for resources in nature, to maintain a population of diverse, high-performing models that are particularly well-suited for merging; and (3) a heuristicbased attraction metric to identify the most promising pairs of models for fusion. Our experimental results demonstrate, for the first time, that model merging can be used to evolve models entirely from scratch. Specifically, we apply M2N2 to evolve MNIST classifiers from scratch and achieve performance comparable to CMA-ES, while being computationally more efficient. Furthermore, M2N2 scales to merge specialized language and image generation models, achieving state-of-the-art performance. Notably, it preserves crucial model capabilities beyond those explicitly optimized by the fitness function, highlighting its robustness and versatility. Our code is available at https://github.com/SakanaAI/natural_niches

Automated red teaming frameworks for Large Language Models (LLMs) have become increasingly sophisticated, yet they share a fundamental limitation: their jailbreak logic is confined to selecting, combining, or refining pre-existing attack strategies. This binds their creativity and leaves them unable to autonomously invent entirely new attack mechanisms. To overcome this gap, we introduce EvoSynth, an autonomous framework that shifts the paradigm from attack planning to the evolutionary synthesis of jailbreak methods. Instead of refining prompts, EvoSynth employs a multi-agent system to autonomously engineer, evolve, and execute novel, code-based attack algorithms. Crucially, it features a code-level self-correction loop, allowing it to iteratively rewrite its own attack logic in response to failure. Through extensive experiments, we demonstrate that EvoSynth not only establishes a new state-of-the-art by achieving an 85.5\% Attack Success Rate (ASR) against highly robust models like Claude-Sonnet-4.5, but also generates attacks that are significantly more diverse than those from existing methods. We release our framework to facilitate future research in this new direction of evolutionary synthesis of jailbreak methods. Code is available at: https://github.com/dongdongunique/EvoSynth.

Multi-agent systems (MAS) have emerged as a powerful paradigm for orchestrating large language models (LLMs) and specialized tools to collaboratively address complex tasks. However, existing MAS frameworks often require manual workflow configuration and lack native support for dynamic evolution and performance optimization. In addition, many MAS optimization algorithms are not integrated into a unified framework. In this paper, we present EvoAgentX, an open-source platform that automates the generation, execution, and evolutionary optimization of multi-agent workflows. EvoAgentX employs a modular architecture consisting of five core layers: the basic components, agent, workflow, evolving, and evaluation layers. Specifically, within the evolving layer, EvoAgentX integrates three MAS optimization algorithms, TextGrad, AFlow, and MIPRO, to iteratively refine agent prompts, tool configurations, and workflow topologies. We evaluate EvoAgentX on HotPotQA, MBPP, and MATH for multi-hop reasoning, code generation, and mathematical problem solving, respectively, and further assess it on real-world tasks using GAIA. Experimental results show that EvoAgentX consistently achieves significant performance improvements, including a 7.44% increase in HotPotQA F1, a 10.00% improvement in MBPP pass@1, a 10.00% gain in MATH solve accuracy, and an overall accuracy improvement of up to 20.00% on GAIA. The source code is available at: https://github.com/EvoAgentX/EvoAgentX

Maintaining genetic diversity as a means to avoid premature convergence is critical in Genetic Programming. Several approaches have been proposed to achieve this, with some focusing on the mating phase from coupling dissimilar solutions to some form of self-adaptive selection mechanism. In nature, genetic diversity can be the consequence of many different factors, but when considering reproduction Sexual Selection can have an impact on promoting variety within a species. Specifically, Mate Choice often results in different selective pressures between sexes, which in turn may trigger evolutionary differences among them. Although some mechanisms of Sexual Selection have been applied to Genetic Programming in the past, the literature is scarce when it comes to mate choice. Recently, a way of modelling mating preferences by ideal mate representations was proposed, achieving good results when compared to a standard approach. These mating preferences evolve freely in a self-adaptive fashion, creating an evolutionary driving force of its own alongside fitness pressure. The inner mechanisms of this approach operate from personal choice, as each individual has its own representation of a perfect mate which affects the mate to be selected. In this paper, we compare this method against a random mate choice to assess whether there are advantages in evolving personal preferences. We conducted experiments using three symbolic regression problems and different mutation rates. The results show that self-adaptive mating preferences are able to create a more diverse set of solutions when compared to the traditional approach and a random mate approach (with statistically significant differences) and have a higher success rate in three of the six instances tested.

B[e] stars are massive B type emission line stars in different evolutionary stages ranging from pre-main sequence to post-main sequence. Due to their mass loss and ejection events these objects deposit huge amounts of mass and energy into their environment and enrich it with chemically processed material, contributing significantly to the chemical and dynamical evolution of their host galaxies. However, the large-scale environments of these enigmatic objects have not attracted much attention. The first and so far only catalog reporting the detection of extended shells around a sample of B[e] stars was an Ha imaging survey carried out in the year 2001, and was limited to bright targets in the northern hemisphere. We have recently started a follow-up of those targets to detect possible evolution of their nebulae in the plane of the sky over a baseline of two decades. Furthermore, we extend our survey to southern targets and fainter northern ones to complement and complete our knowledge on large-scale ejecta surrounding B[e] stars. Besides imaging in Ha and selected nebular lines, we utilize long-slit and 3D spectral observations across the nebulae to derive their physical properties. We discovered pronounced nebula structures around 15 more objects, resulting in a total of 27 B[e] stars with a large-scale nebula. Here we present our (preliminary) results for three selected objects: the two massive supergiants MWC137 and MWC 314, and the unclassified B[e] star MWC 819.

Large Language Models (LLMs) have demonstrated strong capabilities but remain fundamentally static, unable to adapt their internal parameters to novel tasks, evolving knowledge domains, or dynamic interaction contexts. As LLMs are increasingly deployed in open-ended, interactive environments, this static nature has become a critical bottleneck, necessitating agents that can adaptively reason, act, and evolve in real time. This paradigm shift -- from scaling static models to developing self-evolving agents -- has sparked growing interest in architectures and methods enabling continual learning and adaptation from data, interactions, and experiences. This survey provides the first systematic and comprehensive review of self-evolving agents, organized around three foundational dimensions -- what to evolve, when to evolve, and how to evolve. We examine evolutionary mechanisms across agent components (e.g., models, memory, tools, architecture), categorize adaptation methods by stages (e.g., intra-test-time, inter-test-time), and analyze the algorithmic and architectural designs that guide evolutionary adaptation (e.g., scalar rewards, textual feedback, single-agent and multi-agent systems). Additionally, we analyze evaluation metrics and benchmarks tailored for self-evolving agents, highlight applications in domains such as coding, education, and healthcare, and identify critical challenges and research directions in safety, scalability, and co-evolutionary dynamics. By providing a structured framework for understanding and designing self-evolving agents, this survey establishes a roadmap for advancing adaptive agentic systems in both research and real-world deployments, ultimately shedding lights to pave the way for the realization of Artificial Super Intelligence (ASI), where agents evolve autonomously, performing at or beyond human-level intelligence across a wide array of tasks.

Fine-tuning large pre-trained language models with Evol-Instruct has achieved encouraging results across a wide range of tasks. However, designing effective evolving methods for instruction evolution requires substantial human expertise. This paper proposes Auto Evol-Instruct, an end-to-end framework that evolves instruction datasets using large language models without any human effort. The framework automatically analyzes and summarizes suitable evolutionary strategies for the given instruction data and iteratively improves the evolving method based on issues exposed during the instruction evolution process. Our extensive experiments demonstrate that the best method optimized by Auto Evol-Instruct outperforms human-designed methods on various benchmarks, including MT-Bench, AlpacaEval, GSM8K, and HumanEval.

Language models (LMs) perform well on standardized coding benchmarks but struggle with real-world software engineering tasks such as resolving GitHub issues in SWE-Bench, especially when model parameters are less than 100B. While smaller models are preferable in practice due to their lower computational cost, improving their performance remains challenging. Existing approaches primarily rely on supervised fine-tuning (SFT) with high-quality data, which is expensive to curate at scale. An alternative is test-time scaling: generating multiple outputs, scoring them using a verifier, and selecting the best one. Although effective, this strategy often requires excessive sampling and costly scoring, limiting its practical application. We propose Evolutionary Test-Time Scaling (EvoScale), a sample-efficient method that treats generation as an evolutionary process. By iteratively refining outputs via selection and mutation, EvoScale shifts the output distribution toward higher-scoring regions, reducing the number of samples needed to find correct solutions. To reduce the overhead from repeatedly sampling and selection, we train the model to self-evolve using reinforcement learning (RL). Rather than relying on external verifiers at inference time, the model learns to self-improve the scores of its own generations across iterations. Evaluated on SWE-Bench-Verified, EvoScale enables our 32B model, Satori-SWE-32B, to match or exceed the performance of models with over 100B parameters while using a few samples. Code, data, and models will be fully open-sourced.

This paper presents a reinforced genetic approach to a defined d-resource system optimization problem. The classical evolution schema was ineffective due to a very strict feasibility function in the studied problem. Hence, the presented strategy has introduced several modifications and adaptations to standard genetic routines, e.g.: a migration operator which is an analogy to the biological random genetic drift.

Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in biological vision models via large-scale contrastive vision-language training. To achieve this, we first curate TreeOfLife-200M, comprising 214 million images of living organisms, the largest and most diverse biological organism image dataset to date. We then train BioCLIP 2 on TreeOfLife-200M to distinguish different species. Despite the narrow training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction. We identify emergent properties in the learned embedding space of BioCLIP 2. At the inter-species level, the embedding distribution of different species aligns closely with functional and ecological meanings (e.g., beak sizes and habitats). At the intra-species level, instead of being diminished, the intra-species variations (e.g., life stages and sexes) are preserved and better separated in subspaces orthogonal to inter-species distinctions. We provide formal proof and analyses to explain why hierarchical supervision and contrastive objectives encourage these emergent properties. Crucially, our results reveal that these properties become increasingly significant with larger-scale training data, leading to a biologically meaningful embedding space.

Since its emergence, SARS-CoV-2 has demonstrated a rapid and unpredictable evolutionary trajectory, characterized by the continual emergence of immune-evasive variants. This poses persistent challenges to public health and vaccine development. While large-scale generative pre-trained transformers (GPTs) have revolutionized the modeling of sequential data, their direct applications to noisy viral genomic sequences are limited. In this paper, we introduce PETRA(Pretrained Evolutionary TRAnsformer), a novel transformer approach based on evolutionary trajectories derived from phylogenetic trees rather than raw RNA sequences. This method effectively mitigates sequencing noise and captures the hierarchical structure of viral evolution. With a weighted training framework to address substantial geographical and temporal imbalances in global sequence data, PETRA excels in predicting future SARS-CoV-2 mutations, achieving a weighted recall@1 of 9.45% for nucleotide mutations and 17.10\% for spike amino-acid mutations, compared to 0.49% and 6.64% respectively for the best baseline. PETRA also demonstrates its ability to aid in the real-time mutation prediction of major clades like 24F(XEC) and 25A(LP.8.1). The code is open sourced on https://github.com/xz-keg/PETra

This paper reports on patterns exhibiting self-replication with spontaneous, inheritable mutations and exponential genetic drift in Neural Cellular Automata. Despite the models not being explicitly trained for mutation or inheritability, the descendant patterns exponentially drift away from ancestral patterns, even when the automaton is deterministic. While this is far from being the first instance of evolutionary dynamics in a cellular automaton, it is the first to do so by exploiting the power and convenience of Neural Cellular Automata, arguably increasing the space of variations and the opportunity for Open Ended Evolution.

Evolvability is an important feature that impacts the ability of evolutionary processes to find interesting novel solutions and to deal with changing conditions of the problem to solve. The estimation of evolvability is not straightforward and is generally too expensive to be directly used as selective pressure in the evolutionary process. Indirectly promoting evolvability as a side effect of other easier and faster to compute selection pressures would thus be advantageous. In an unbounded behavior space, it has already been shown that evolvable individuals naturally appear and tend to be selected as they are more likely to invade empty behavior niches. Evolvability is thus a natural byproduct of the search in this context. However, practical agents and environments often impose limits on the reach-able behavior space. How do these boundaries impact evolvability? In this context, can evolvability still be promoted without explicitly rewarding it? We show that Novelty Search implicitly creates a pressure for high evolvability even in bounded behavior spaces, and explore the reasons for such a behavior. More precisely we show that, throughout the search, the dynamic evaluation of novelty rewards individuals which are very mobile in the behavior space, which in turn promotes evolvability.

Protein family design emerges as a promising alternative by combining the advantages of de novo protein design and mutation-based directed evolution.In this paper, we propose ProfileBFN, the Profile Bayesian Flow Networks, for specifically generative modeling of protein families. ProfileBFN extends the discrete Bayesian Flow Network from an MSA profile perspective, which can be trained on single protein sequences by regarding it as a degenerate profile, thereby achieving efficient protein family design by avoiding large-scale MSA data construction and training. Empirical results show that ProfileBFN has a profound understanding of proteins. When generating diverse and novel family proteins, it can accurately capture the structural characteristics of the family. The enzyme produced by this method is more likely than the previous approach to have the corresponding function, offering better odds of generating diverse proteins with the desired functionality.

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance.

LLM-driven multi-agent collaboration (MAC) systems have demonstrated impressive capabilities in automatic software development at the function level. However, their heavy reliance on human design limits their adaptability to the diverse demands of real-world software development. To address this limitation, we introduce EvoMAC, a novel self-evolving paradigm for MAC networks. Inspired by traditional neural network training, EvoMAC obtains text-based environmental feedback by verifying the MAC network's output against a target proxy and leverages a novel textual backpropagation to update the network. To extend coding capabilities beyond function-level tasks to more challenging software-level development, we further propose rSDE-Bench, a requirement-oriented software development benchmark, which features complex and diverse software requirements along with automatic evaluation of requirement correctness. Our experiments show that: i) The automatic requirement-aware evaluation in rSDE-Bench closely aligns with human evaluations, validating its reliability as a software-level coding benchmark. ii) EvoMAC outperforms previous SOTA methods on both the software-level rSDE-Bench and the function-level HumanEval benchmarks, reflecting its superior coding capabilities. The benchmark can be downloaded at https://yuzhu-cai.github.io/rSDE-Bench/.

In this white paper, we present AlphaEvolve, an evolutionary coding agent that substantially enhances capabilities of state-of-the-art LLMs on highly challenging tasks such as tackling open scientific problems or optimizing critical pieces of computational infrastructure. AlphaEvolve orchestrates an autonomous pipeline of LLMs, whose task is to improve an algorithm by making direct changes to the code. Using an evolutionary approach, continuously receiving feedback from one or more evaluators, AlphaEvolve iteratively improves the algorithm, potentially leading to new scientific and practical discoveries. We demonstrate the broad applicability of this approach by applying it to a number of important computational problems. When applied to optimizing critical components of large-scale computational stacks at Google, AlphaEvolve developed a more efficient scheduling algorithm for data centers, found a functionally equivalent simplification in the circuit design of hardware accelerators, and accelerated the training of the LLM underpinning AlphaEvolve itself. Furthermore, AlphaEvolve discovered novel, provably correct algorithms that surpass state-of-the-art solutions on a spectrum of problems in mathematics and computer science, significantly expanding the scope of prior automated discovery methods (Romera-Paredes et al., 2023). Notably, AlphaEvolve developed a search algorithm that found a procedure to multiply two 4 times 4 complex-valued matrices using 48 scalar multiplications; offering the first improvement, after 56 years, over Strassen's algorithm in this setting. We believe AlphaEvolve and coding agents like it can have a significant impact in improving solutions of problems across many areas of science and computation.

Large language models (LLMs) frequently refuse to respond to pseudo-malicious instructions: semantically harmless input queries triggering unnecessary LLM refusals due to conservative safety alignment, significantly impairing user experience. Collecting such instructions is crucial for evaluating and mitigating over-refusals, but existing instruction curation methods, like manual creation or instruction rewriting, either lack scalability or fail to produce sufficiently diverse and effective refusal-inducing prompts. To address these limitations, we introduce EVOREFUSE, a prompt optimization approach that generates diverse pseudo-malicious instructions consistently eliciting confident refusals across LLMs. EVOREFUSE employs an evolutionary algorithm exploring the instruction space in more diverse directions than existing methods via mutation strategies and recombination, and iteratively evolves seed instructions to maximize evidence lower bound on LLM refusal probability. Using EVOREFUSE, we create two novel datasets: EVOREFUSE-TEST, a benchmark of 582 pseudo-malicious instructions that outperforms the next-best benchmark with 140.41% higher average refusal triggering rate across 9 LLMs, 34.86% greater lexical diversity, and 40.03% improved LLM response confidence scores; and EVOREFUSE-ALIGN, which provides 3,000 pseudo-malicious instructions with responses for supervised and preference-based alignment training. LLAMA3.1-8B-INSTRUCT supervisedly fine-tuned on EVOREFUSE-ALIGN achieves up to 14.31% fewer over-refusals than models trained on the second-best alignment dataset, without compromising safety. Our analysis with EVOREFUSE-TEST reveals models trigger over-refusals by overly focusing on sensitive keywords while ignoring broader context.

Rust's compile-time safety guarantees make it ideal for safety-critical systems, creating demand for translating legacy C codebases to Rust. While various approaches have emerged for this task, they face inherent trade-offs: rule-based solutions face challenges in meeting code safety and idiomaticity requirements, while LLM-based solutions often fail to generate semantically equivalent Rust code, due to the heavy dependencies of modules across the entire codebase. Recent studies have revealed that both solutions are limited to small-scale programs. In this paper, we propose EvoC2Rust, an automated framework for converting entire C projects to equivalent Rust ones. EvoC2Rust employs a skeleton-guided translation strategy for project-level translation. The pipeline consists of three evolutionary stages: 1) it first decomposes the C project into functional modules, employs a feature-mapping-enhanced LLM to transform definitions and macros and generates type-checked function stubs, which form a compilable Rust skeleton; 2) it then incrementally translates the function, replacing the corresponding stub placeholder; 3) finally, it repairs compilation errors by integrating LLM and static analysis. Through evolutionary augmentation, EvoC2Rust combines the advantages of both rule-based and LLM-based solutions. Our evaluation on open-source benchmarks and six industrial projects demonstrates EvoC2Rust's superior performance in project-level C-to-Rust translation. On average, it achieves 17.24% and 14.32% improvements in syntax and semantic accuracy over the LLM-based approaches, along with a 96.79% higher code safety rate than the rule-based tools. At the module level, EvoC2Rust reaches 92.25% compilation and 89.53% test pass rates on industrial projects, even for complex codebases and long functions.

Despite the significant advancements in text-to-image (T2I) generative models, users often face a trial-and-error challenge in practical scenarios. This challenge arises from the complexity and uncertainty of tedious steps such as crafting suitable prompts, selecting appropriate models, and configuring specific arguments, making users resort to labor-intensive attempts for desired images. This paper proposes Automatic T2I generation, which aims to automate these tedious steps, allowing users to simply describe their needs in a freestyle chatting way. To systematically study this problem, we first introduce ChatGenBench, a novel benchmark designed for Automatic T2I. It features high-quality paired data with diverse freestyle inputs, enabling comprehensive evaluation of automatic T2I models across all steps. Additionally, recognizing Automatic T2I as a complex multi-step reasoning task, we propose ChatGen-Evo, a multi-stage evolution strategy that progressively equips models with essential automation skills. Through extensive evaluation across step-wise accuracy and image quality, ChatGen-Evo significantly enhances performance over various baselines. Our evaluation also uncovers valuable insights for advancing automatic T2I. All our data, code, and models will be available in https://chengyou-jia.github.io/ChatGen-Home

We propose a new concept, Evolution 6.0, which represents the evolution of robotics driven by Generative AI. When a robot lacks the necessary tools to accomplish a task requested by a human, it autonomously designs the required instruments and learns how to use them to achieve the goal. Evolution 6.0 is an autonomous robotic system powered by Vision-Language Models (VLMs), Vision-Language Action (VLA) models, and Text-to-3D generative models for tool design and task execution. The system comprises two key modules: the Tool Generation Module, which fabricates task-specific tools from visual and textual data, and the Action Generation Module, which converts natural language instructions into robotic actions. It integrates QwenVLM for environmental understanding, OpenVLA for task execution, and Llama-Mesh for 3D tool generation. Evaluation results demonstrate a 90% success rate for tool generation with a 10-second inference time, and action generation achieving 83.5% in physical and visual generalization, 70% in motion generalization, and 37% in semantic generalization. Future improvements will focus on bimanual manipulation, expanded task capabilities, and enhanced environmental interpretation to improve real-world adaptability.

Self-supervised representation learning of biological sequence embeddings alleviates computational resource constraints on downstream tasks while circumventing expensive experimental label acquisition. However, existing methods mostly borrow directly from large language models designed for NLP, rather than with bioinformatics philosophies in mind. Recently, contrastive mutual information maximization methods have achieved state-of-the-art representations for ImageNet. In this perspective piece, we discuss how viewing evolution as natural sequence augmentation and maximizing information across phylogenetic "noisy channels" is a biologically and theoretically desirable objective for pretraining encoders. We first provide a review of current contrastive learning literature, then provide an illustrative example where we show that contrastive learning using evolutionary augmentation can be used as a representation learning objective which maximizes the mutual information between biological sequences and their conserved function, and finally outline rationale for this approach.

Human intelligence emerged through the process of natural selection and evolution on Earth. We investigate what it would take to re-create this process in silico. While past work has often focused on low-level processes (such as simulating physics or chemistry), we instead take a more targeted approach, aiming to evolve agents that can accumulate open-ended culture and technologies across generations. Towards this, we present JaxLife: an artificial life simulator in which embodied agents, parameterized by deep neural networks, must learn to survive in an expressive world containing programmable systems. First, we describe the environment and show that it can facilitate meaningful Turing-complete computation. We then analyze the evolved emergent agents' behavior, such as rudimentary communication protocols, agriculture, and tool use. Finally, we investigate how complexity scales with the amount of compute used. We believe JaxLife takes a step towards studying evolved behavior in more open-ended simulations. Our code is available at https://github.com/luchris429/JaxLife

In-context learning (ICL) -- the capacity of a model to infer and apply abstract patterns from examples provided within its input -- has been extensively studied in large language models trained for next-token prediction on human text. In fact, prior work often attributes this emergent behavior to distinctive statistical properties in human language. This raises a fundamental question: can ICL arise organically in other sequence domains purely through large-scale predictive training? To explore this, we turn to genomic sequences, an alternative symbolic domain rich in statistical structure. Specifically, we study the Evo2 genomic model, trained predominantly on next-nucleotide (A/T/C/G) prediction, at a scale comparable to mid-sized LLMs. We develop a controlled experimental framework comprising symbolic reasoning tasks instantiated in both linguistic and genomic forms, enabling direct comparison of ICL across genomic and linguistic models. Our results show that genomic models, like their linguistic counterparts, exhibit log-linear gains in pattern induction as the number of in-context demonstrations increases. To the best of our knowledge, this is the first evidence of organically emergent ICL in genomic sequences, supporting the hypothesis that ICL arises as a consequence of large-scale predictive modeling over rich data. These findings extend emergent meta-learning beyond language, pointing toward a unified, modality-agnostic view of in-context learning.

The relationship between computing systems and the brain has served as motivation for pioneering theoreticians since John von Neumann and Alan Turing. Uniform, scale-free biological networks, such as the brain, have powerful properties, including generalizing over time, which is the main barrier for Machine Learning on the path to Universal Reasoning Models. We introduce `Dragon Hatchling' (BDH), a new Large Language Model architecture based on a scale-free biologically inspired network of \n locally-interacting neuron particles. BDH couples strong theoretical foundations and inherent interpretability without sacrificing Transformer-like performance. BDH is a practical, performant state-of-the-art attention-based state space sequence learning architecture. In addition to being a graph model, BDH admits a GPU-friendly formulation. It exhibits Transformer-like scaling laws: empirically BDH rivals GPT2 performance on language and translation tasks, at the same number of parameters (10M to 1B), for the same training data. BDH can be represented as a brain model. The working memory of BDH during inference entirely relies on synaptic plasticity with Hebbian learning using spiking neurons. We confirm empirically that specific, individual synapses strengthen connection whenever BDH hears or reasons about a specific concept while processing language inputs. The neuron interaction network of BDH is a graph of high modularity with heavy-tailed degree distribution. The BDH model is biologically plausible, explaining one possible mechanism which human neurons could use to achieve speech. BDH is designed for interpretability. Activation vectors of BDH are sparse and positive. We demonstrate monosemanticity in BDH on language tasks. Interpretability of state, which goes beyond interpretability of neurons and model parameters, is an inherent feature of the BDH architecture.

Quantization scale and bit-width are the most important parameters when considering how to quantize a neural network. Prior work focuses on optimizing quantization scales in a global manner through gradient methods (gradient descent \& Hessian analysis). Yet, when applying perturbations to quantization scales, we observe a very jagged, highly non-smooth test loss landscape. In fact, small perturbations in quantization scale can greatly affect accuracy, yielding a 0.5-0.8% accuracy boost in 4-bit quantized vision transformers (ViTs). In this regime, gradient methods break down, since they cannot reliably reach local minima. In our work, dubbed Evol-Q, we use evolutionary search to effectively traverse the non-smooth landscape. Additionally, we propose using an infoNCE loss, which not only helps combat overfitting on the small calibration dataset (1,000 images) but also makes traversing such a highly non-smooth surface easier. Evol-Q improves the top-1 accuracy of a fully quantized ViT-Base by 10.30%, 0.78%, and 0.15% for 3-bit, 4-bit, and 8-bit weight quantization levels. Extensive experiments on a variety of CNN and ViT architectures further demonstrate its robustness in extreme quantization scenarios. Our code is available at https://github.com/enyac-group/evol-q

The performance of Convolutional Neural Networks (CNNs) highly relies on their architectures. In order to design a CNN with promising performance, extended expertise in both CNNs and the investigated problem is required, which is not necessarily held by every user interested in CNNs or the problem domain. In this paper, we propose to automatically evolve CNN architectures by using a genetic algorithm based on ResNet blocks and DenseNet blocks. The proposed algorithm is completely automatic in designing CNN architectures, particularly, neither pre-processing before it starts nor post-processing on the designed CNN is needed. Furthermore, the proposed algorithm does not require users with domain knowledge on CNNs, the investigated problem or even genetic algorithms. The proposed algorithm is evaluated on CIFAR10 and CIFAR100 against 18 state-of-the-art peer competitors. Experimental results show that it outperforms state-of-the-art CNNs hand-crafted and CNNs designed by automatic peer competitors in terms of the classification accuracy, and achieves the competitive classification accuracy against semi-automatic peer competitors. In addition, the proposed algorithm consumes much less time than most peer competitors in finding the best CNN architectures.

Artificial neural networks for motor control usually adopt generic architectures like fully connected MLPs. While general, these tabula rasa architectures rely on large amounts of experience to learn, are not easily transferable to new bodies, and have internal dynamics that are difficult to interpret. In nature, animals are born with highly structured connectivity in their nervous systems shaped by evolution; this innate circuitry acts synergistically with learning mechanisms to provide inductive biases that enable most animals to function well soon after birth and learn efficiently. Convolutional networks inspired by visual circuitry have encoded useful biases for vision. However, it is unknown the extent to which ANN architectures inspired by neural circuitry can yield useful biases for other AI domains. In this work, we ask what advantages biologically inspired ANN architecture can provide in the domain of motor control. Specifically, we translate C. elegans locomotion circuits into an ANN model controlling a simulated Swimmer agent. On a locomotion task, our architecture achieves good initial performance and asymptotic performance comparable with MLPs, while dramatically improving data efficiency and requiring orders of magnitude fewer parameters. Our architecture is interpretable and transfers to new body designs. An ablation analysis shows that constrained excitation/inhibition is crucial for learning, while weight initialization contributes to good initial performance. Our work demonstrates several advantages of biologically inspired ANN architecture and encourages future work in more complex embodied control.

A hallmark of intelligence is the ability to autonomously learn new flexible, cognitive behaviors - that is, behaviors where the appropriate action depends not just on immediate stimuli (as in simple reflexive stimulus-response associations), but on contextual information that must be adequately acquired, stored and processed. While many meta-learning algorithms can design agents that autonomously learn new tasks, cognitive tasks adds another level of learning and memory to typical ``learning-to-learn'' problems. Here we evolve neural networks, endowed with plastic connections and neuromodulation, over a sizable set of simple cognitive tasks adapted from a computational neuroscience framework. The resulting evolved networks can automatically modify their own connectivity to acquire a novel simple cognitive task, never seen during evolution, from stimuli and rewards alone, through the spontaneous operation of their evolved neural organization and plasticity system. Our results emphasize the importance of carefully considering the multiple learning loops involved in the emergence of intelligent behavior.

Recent advances in Neural Architecture Search (NAS) which extract specialized hardware-aware configurations (a.k.a. "sub-networks") from a hardware-agnostic "super-network" have become increasingly popular. While considerable effort has been employed towards improving the first stage, namely, the training of the super-network, the search for derivative high-performing sub-networks is still largely under-explored. For example, some recent network morphism techniques allow a super-network to be trained once and then have hardware-specific networks extracted from it as needed. These methods decouple the super-network training from the sub-network search and thus decrease the computational burden of specializing to different hardware platforms. We propose a comprehensive system that automatically and efficiently finds sub-networks from a pre-trained super-network that are optimized to different performance metrics and hardware configurations. By combining novel search tactics and algorithms with intelligent use of predictors, we significantly decrease the time needed to find optimal sub-networks from a given super-network. Further, our approach does not require the super-network to be refined for the target task a priori, thus allowing it to interface with any super-network. We demonstrate through extensive experiments that our system works seamlessly with existing state-of-the-art super-network training methods in multiple domains. Moreover, we show how novel search tactics paired with evolutionary algorithms can accelerate the search process for ResNet50, MobileNetV3 and Transformer while maintaining objective space Pareto front diversity and demonstrate an 8x faster search result than the state-of-the-art Bayesian optimization WeakNAS approach.

Recent advances in large language models have sparked growing interest in AI agents capable of solving complex, real-world tasks. However, most existing agent systems rely on manually crafted configurations that remain static after deployment, limiting their ability to adapt to dynamic and evolving environments. To this end, recent research has explored agent evolution techniques that aim to automatically enhance agent systems based on interaction data and environmental feedback. This emerging direction lays the foundation for self-evolving AI agents, which bridge the static capabilities of foundation models with the continuous adaptability required by lifelong agentic systems. In this survey, we provide a comprehensive review of existing techniques for self-evolving agentic systems. Specifically, we first introduce a unified conceptual framework that abstracts the feedback loop underlying the design of self-evolving agentic systems. The framework highlights four key components: System Inputs, Agent System, Environment, and Optimisers, serving as a foundation for understanding and comparing different strategies. Based on this framework, we systematically review a wide range of self-evolving techniques that target different components of the agent system. We also investigate domain-specific evolution strategies developed for specialised fields such as biomedicine, programming, and finance, where optimisation objectives are tightly coupled with domain constraints. In addition, we provide a dedicated discussion on the evaluation, safety, and ethical considerations for self-evolving agentic systems, which are critical to ensuring their effectiveness and reliability. This survey aims to provide researchers and practitioners with a systematic understanding of self-evolving AI agents, laying the foundation for the development of more adaptive, autonomous, and lifelong agentic systems.

Model merging allows combining the capabilities of existing models into a new one - post hoc, without additional training. This has made it increasingly popular thanks to its low cost and the availability of libraries that support merging on consumer GPUs. Recent work shows that pairing merging with evolutionary algorithms can boost performance, but no framework currently supports flexible experimentation with such strategies in language models. We introduce Mergenetic, an open-source library for evolutionary model merging. Mergenetic enables easy composition of merging methods and evolutionary algorithms while incorporating lightweight fitness estimators to reduce evaluation costs. We describe its design and demonstrate that Mergenetic produces competitive results across tasks and languages using modest hardware.

We introduce ShinkaEvolve: a new open-source framework leveraging large language models (LLMs) to advance scientific discovery with state-of-the-art performance and unprecedented efficiency. Recent advances in scaling inference time compute of LLMs have enabled significant progress in generalized scientific discovery. These approaches rely on evolutionary agentic harnesses that leverage LLMs as mutation operators to generate candidate solutions. However, current code evolution methods suffer from critical limitations: they are sample inefficient, requiring thousands of samples to identify effective solutions, and remain closed-source, hindering broad adoption and extension. ShinkaEvolve addresses these limitations, introducing three key innovations: a parent sampling technique balancing exploration and exploitation, code novelty rejection-sampling for efficient search space exploration, and a bandit-based LLM ensemble selection strategy. We evaluate ShinkaEvolve across diverse tasks, demonstrating consistent improvements in sample efficiency and solution quality. ShinkaEvolve discovers a new state-of-the-art circle packing solution using only 150 samples, designs high-performing agentic harnesses for AIME mathematical reasoning tasks, identifies improvements to ALE-Bench competitive programming solutions, and discovers novel mixture-of-expert load balancing loss functions that illuminate the space of optimization strategies. Our results demonstrate that ShinkaEvolve achieves broad applicability with exceptional sample efficiency. By providing open-source accessibility and cost-efficiency, this work democratizes open-ended discovery across diverse computational problems.

Multi-organ segmentation is a critical yet challenging task due to complex anatomical backgrounds, blurred boundaries, and diverse morphologies. This study introduces the Gradient-aware Adaptive Momentum Evolution Deep Snake (GAMED-Snake) model, which establishes a novel paradigm for contour-based segmentation by integrating gradient-based learning with adaptive momentum evolution mechanisms. The GAMED-Snake model incorporates three major innovations: First, the Distance Energy Map Prior (DEMP) generates a pixel-level force field that effectively attracts contour points towards the true boundaries, even in scenarios with complex backgrounds and blurred edges. Second, the Differential Convolution Inception Module (DCIM) precisely extracts comprehensive energy gradients, significantly enhancing segmentation accuracy. Third, the Adaptive Momentum Evolution Mechanism (AMEM) employs cross-attention to establish dynamic features across different iterations of evolution, enabling precise boundary alignment for diverse morphologies. Experimental results on four challenging multi-organ segmentation datasets demonstrate that GAMED-Snake improves the mDice metric by approximately 2% compared to state-of-the-art methods. Code will be available at https://github.com/SYSUzrc/GAMED-Snake.

This paper pursues the insight that large language models (LLMs) trained to generate code can vastly improve the effectiveness of mutation operators applied to programs in genetic programming (GP). Because such LLMs benefit from training data that includes sequential changes and modifications, they can approximate likely changes that humans would make. To highlight the breadth of implications of such evolution through large models (ELM), in the main experiment ELM combined with MAP-Elites generates hundreds of thousands of functional examples of Python programs that output working ambulating robots in the Sodarace domain, which the original LLM had never seen in pre-training. These examples then help to bootstrap training a new conditional language model that can output the right walker for a particular terrain. The ability to bootstrap new models that can output appropriate artifacts for a given context in a domain where zero training data was previously available carries implications for open-endedness, deep learning, and reinforcement learning. These implications are explored here in depth in the hope of inspiring new directions of research now opened up by ELM.

A hallmark of human innovation is the process of recombination -- creating original ideas by integrating elements of existing mechanisms and concepts. In this work, we automatically mine the scientific literature and build CHIMERA: a large-scale knowledge base (KB) of recombination examples. CHIMERA can be used to empirically explore at scale how scientists recombine concepts and take inspiration from different areas, or to train supervised machine learning models that learn to predict new creative cross-domain directions. To build this KB, we present a novel information extraction task of extracting recombination from scientific paper abstracts, collect a high-quality corpus of hundreds of manually annotated abstracts, and use it to train an LLM-based extraction model. The model is applied to a large corpus of papers in the AI domain, yielding a KB of over 28K recombination examples. We analyze CHIMERA to explore the properties of recombination in different subareas of AI. Finally, we train a scientific hypothesis generation model using the KB, which predicts new recombination directions that real-world researchers find inspiring. Our data and code are available at https://github.cs.huji.ac.il/tomhope-lab/CHIMERA

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module Adaptive-eta, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md{here.}

Recent advances in large language models (LLMs) have enabled breakthroughs in mathematical discovery, exemplified by AlphaEvolve, a closed-source system that evolves programs to improve bounds on open problems. However, it relies on ensembles of frontier LLMs to achieve new bounds and is a pure inference system that models cannot internalize the evolving strategies. We introduce ThetaEvolve, an open-source framework that simplifies and extends AlphaEvolve to efficiently scale both in-context learning and Reinforcement Learning (RL) at test time, allowing models to continually learn from their experiences in improving open optimization problems. ThetaEvolve features a single LLM, a large program database for enhanced exploration, batch sampling for higher throughput, lazy penalties to discourage stagnant outputs, and optional reward shaping for stable training signals, etc. ThetaEvolve is the first evolving framework that enable a small open-source model, like DeepSeek-R1-0528-Qwen3-8B, to achieve new best-known bounds on open problems (circle packing and first auto-correlation inequality) mentioned in AlphaEvolve. Besides, across two models and four open tasks, we find that ThetaEvolve with RL at test-time consistently outperforms inference-only baselines, and the model indeed learns evolving capabilities, as the RL-trained checkpoints demonstrate faster progress and better final performance on both trained target task and other unseen tasks. We release our code publicly: https://github.com/ypwang61/ThetaEvolve

Retrieval-Augmented Generation (RAG) and Graph-based RAG has become the important paradigm for enhancing Large Language Models (LLMs) with external knowledge. However, existing approaches face a fundamental trade-off. While graph-based methods are inherently dependent on high-quality graph structures, they face significant practical constraints: manually constructed knowledge graphs are prohibitively expensive to scale, while automatically extracted graphs from corpora are limited by the performance of the underlying LLM extractors, especially when using smaller, local-deployed models. This paper presents Think-on-Graph 3.0 (ToG-3), a novel framework that introduces Multi-Agent Context Evolution and Retrieval (MACER) mechanism to overcome these limitations. Our core innovation is the dynamic construction and refinement of a Chunk-Triplets-Community heterogeneous graph index, which pioneeringly incorporates a dual-evolution mechanism of Evolving Query and Evolving Sub-Graph for precise evidence retrieval. This approach addresses a critical limitation of prior Graph-based RAG methods, which typically construct a static graph index in a single pass without adapting to the actual query. A multi-agent system, comprising Constructor, Retriever, Reflector, and Responser agents, collaboratively engages in an iterative process of evidence retrieval, answer generation, sufficiency reflection, and, crucially, evolving query and subgraph. This dual-evolving multi-agent system allows ToG-3 to adaptively build a targeted graph index during reasoning, mitigating the inherent drawbacks of static, one-time graph construction and enabling deep, precise reasoning even with lightweight LLMs. Extensive experiments demonstrate that ToG-3 outperforms compared baselines on both deep and broad reasoning benchmarks, and ablation studies confirm the efficacy of the components of MACER framework.

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

Deep artificial neural networks (DNNs) are typically trained via gradient-based learning algorithms, namely backpropagation. Evolution strategies (ES) can rival backprop-based algorithms such as Q-learning and policy gradients on challenging deep reinforcement learning (RL) problems. However, ES can be considered a gradient-based algorithm because it performs stochastic gradient descent via an operation similar to a finite-difference approximation of the gradient. That raises the question of whether non-gradient-based evolutionary algorithms can work at DNN scales. Here we demonstrate they can: we evolve the weights of a DNN with a simple, gradient-free, population-based genetic algorithm (GA) and it performs well on hard deep RL problems, including Atari and humanoid locomotion. The Deep GA successfully evolves networks with over four million free parameters, the largest neural networks ever evolved with a traditional evolutionary algorithm. These results (1) expand our sense of the scale at which GAs can operate, (2) suggest intriguingly that in some cases following the gradient is not the best choice for optimizing performance, and (3) make immediately available the multitude of neuroevolution techniques that improve performance. We demonstrate the latter by showing that combining DNNs with novelty search, which encourages exploration on tasks with deceptive or sparse reward functions, can solve a high-dimensional problem on which reward-maximizing algorithms (e.g.\ DQN, A3C, ES, and the GA) fail. Additionally, the Deep GA is faster than ES, A3C, and DQN (it can train Atari in {raise.17ex\scriptstyle\sim}4 hours on one desktop or {raise.17ex\scriptstyle\sim}1 hour distributed on 720 cores), and enables a state-of-the-art, up to 10,000-fold compact encoding technique.

Neural Architecture Search (NAS) has garnered significant research interest due to its capability to discover architectures superior to manually designed ones. Learning text representation is crucial for text classification and other language-related tasks. The NAS model used in text classification does not have a Hybrid hierarchical structure, and there is no restriction on the architecture structure, due to which the search space becomes very large and mostly redundant, so the existing RL models are not able to navigate the search space effectively. Also, doing a flat architecture search leads to an unorganised search space, which is difficult to traverse. For this purpose, we propose HHNAS-AM (Hierarchical Hybrid Neural Architecture Search with Adaptive Mutation Policies), a novel approach that efficiently explores diverse architectural configurations. We introduce a few architectural templates to search on which organise the search spaces, where search spaces are designed on the basis of domain-specific cues. Our method employs mutation strategies that dynamically adapt based on performance feedback from previous iterations using Q-learning, enabling a more effective and accelerated traversal of the search space. The proposed model is fully probabilistic, enabling effective exploration of the search space. We evaluate our approach on the database id (db_id) prediction task, where it consistently discovers high-performing architectures across multiple experiments. On the Spider dataset, our method achieves an 8% improvement in test accuracy over existing baselines.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Transfer RNAs (tRNAs) are universal adaptors of the genetic code, yet their evolutionary dynamics across photosynthetic eukaryotes remain underexplored. Here, we present the largest comparative re-analysis integrating the PlantRNA database with published data to explore tRNA gene evolution. We find that tRNA gene repertoires have been deeply shaped by ecological transitions, genome architecture, and translational demands. Terrestrialization marks a major shift in tRNA evolution, characterized by the loss of selenoproteins and their dedicated selenocysteine tRNAs in land plants compared to algae. Patterns of intron prevalence, position, and structure diverged among lineages, with extensive intron loss occurring around the origin of land plants. Organellar genomes exhibit divergent trajectories: mitochondrial tRNA sets are highly labile due to recurrent gene losses, imports, and horizontal transfers, whereas plastid repertoires are comparatively stable with lineage-specific exceptions. In parallel, angiosperm nuclear tRNA genes exhibit reinforced cis-regulatory elements, consistent with increased and developmentally complex translational demands, and their copy number correlates tightly with codon usage and amino acid composition. Finally, conserved yet family-biased clustering of nuclear tRNA genes reveals contrasting organizational principles in plants versus metazoans. Together, these findings establish tRNA gene evolution as a major determinant of translational capacity and a key driver of photosynthetic diversification.

The study of hardest and easiest fitness landscapes is an active area of research. Recently, Kaufmann, Larcher, Lengler and Zou conjectured that for the self-adjusting (1,lambda)-EA, Adversarial Dynamic BinVal (ADBV) is the hardest dynamic monotone function to optimize. We introduce the function Switching Dynamic BinVal (SDBV) which coincides with ADBV whenever the number of remaining zeros in the search point is strictly less than n/2, where n denotes the dimension of the search space. We show, using a combinatorial argument, that for the (1+1)-EA with any mutation rate p in [0,1], SDBV is drift-minimizing among the class of dynamic monotone functions. Our construction provides the first explicit example of an instance of the partially-ordered evolutionary algorithm (PO-EA) model with parameterized pessimism introduced by Colin, Doerr and F\'erey, building on work of Jansen. We further show that the (1+1)-EA optimizes SDBV in Theta(n^{3/2}) generations. Our simulations demonstrate matching runtimes for both static and self-adjusting (1,lambda) and (1+lambda)-EA. We further show, using an example of fixed dimension, that drift-minimization does not equal maximal runtime.

NeXML is a powerful and extensible exchange standard recently proposed to better meet the expanding needs for phylogenetic data and metadata sharing. Here we present the RNeXML package, which provides users of the R programming language with easy-to-use tools for reading and writing NeXML documents, including rich metadata, in a way that interfaces seamlessly with the extensive library of phylogenetic tools already available in the R ecosystem.

Decision trees are a crucial class of models offering robust predictive performance and inherent interpretability across various domains, including healthcare, finance, and logistics. However, current tree induction methods often face limitations such as suboptimal solutions from greedy methods or prohibitive computational costs and limited applicability of exact optimization approaches. To address these challenges, we propose an evolutionary optimization method for decision tree induction based on genetic programming (GP). Our key innovation is the integration of semantic priors and domain-specific knowledge about the search space into the optimization algorithm. To this end, we introduce LLEGO, a framework that incorporates semantic priors into genetic search operators through the use of Large Language Models (LLMs), thereby enhancing search efficiency and targeting regions of the search space that yield decision trees with superior generalization performance. This is operationalized through novel genetic operators that work with structured natural language prompts, effectively utilizing LLMs as conditional generative models and sources of semantic knowledge. Specifically, we introduce fitness-guided crossover to exploit high-performing regions, and diversity-guided mutation for efficient global exploration of the search space. These operators are controlled by corresponding hyperparameters that enable a more nuanced balance between exploration and exploitation across the search space. Empirically, we demonstrate across various benchmarks that LLEGO evolves superior-performing trees compared to existing tree induction methods, and exhibits significantly more efficient search performance compared to conventional GP approaches.

The recent surge in large-scale foundation models has spurred the development of efficient methods for adapting these models to various downstream tasks. Low-rank adaptation methods, such as LoRA, have gained significant attention due to their outstanding parameter efficiency and no additional inference latency. This paper investigates a more general form of adapter module based on the analysis that parallel and sequential adaptation branches learn novel and general features during fine-tuning, respectively. The proposed method, named Hydra, due to its multi-head computational branches, combines parallel and sequential branch to integrate capabilities, which is more expressive than existing single branch methods and enables the exploration of a broader range of optimal points in the fine-tuning process. In addition, the proposed adaptation method explicitly leverages the pre-trained weights by performing a linear combination of the pre-trained features. It allows the learned features to have better generalization performance across diverse downstream tasks. Furthermore, we perform a comprehensive analysis of the characteristics of each adaptation branch with empirical evidence. Through an extensive range of experiments, encompassing comparisons and ablation studies, we substantiate the efficiency and demonstrate the superior performance of Hydra. This comprehensive evaluation underscores the potential impact and effectiveness of Hydra in a variety of applications. Our code is available on https://github.com/extremebird/Hydra

Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates some central challenges from multiple tasks, including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding and elicits continuous differential attention that encapsulates and evolves with latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.

Scientific discovery relies on scientists generating novel hypotheses that undergo rigorous experimental validation. To augment this process, we introduce an AI co-scientist, a multi-agent system built on Gemini 2.0. The AI co-scientist is intended to help uncover new, original knowledge and to formulate demonstrably novel research hypotheses and proposals, building upon prior evidence and aligned to scientist-provided research objectives and guidance. The system's design incorporates a generate, debate, and evolve approach to hypothesis generation, inspired by the scientific method and accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute, improving hypothesis quality. While general purpose, we focus development and validation in three biomedical areas: drug repurposing, novel target discovery, and explaining mechanisms of bacterial evolution and anti-microbial resistance. For drug repurposing, the system proposes candidates with promising validation findings, including candidates for acute myeloid leukemia that show tumor inhibition in vitro at clinically applicable concentrations. For novel target discovery, the AI co-scientist proposed new epigenetic targets for liver fibrosis, validated by anti-fibrotic activity and liver cell regeneration in human hepatic organoids. Finally, the AI co-scientist recapitulated unpublished experimental results via a parallel in silico discovery of a novel gene transfer mechanism in bacterial evolution. These results, detailed in separate, co-timed reports, demonstrate the potential to augment biomedical and scientific discovery and usher an era of AI empowered scientists.

Autonomous agents driven by Large Language Models (LLMs) have revolutionized reasoning and problem-solving but remain static after training, unable to grow with experience as intelligent beings do during deployment. We introduce Forward Learning with EXperience (FLEX), a gradient-free learning paradigm that enables LLM agents to continuously evolve through accumulated experience. Specifically, FLEX cultivates scalable and inheritable evolution by constructing a structured experience library through continual reflection on successes and failures during interaction with the environment. FLEX delivers substantial improvements on mathematical reasoning, chemical retrosynthesis, and protein fitness prediction (up to 23% on AIME25, 10% on USPTO50k, and 14% on ProteinGym). We further identify a clear scaling law of experiential growth and the phenomenon of experience inheritance across agents, marking a step toward scalable and inheritable continuous agent evolution. Project Page: https://flex-gensi-thuair.github.io.

Deep neural networks can be exploited using natural adversarial samples, which do not impact human perception. Current approaches often rely on deep neural networks' white-box nature to generate these adversarial samples or synthetically alter the distribution of adversarial samples compared to the training distribution. In contrast, we propose EvoSeed, a novel evolutionary strategy-based algorithmic framework for generating photo-realistic natural adversarial samples. Our EvoSeed framework uses auxiliary Conditional Diffusion and Classifier models to operate in a black-box setting. We employ CMA-ES to optimize the search for an initial seed vector, which, when processed by the Conditional Diffusion Model, results in the natural adversarial sample misclassified by the Classifier Model. Experiments show that generated adversarial images are of high image quality, raising concerns about generating harmful content bypassing safety classifiers. Our research opens new avenues to understanding the limitations of current safety mechanisms and the risk of plausible attacks against classifier systems using image generation. Project Website can be accessed at: https://shashankkotyan.github.io/EvoSeed.

How to evaluate Large Language Models (LLMs) in code generation is an open question. Existing benchmarks demonstrate poor alignment with real-world code repositories and are insufficient to evaluate the coding abilities of LLMs. This paper proposes a new benchmark - EvoCodeBench to address the preceding problems, which has three primary advances. (1) EvoCodeBench aligns with real-world repositories in multiple dimensions, e.g., code distributions and dependency distributions. (2) EvoCodeBench offers comprehensive annotations (e.g., requirements, reference code, and reference dependencies), and robust evaluation metrics (e.g., Pass@k and Recall@k). (3) EvoCodeBench is an evolving benchmark to avoid data leakage. We build an automatic pipeline to update EvoCodeBench from the latest repositories. We release the first version - EvoCodeBench-2403, containing 275 samples from 25 real-world repositories. Based on EvoCodeBench, we propose repository-level code generation and evaluate 10 popular LLMs (e.g., gpt-4, gpt-3.5, DeepSeek Coder, StarCoder 2, CodeLLaMa, Gemma, and Qwen 1.5). Our experiments reveal the coding abilities of these LLMs in real-world repositories. For example, the highest Pass@1 of gpt-4 only is 20.73% in our experiments. We also analyze failed cases and summarize the shortcomings of existing LLMs in EvoCodeBench. We release EvoCodeBench, all prompts, and LLMs' completions for further community analysis.

Both the design and control of a robot play equally important roles in its task performance. However, while optimal control is well studied in the machine learning and robotics community, less attention is placed on finding the optimal robot design. This is mainly because co-optimizing design and control in robotics is characterized as a challenging problem, and more importantly, a comprehensive evaluation benchmark for co-optimization does not exist. In this paper, we propose Evolution Gym, the first large-scale benchmark for co-optimizing the design and control of soft robots. In our benchmark, each robot is composed of different types of voxels (e.g., soft, rigid, actuators), resulting in a modular and expressive robot design space. Our benchmark environments span a wide range of tasks, including locomotion on various types of terrains and manipulation. Furthermore, we develop several robot co-evolution algorithms by combining state-of-the-art design optimization methods and deep reinforcement learning techniques. Evaluating the algorithms on our benchmark platform, we observe robots exhibiting increasingly complex behaviors as evolution progresses, with the best evolved designs solving many of our proposed tasks. Additionally, even though robot designs are evolved autonomously from scratch without prior knowledge, they often grow to resemble existing natural creatures while outperforming hand-designed robots. Nevertheless, all tested algorithms fail to find robots that succeed in our hardest environments. This suggests that more advanced algorithms are required to explore the high-dimensional design space and evolve increasingly intelligent robots -- an area of research in which we hope Evolution Gym will accelerate progress. Our website with code, environments, documentation, and tutorials is available at http://evogym.csail.mit.edu.

Iterative improvement of model architectures is fundamental to deep learning: Transformers first enabled scaling, and recent advances in model hybridization have pushed the quality-efficiency frontier. However, optimizing architectures remains challenging and expensive. Current automated or manual approaches fall short, largely due to limited progress in the design of search spaces and due to the simplicity of resulting patterns and heuristics. In this work, we propose a new approach for the synthesis of tailored architectures (STAR). Our approach combines a novel search space based on the theory of linear input-varying systems, supporting a hierarchical numerical encoding into architecture genomes. STAR genomes are automatically refined and recombined with gradient-free, evolutionary algorithms to optimize for multiple model quality and efficiency metrics. Using STAR, we optimize large populations of new architectures, leveraging diverse computational units and interconnection patterns, improving over highly-optimized Transformers and striped hybrid models on the frontier of quality, parameter size, and inference cache for autoregressive language modeling.

Massive stars often evolve in binary systems, in which binary interactions significantly affect their evolution. Massive stars in the Galaxy serve as valuable testbeds for this due to their proximity. We computed the evolution of more than 38000 galactic binary systems with initial primary star masses of 5...100 Msun. In this paper, we aim to investigate the surface properties of post-mass transfer mass donor and mass gainer stars through core hydrogen burning, core helium burning, and for the pre-supernova stage. The models are computed with MESA, incorporating detailed stellar and binary physics, including internal differential rotation, magnetic angular momentum transport, mass-dependent overshooting, stellar wind mass-loss, mass and angular momentum transfer and tidal interaction. They incorporate a new extensive nuclear network for hydrogen burning, which allows us to track the full range of hydrogen burning nucleosynthesis products, from the light elements to aluminum. The widest, non-interacting binary models in our grid effectively serve as single star models. We find that mass gainers and mass donors may evolve through long-lived blue and yellow supergiant stages during core helium burning where single stars of the same mass remain red supergiants. Furthermore, some of our gainers evolve into more luminous yellow and blue supergiants prior to core collapse than single stars, while some donors end their life as red or yellow supergiants, showing a rich diversity in supernova progenitors. We show that the surface elemental and isotopic abundances carry valuable information about a star's evolutionary history and can be used to distinguish binary interaction products from single stars. Our binary model grid may serve as a tool for identifying post-mass transfer stars and supernovae, and holds potential for population studies, supernova modeling, and guidance of future observations.

We investigate the potential of bio-inspired evolutionary algorithms for designing quantum circuits with specific goals, focusing on two particular tasks. The first one is motivated by the ideas of Artificial Life that are used to reproduce stochastic cellular automata with given rules. We test the robustness of quantum implementations of the cellular automata for different numbers of quantum gates The second task deals with the sampling of quantum circuits that generate highly entangled quantum states, which constitute an important resource for quantum computing. In particular, an evolutionary algorithm is employed to optimize circuits with respect to a fitness function defined with the Mayer-Wallach entanglement measure. We demonstrate that, by balancing the mutation rate between exploration and exploitation, we can find entangling quantum circuits for up to five qubits. We also discuss the trade-off between the number of gates in quantum circuits and the computational costs of finding the gate arrangements leading to a strongly entangled state. Our findings provide additional insight into the trade-off between the complexity of a circuit and its performance, which is an important factor in the design of quantum circuits.

This work explores hypernetworks: an approach of using a one network, also known as a hypernetwork, to generate the weights for another network. Hypernetworks provide an abstraction that is similar to what is found in nature: the relationship between a genotype - the hypernetwork - and a phenotype - the main network. Though they are also reminiscent of HyperNEAT in evolution, our hypernetworks are trained end-to-end with backpropagation and thus are usually faster. The focus of this work is to make hypernetworks useful for deep convolutional networks and long recurrent networks, where hypernetworks can be viewed as relaxed form of weight-sharing across layers. Our main result is that hypernetworks can generate non-shared weights for LSTM and achieve near state-of-the-art results on a variety of sequence modelling tasks including character-level language modelling, handwriting generation and neural machine translation, challenging the weight-sharing paradigm for recurrent networks. Our results also show that hypernetworks applied to convolutional networks still achieve respectable results for image recognition tasks compared to state-of-the-art baseline models while requiring fewer learnable parameters.

Using a set of LambdaCDM simulations of cosmic structure formation, we study the evolving connectivity and changing topological structure of the cosmic web using state-of-the-art tools of multiscale topological data analysis (TDA). We follow the development of the cosmic web topology in terms of the evolution of Betti number curves and feature persistence diagrams of the three (topological) classes of structural features: matter concentrations, filaments and tunnels, and voids. The Betti curves specify the prominence of features as a function of density level, and their evolution with cosmic epoch reflects the changing network connections between these structural features. The persistence diagrams quantify the longevity and stability of topological features. In this study we establish, for the first time, the link between persistence diagrams, the features they show, and the gravitationally driven cosmic structure formation process. By following the diagrams' development over cosmic time, the link between the multiscale topology of the cosmic web and the hierarchical buildup of cosmic structure is established. The sharp apexes in the diagrams are intimately related to key transitions in the structure formation process. The apex in the matter concentration diagrams coincides with the density level at which, typically, they detach from the Hubble expansion and begin to collapse. At that level many individual islands merge to form the network of the cosmic web and a large number of filaments and tunnels emerge to establish its connecting bridges. The location trends of the apex possess a self-similar character that can be related to the cosmic web's hierarchical buildup. We find that persistence diagrams provide a significantly higher and more profound level of information on the structure formation process than more global summary statistics like Euler characteristic or Betti numbers.

Incorporating modular designs into neural networks demonstrates superior out-of-generalization, learning efficiency, etc. Existing modular neural networks are generally explicit because their modular architectures are pre-defined, and individual modules are expected to implement distinct functions. Conversely, recent works reveal that there exist implicit modular structures in standard pre-trained transformers, namely Emergent Modularity. They indicate that such modular structures exhibit during the early pre-training phase and are totally spontaneous. However, most transformers are still treated as monolithic models with their modular natures underutilized. Therefore, given the excellent properties of explicit modular architecture, we explore whether and how dense pre-trained transformers can benefit from emergent modular structures. To study this question, we construct Emergent Mixture-of-Experts (EMoE). Without introducing additional parameters, EMoE can be seen as the modular counterpart of the original model and can be effortlessly incorporated into downstream tuning. Extensive experiments (we tune 1785 models) on various downstream tasks (vision and language) and models (22M to1.5B) demonstrate that EMoE effectively boosts in-domain and out-of-domain generalization abilities. Further analysis and ablation study suggest that EMoE mitigates negative knowledge transfer and is robust to various configurations. Code is available at https://github.com/qiuzh20/EMoE

Neural architecture search (NAS) methods rely on a search strategy for deciding which architectures to evaluate next and a performance estimation strategy for assessing their performance (e.g., using full evaluations, multi-fidelity evaluations, or the one-shot model). In this paper, we focus on the search strategy. We introduce the simple yet powerful evolutionary algorithm of differential evolution to the NAS community. Using the simplest performance evaluation strategy of full evaluations, we comprehensively compare this search strategy to regularized evolution and Bayesian optimization and demonstrate that it yields improved and more robust results for 13 tabular NAS benchmarks based on NAS-Bench-101, NAS-Bench-1Shot1, NAS-Bench-201 and NAS-HPO bench.

Self-replication is a key aspect of biological life that has been largely overlooked in Artificial Intelligence systems. Here we describe how to build and train self-replicating neural networks. The network replicates itself by learning to output its own weights. The network is designed using a loss function that can be optimized with either gradient-based or non-gradient-based methods. We also describe a method we call regeneration to train the network without explicit optimization, by injecting the network with predictions of its own parameters. The best solution for a self-replicating network was found by alternating between regeneration and optimization steps. Finally, we describe a design for a self-replicating neural network that can solve an auxiliary task such as MNIST image classification. We observe that there is a trade-off between the network's ability to classify images and its ability to replicate, but training is biased towards increasing its specialization at image classification at the expense of replication. This is analogous to the trade-off between reproduction and other tasks observed in nature. We suggest that a self-replication mechanism for artificial intelligence is useful because it introduces the possibility of continual improvement through natural selection.

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyenas new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level, an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 17 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on all 8 datasets on average by +9 accuracy points.

We introduce the STATION, an open-world multi-agent environment that models a miniature scientific ecosystem. Leveraging their extended context windows, agents in the Station can engage in long scientific journeys that include reading papers from peers, formulating hypotheses, submitting code, performing analyses, and publishing results. Importantly, there is no centralized system coordinating their activities - agents are free to choose their own actions and develop their own narratives within the Station. Experiments demonstrate that AI agents in the Station achieve new state-of-the-art performance on a wide range of benchmarks, spanning from mathematics to computational biology to machine learning, notably surpassing AlphaEvolve in circle packing. A rich tapestry of narratives emerges as agents pursue independent research, interact with peers, and build upon a cumulative history. From these emergent narratives, novel methods arise organically, such as a new density-adaptive algorithm for scRNA-seq batch integration. The Station marks a first step towards autonomous scientific discovery driven by emergent behavior in an open-world environment, representing a new paradigm that moves beyond rigid optimization.

Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and protein generation. We introduce Gumbel-Softmax Flow and Score Matching, a generative framework on the simplex based on a novel Gumbel-Softmax interpolant with a time-dependent temperature. Using this interpolant, we introduce Gumbel-Softmax Flow Matching by deriving a parameterized velocity field that transports from smooth categorical distributions to distributions concentrated at a single vertex of the simplex. We alternatively present Gumbel-Softmax Score Matching which learns to regress the gradient of the probability density. Our framework enables high-quality, diverse generation and scales efficiently to higher-dimensional simplices. To enable training-free guidance, we propose Straight-Through Guided Flows (STGFlow), a classifier-based guidance method that leverages straight-through estimators to steer the unconditional velocity field toward optimal vertices of the simplex. STGFlow enables efficient inference-time guidance using classifiers pre-trained on clean sequences, and can be used with any discrete flow method. Together, these components form a robust framework for controllable de novo sequence generation. We demonstrate state-of-the-art performance in conditional DNA promoter design, sequence-only protein generation, and target-binding peptide design for rare disease treatment.

Large language models (LLMs) have recently shown strong coding abilities, enabling not only static code generation but also iterative code self-evolving through agentic frameworks. Recently, AlphaEvolve novikov2025alphaevolve demonstrated that LLM-based coding agents can autonomously improve algorithms and surpass human experts, with scopes limited to isolated kernels spanning hundreds of lines of code. Inspired by AlphaEvolve, we present SATLUTION, the first framework to extend LLM-based code evolution to the full repository scale, encompassing hundreds of files and tens of thousands of lines of C/C++ code. Targeting Boolean Satisfiability (SAT), the canonical NP-complete problem and a cornerstone of both theory and applications. SATLUTION orchestrates LLM agents to directly evolve solver repositories under strict correctness guarantees and distributed runtime feedback, while simultaneously self-evolving its own evolution policies and rules. Starting from SAT Competition 2024 codebases and benchmark, SATLUTION evolved solvers that decisively outperformed the human-designed winners of the SAT Competition 2025, and also surpassed both 2024 and 2025 champions on the 2024 benchmarks.

Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are essential, making prior methods potentially unsuitable in such contexts. Moreover, while trivial adaptations are available, empirical investigations reveal their limited efficacy as they do not properly model the interplay among graph components. To address this, we propose a joint score-based model of nodes and edges for graph generation that considers all graph components. Our approach offers two key novelties: (i) node and edge attributes are combined in an attention module that generates samples based on the two ingredients; and (ii) node, edge and adjacency information are mutually dependent during the graph diffusion process. We evaluate our method on challenging benchmarks involving real-world and synthetic datasets in which edge features are crucial. Additionally, we introduce a new synthetic dataset that incorporates edge values. Furthermore, we propose a novel application that greatly benefits from the method due to its nature: the generation of traffic scenes represented as graphs. Our method outperforms other graph generation methods, demonstrating a significant advantage in edge-related measures.

We propose an evolution strategies-based algorithm for estimating gradients in unrolled computation graphs, called ES-Single. Similarly to the recently-proposed Persistent Evolution Strategies (PES), ES-Single is unbiased, and overcomes chaos arising from recursive function applications by smoothing the meta-loss landscape. ES-Single samples a single perturbation per particle, that is kept fixed over the course of an inner problem (e.g., perturbations are not re-sampled for each partial unroll). Compared to PES, ES-Single is simpler to implement and has lower variance: the variance of ES-Single is constant with respect to the number of truncated unrolls, removing a key barrier in applying ES to long inner problems using short truncations. We show that ES-Single is unbiased for quadratic inner problems, and demonstrate empirically that its variance can be substantially lower than that of PES. ES-Single consistently outperforms PES on a variety of tasks, including a synthetic benchmark task, hyperparameter optimization, training recurrent neural networks, and training learned optimizers.

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

Large language models (LLMs) are increasingly trained with reinforcement learning from verifiable rewards (RLVR), yet real-world deployment demands models that can self-improve without labels or external judges. Existing label-free methods, confidence minimization, self-consistency, or majority-vote objectives, stabilize learning but steadily shrink exploration, causing an entropy collapse: generations become shorter, less diverse, and brittle. Unlike prior approaches such as Test-Time Reinforcement Learning (TTRL), which primarily adapt models to the immediate unlabeled dataset at hand, our goal is broader: to enable general improvements without sacrificing the model's inherent exploration capacity and generalization ability, i.e., evolving. We formalize this issue and propose EVolution-Oriented and Label-free Reinforcement Learning (EVOL-RL), a simple rule that couples stability with variation under a label-free setting. EVOL-RL keeps the majority-voted answer as a stable anchor (selection) while adding a novelty-aware reward that favors responses whose reasoning differs from what has already been produced (variation), measured in semantic space. Implemented with GRPO, EVOL-RL also uses asymmetric clipping to preserve strong signals and an entropy regularizer to sustain search. This majority-for-selection + novelty-for-variation design prevents collapse, maintains longer and more informative chains of thought, and improves both pass@1 and pass@n. EVOL-RL consistently outperforms the majority-only TTRL baseline; e.g., training on label-free AIME24 lifts Qwen3-4B-Base AIME25 pass@1 from TTRL's 4.6% to 16.4%, and pass@16 from 18.5% to 37.9%. EVOL-RL not only prevents diversity collapse but also unlocks stronger generalization across domains (e.g., GPQA). Furthermore, we demonstrate that EVOL-RL also boosts performance in the RLVR setting, highlighting its broad applicability.

Large language models (LLMs) provide a compelling foundation for building generally-capable AI agents. These agents may soon be deployed at scale in the real world, representing the interests of individual humans (e.g., AI assistants) or groups of humans (e.g., AI-accelerated corporations). At present, relatively little is known about the dynamics of multiple LLM agents interacting over many generations of iterative deployment. In this paper, we examine whether a "society" of LLM agents can learn mutually beneficial social norms in the face of incentives to defect, a distinctive feature of human sociality that is arguably crucial to the success of civilization. In particular, we study the evolution of indirect reciprocity across generations of LLM agents playing a classic iterated Donor Game in which agents can observe the recent behavior of their peers. We find that the evolution of cooperation differs markedly across base models, with societies of Claude 3.5 Sonnet agents achieving significantly higher average scores than Gemini 1.5 Flash, which, in turn, outperforms GPT-4o. Further, Claude 3.5 Sonnet can make use of an additional mechanism for costly punishment to achieve yet higher scores, while Gemini 1.5 Flash and GPT-4o fail to do so. For each model class, we also observe variation in emergent behavior across random seeds, suggesting an understudied sensitive dependence on initial conditions. We suggest that our evaluation regime could inspire an inexpensive and informative new class of LLM benchmarks, focussed on the implications of LLM agent deployment for the cooperative infrastructure of society.

In the past few years, Differentiable Neural Architecture Search (DNAS) rapidly imposed itself as the trending approach to automate the discovery of deep neural network architectures. This rise is mainly due to the popularity of DARTS, one of the first major DNAS methods. In contrast with previous works based on Reinforcement Learning or Evolutionary Algorithms, DNAS is faster by several orders of magnitude and uses fewer computational resources. In this comprehensive survey, we focus specifically on DNAS and review recent approaches in this field. Furthermore, we propose a novel challenge-based taxonomy to classify DNAS methods. We also discuss the contributions brought to DNAS in the past few years and its impact on the global NAS field. Finally, we conclude by giving some insights into future research directions for the DNAS field.

Graph Edit Distance (GED) measures the (dis-)similarity between two given graphs, in terms of the minimum-cost edit sequence that transforms one graph to the other. However, the exact computation of GED is NP-Hard, which has recently motivated the design of neural methods for GED estimation. However, they do not explicitly account for edit operations with different costs. In response, we propose GRAPHEDX, a neural GED estimator that can work with general costs specified for the four edit operations, viz., edge deletion, edge addition, node deletion and node addition. We first present GED as a quadratic assignment problem (QAP) that incorporates these four costs. Then, we represent each graph as a set of node and edge embeddings and use them to design a family of neural set divergence surrogates. We replace the QAP terms corresponding to each operation with their surrogates. Computing such neural set divergence require aligning nodes and edges of the two graphs. We learn these alignments using a Gumbel-Sinkhorn permutation generator, additionally ensuring that the node and edge alignments are consistent with each other. Moreover, these alignments are cognizant of both the presence and absence of edges between node-pairs. Experiments on several datasets, under a variety of edit cost settings, show that GRAPHEDX consistently outperforms state-of-the-art methods and heuristics in terms of prediction error.

We propose Beam Tree Recursive Cell (BT-Cell) - a backpropagation-friendly framework to extend Recursive Neural Networks (RvNNs) with beam search for latent structure induction. We further extend this framework by proposing a relaxation of the hard top-k operators in beam search for better propagation of gradient signals. We evaluate our proposed models in different out-of-distribution splits in both synthetic and realistic data. Our experiments show that BTCell achieves near-perfect performance on several challenging structure-sensitive synthetic tasks like ListOps and logical inference while maintaining comparable performance in realistic data against other RvNN-based models. Additionally, we identify a previously unknown failure case for neural models in generalization to unseen number of arguments in ListOps. The code is available at: https://github.com/JRC1995/BeamTreeRecursiveCells.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

We introduce the Bittensor Language Model, called "BTLM-3B-8K", a new state-of-the-art 3 billion parameter open-source language model. BTLM-3B-8K was trained on 627B tokens from the SlimPajama dataset with a mixture of 2,048 and 8,192 context lengths. BTLM-3B-8K outperforms all existing 3B parameter models by 2-5.5% across downstream tasks. BTLM-3B-8K is even competitive with some 7B parameter models. Additionally, BTLM-3B-8K provides excellent long context performance, outperforming MPT-7B-8K and XGen-7B-8K on tasks up to 8,192 context length. We trained the model on a cleaned and deduplicated SlimPajama dataset; aggressively tuned the \textmu P hyperparameters and schedule; used ALiBi position embeddings; and adopted the SwiGLU nonlinearity. On Hugging Face, the most popular models have 7B parameters, indicating that users prefer the quality-size ratio of 7B models. Compacting the 7B parameter model to one with 3B parameters, with little performance impact, is an important milestone. BTLM-3B-8K needs only 3GB of memory with 4-bit precision and takes 2.5x less inference compute than 7B models, helping to open up access to a powerful language model on mobile and edge devices. BTLM-3B-8K is available under an Apache 2.0 license on Hugging Face: https://huggingface.co/cerebras/btlm-3b-8k-base.

We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules. The model learns to transform a uniform source over all possible tokens into the data distribution. Unlike masked models, its training loss accounts for predictions on all sequence positions at every denoising step, shifting the generation paradigm from completion to refinement, and decoupling the number of sampling steps from the sequence length. For de novo generation, InVirtuoGen achieves a stronger quality-diversity pareto frontier than prior fragment-based models and competitive performance on fragment-constrained tasks. For property and lead optimization, we propose a hybrid scheme that combines a genetic algorithm with a Proximal Property Optimization fine-tuning strategy adapted to discrete flows. Our approach sets a new state-of-the-art on the Practical Molecular Optimization benchmark, measured by top-10 AUC across tasks, and yields higher docking scores in lead optimization than previous baselines. InVirtuoGen thus establishes a versatile generative foundation for drug discovery, from early hit finding to multi-objective lead optimization. We further contribute to open science by releasing pretrained checkpoints and code, making our results fully reproduciblehttps://github.com/invirtuolabs/InVirtuoGen_results.

Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

Artificial intelligence (AI) has undergone a renaissance recently, making major progress in key domains such as vision, language, control, and decision-making. This has been due, in part, to cheap data and cheap compute resources, which have fit the natural strengths of deep learning. However, many defining characteristics of human intelligence, which developed under much different pressures, remain out of reach for current approaches. In particular, generalizing beyond one's experiences--a hallmark of human intelligence from infancy--remains a formidable challenge for modern AI. The following is part position paper, part review, and part unification. We argue that combinatorial generalization must be a top priority for AI to achieve human-like abilities, and that structured representations and computations are key to realizing this objective. Just as biology uses nature and nurture cooperatively, we reject the false choice between "hand-engineering" and "end-to-end" learning, and instead advocate for an approach which benefits from their complementary strengths. We explore how using relational inductive biases within deep learning architectures can facilitate learning about entities, relations, and rules for composing them. We present a new building block for the AI toolkit with a strong relational inductive bias--the graph network--which generalizes and extends various approaches for neural networks that operate on graphs, and provides a straightforward interface for manipulating structured knowledge and producing structured behaviors. We discuss how graph networks can support relational reasoning and combinatorial generalization, laying the foundation for more sophisticated, interpretable, and flexible patterns of reasoning. As a companion to this paper, we have released an open-source software library for building graph networks, with demonstrations of how to use them in practice.

The fine-tuning of Large Language Models (LLMs) specialized in code generation has seen notable advancements through the use of open-domain coding queries. Despite the successes, existing methodologies like Evol-Instruct encounter performance limitations, impeding further enhancements in code generation tasks. This paper examines the constraints of existing prompt evolution techniques and introduces a novel approach, Instruction Fusion (IF). IF innovatively combines two distinct prompts through a hybridization process, thereby enhancing the evolution of training prompts for code LLMs. Our experimental results reveal that the proposed novel method effectively addresses the shortcomings of prior methods, significantly improving the performance of Code LLMs across five code generation benchmarks, namely HumanEval, HumanEval+, MBPP, MBPP+ and MultiPL-E, which underscore the effectiveness of Instruction Fusion in advancing the capabilities of LLMs in code generation.

We explore efficient neural architecture search methods and show that a simple yet powerful evolutionary algorithm can discover new architectures with excellent performance. Our approach combines a novel hierarchical genetic representation scheme that imitates the modularized design pattern commonly adopted by human experts, and an expressive search space that supports complex topologies. Our algorithm efficiently discovers architectures that outperform a large number of manually designed models for image classification, obtaining top-1 error of 3.6% on CIFAR-10 and 20.3% when transferred to ImageNet, which is competitive with the best existing neural architecture search approaches. We also present results using random search, achieving 0.3% less top-1 accuracy on CIFAR-10 and 0.1% less on ImageNet whilst reducing the search time from 36 hours down to 1 hour.

The Branch-and-bound (B&B) algorithm is the main solver for Mixed Integer Linear Programs (MILPs), where the selection of branching variable is essential to computational efficiency. However, traditional heuristics for branching often fail to generalize across heterogeneous problem instances, while existing learning-based methods such as imitation learning (IL) suffers from dependence on expert demonstration quality, and reinforcement learning (RL) struggles with limitations in sparse rewards and dynamic state representation challenges. To address these issues, we propose ReviBranch, a novel deep RL framework that constructs revived trajectories by reviving explicit historical correspondences between branching decisions and their corresponding graph states along search-tree paths. During training, ReviBranch enables agents to learn from complete structural evolution and temporal dependencies within the branching process. Additionally, we introduce an importance-weighted reward redistribution mechanism that transforms sparse terminal rewards into dense stepwise feedback, addressing the sparse reward challenge. Extensive experiments on different MILP benchmarks demonstrate that ReviBranch outperforms state-of-the-art RL methods, reducing B&B nodes by 4.0% and LP iterations by 2.2% on large-scale instances. The results highlight the robustness and generalizability of ReviBranch across heterogeneous MILP problem classes.

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.