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Jul 10

From the RNA world to land plants: Evolutionary insights from tRNA genes

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.

  • 4 authors
·
Nov 3, 2025

daVinci-Agency: Unlocking Long-Horizon Agency Data-Efficiently

While Large Language Models (LLMs) excel at short-term tasks, scaling them to long-horizon agentic workflows remains challenging. The core bottleneck lies in the scarcity of training data that captures authentic long-dependency structures and cross-stage evolutionary dynamics--existing synthesis methods either confine to single-feature scenarios constrained by model distribution, or incur prohibitive human annotation costs, failing to provide scalable, high-quality supervision. We address this by reconceptualizing data synthesis through the lens of real-world software evolution. Our key insight: Pull Request (PR) sequences naturally embody the supervision signals for long-horizon learning. They decompose complex objectives into verifiable submission units, maintain functional coherence across iterations, and encode authentic refinement patterns through bug-fix histories. Building on this, we propose daVinci-Agency, which systematically mines structured supervision from chain-of-PRs through three interlocking mechanisms: (1) progressive task decomposition via continuous commits, (2) long-term consistency enforcement through unified functional objectives, and (3) verifiable refinement from authentic bug-fix trajectories. Unlike synthetic trajectories that treat each step independently, daVinci-Agency's PR-grounded structure inherently preserves the causal dependencies and iterative refinements essential for teaching persistent goal-directed behavior and enables natural alignment with project-level, full-cycle task modeling. The resulting trajectories are substantial--averaging 85k tokens and 116 tool calls--yet remarkably data-efficient: fine-tuning GLM-4.6 on 239 daVinci-Agency samples yields broad improvements across benchmarks, notably achieving a 47% relative gain on Toolathlon. Beyond benchmark performance, our analysis confirms...

GAIR SII - GAIR
·
Feb 2 3

A Survey of Self-Evolving Agents: On Path to Artificial Super Intelligence

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.

  • 27 authors
·
Jul 28, 2025 4

Ideas Have Genomes: Benchmarking Scientific Lineage Reasoning and Lineage-Grounded Idea Generation

Scientific ideas rarely start from a blank page. They inherit mechanisms, repair known limitations, and recombine pieces of earlier work, much like biological genomes. Current benchmarks still say little about whether AI systems can follow this inheritance structure. We present IdeaGene-Bench (IG-Bench), a benchmark for scientific lineage reasoning and lineage-grounded idea generation. IG-Bench is organized around the IdeaGene framework: each paper or proposal is represented as a set of minimal, typed, evidence-grounded Idea Genome objects, and a GenomeDiff aligns these objects to record inheritance, mutation, loss, external import, and novel insertion under six operational evolutionary dynamics. The benchmark contains 1,961 golden lineage traces, 1,085 curated Idea Genome objects, and 920 pairwise GenomeDiff records across 10 scientific domains. It supports two evaluations. IG-Exam (42 task types, 1,029 instances) tests closed-form lineage reasoning across Idea Genome abstraction, inheritance tracing, evolutionary reasoning, and lineage verification. IG-Arena evaluates generation with a lineage-conditioned Population-Evolution Score(PES), asking whether a proposal can be inserted as a coherent descendant of a given lineage population: it should inherit the right Idea Genome objects, vary meaningfully from nearby work, and offer selection value for future research. Experiments on 14 LLM-based scientists expose a compositional bottleneck. The strongest system reaches only 27.3% exact accuracy on lineage reasoning, and structured lineage context reshuffles system rankings rather than helping every participant uniformly.

A Co-Evolutionary Theory of Human-AI Coexistence: Mutualism, Governance, and Dynamics in Complex Societies

Classical robot ethics is often framed around obedience, most famously through Asimov's laws. This framing is too narrow for contemporary AI systems, which are adaptive, generative, embodied, and embedded in physical, psychological, and social worlds. We argue that future human-AI relations should be understood not as master-tool obedience, but as conditional mutualism under governance: a co-evolutionary relationship in which humans and AI systems can develop, specialize, and coordinate while institutions keep the relation reciprocal, reversible, psychologically safe, and socially legitimate. We synthesize concepts from computability, machine learning, foundation models, embodied AI, alignment, human-robot interaction, ecological mutualism, coevolution, and polycentric governance. We then formalize coexistence as a multiplex dynamical system across physical, psychological, and social layers, with reciprocal supply-demand coupling, conflict penalties, developmental freedom, and governance regularization. The model gives conditions for existence, uniqueness, and global asymptotic stability of equilibria. Deterministic ODE simulations, basin sweeps, sensitivity analyses, governance-regime comparisons, shock tests, and local stability checks show that governed mutualism reaches high coexistence with zero domination, while absent or excessive governance can produce domination, weak-benefit lock-in, or suppressed development. The results suggest that human-AI coexistence should be designed as a co-evolutionary governance problem, not a one-shot obedience problem.

  • 1 authors
·
Apr 26

OR-Agent: Bridging Evolutionary Search and Structured Research for Automated Algorithm Discovery

Automating scientific discovery in complex, experiment-driven domains requires more than iterative mutation of programs; it demands structured hypothesis management, environment interaction, and principled reflection. We present OR-Agent, a configurable multi-agent research framework designed for automated exploration in rich experimental environments. OR-Agent organizes research as a structured tree-based workflow that explicitly models branching hypothesis generation and systematic backtracking, enabling controlled management of research trajectories beyond simple mutation-crossover loops. At its core, we introduce an evolutionary-systematic ideation mechanism that unifies evolutionary selection of research starting points, comprehensive research plan generation, and coordinated exploration within a research tree. We introduce a hierarchical optimization-inspired reflection system in which short-term reflections act as verbal gradients, long-term reflections as verbal momentum, and memory compression as semantic weight decay, collectively forming a principled mechanism for governing research dynamics. We conduct extensive experiments across classical combinatorial optimization benchmarks as well as simulation-based cooperative driving scenarios. Results demonstrate that OR-Agent outperforms strong evolutionary baselines while providing a general, extensible, and inspectable framework for AI-assisted scientific discovery. All code and experimental data are publicly available at https://github.com/qiliuchn/OR-Agent.

  • 4 authors
·
Feb 14

Metal-Sci: A Scientific Compute Benchmark for Evolutionary LLM Kernel Search on Apple Silicon

We present Metal-Sci, a 10-task benchmark of scientific Apple Silicon Metal compute kernels spanning six optimization regimes (stencils, all-pairs in n-body problems, multi-field Boltzmann, neighbor-list molecular dynamics, multi-kernel PDE, FFT). Each task ships a CPU reference, a roofline-anchored fitness function, and a held-out generalization size. We pair the benchmark with a lightweight harness for automatic kernel search that runtime-compiles each candidate, scores it against the roofline across multiple sizes, and feeds structured compile and per-size correctness diagnostics back to a frozen LLM driving a (1{+}1) evolutionary loop. We report matched single-model sweeps of Claude Opus 4.7, Gemini 3.1 Pro, and GPT 5.5 on M1 Pro: in-distribution self-speedups span 1.00times to 10.7times. Beyond raw speedup, our central methodological claim is structural: the held-out gate scoring function Φ_T (evaluated once at end-of-run on a configuration the agent never sees during search) functions as a cheap mechanical oversight primitive on this automatic search loop, catching e.g. an Opus template <uint D> HMC win that returns wrong samples at unseen dimensions, and a GPT FFT3D best that wins in-distribution at 2.95times speedup but collapses to 0.23times on a 256^3 held-out cube, a silent regression that the in-distribution score alone cannot see. Code at https://github.com/vicgalle/metal-sci-kernels

  • 1 authors
·
May 9 1

Cognitio Emergens: Agency, Dimensions, and Dynamics in Human-AI Knowledge Co-Creation

Scientific knowledge creation is fundamentally transforming as humans and AI systems evolve beyond tool-user relationships into co-evolutionary epistemic partnerships. When AlphaFold revolutionized protein structure prediction, researchers described engaging with an epistemic partner that reshaped how they conceptualized fundamental relationships. This article introduces Cognitio Emergens (CE), a framework addressing critical limitations in existing models that focus on static roles or narrow metrics while failing to capture how scientific understanding emerges through recursive human-AI interaction over time. CE integrates three components addressing these limitations: Agency Configurations describing how authority distributes between humans and AI (Directed, Contributory, Partnership), with partnerships dynamically oscillating between configurations rather than following linear progression; Epistemic Dimensions capturing six specific capabilities emerging through collaboration across Discovery, Integration, and Projection axes, creating distinctive "capability signatures" that guide development; and Partnership Dynamics identifying forces shaping how these relationships evolve, particularly the risk of epistemic alienation where researchers lose interpretive control over knowledge they formally endorse. Drawing from autopoiesis theory, social systems theory, and organizational modularity, CE reveals how knowledge co-creation emerges through continuous negotiation of roles, values, and organizational structures. By reconceptualizing human-AI scientific collaboration as fundamentally co-evolutionary, CE offers a balanced perspective that neither uncritically celebrates nor unnecessarily fears AI's evolving role, instead providing conceptual tools for cultivating partnerships that maintain meaningful human participation while enabling transformative scientific breakthroughs.

  • 1 authors
·
May 5, 2025 1

Agentic End-to-End De Novo Protein Design for Tailored Dynamics Using a Language Diffusion Model

Proteins are dynamic molecular machines whose biological functions, spanning enzymatic catalysis, signal transduction, and structural adaptation, are intrinsically linked to their motions. Designing proteins with targeted dynamic properties, however, remains a challenge due to the complex, degenerate relationships between sequence, structure, and molecular motion. Here, we introduce VibeGen, a generative AI framework that enables end-to-end de novo protein design conditioned on normal mode vibrations. VibeGen employs an agentic dual-model architecture, comprising a protein designer that generates sequence candidates based on specified vibrational modes and a protein predictor that evaluates their dynamic accuracy. This approach synergizes diversity, accuracy, and novelty during the design process. Via full-atom molecular simulations as direct validation, we demonstrate that the designed proteins accurately reproduce the prescribed normal mode amplitudes across the backbone while adopting various stable, functionally relevant structures. Notably, generated sequences are de novo, exhibiting no significant similarity to natural proteins, thereby expanding the accessible protein space beyond evolutionary constraints. Our work integrates protein dynamics into generative protein design, and establishes a direct, bidirectional link between sequence and vibrational behavior, unlocking new pathways for engineering biomolecules with tailored dynamical and functional properties. This framework holds broad implications for the rational design of flexible enzymes, dynamic scaffolds, and biomaterials, paving the way toward dynamics-informed AI-driven protein engineering.

  • 2 authors
·
Feb 14, 2025 2

Advances and Challenges in Foundation Agents: From Brain-Inspired Intelligence to Evolutionary, Collaborative, and Safe Systems

The advent of large language models (LLMs) has catalyzed a transformative shift in artificial intelligence, paving the way for advanced intelligent agents capable of sophisticated reasoning, robust perception, and versatile action across diverse domains. As these agents increasingly drive AI research and practical applications, their design, evaluation, and continuous improvement present intricate, multifaceted challenges. This survey provides a comprehensive overview, framing intelligent agents within a modular, brain-inspired architecture that integrates principles from cognitive science, neuroscience, and computational research. We structure our exploration into four interconnected parts. First, we delve into the modular foundation of intelligent agents, systematically mapping their cognitive, perceptual, and operational modules onto analogous human brain functionalities, and elucidating core components such as memory, world modeling, reward processing, and emotion-like systems. Second, we discuss self-enhancement and adaptive evolution mechanisms, exploring how agents autonomously refine their capabilities, adapt to dynamic environments, and achieve continual learning through automated optimization paradigms, including emerging AutoML and LLM-driven optimization strategies. Third, we examine collaborative and evolutionary multi-agent systems, investigating the collective intelligence emerging from agent interactions, cooperation, and societal structures, highlighting parallels to human social dynamics. Finally, we address the critical imperative of building safe, secure, and beneficial AI systems, emphasizing intrinsic and extrinsic security threats, ethical alignment, robustness, and practical mitigation strategies necessary for trustworthy real-world deployment.

  • 47 authors
·
Mar 31, 2025 8

Digital Red Queen: Adversarial Program Evolution in Core War with LLMs

Large language models (LLMs) are increasingly being used to evolve solutions to problems in many domains, in a process inspired by biological evolution. However, unlike biological evolution, most LLM-evolution frameworks are formulated as static optimization problems, overlooking the open-ended adversarial dynamics that characterize real-world evolutionary processes. Here, we study Digital Red Queen (DRQ), a simple self-play algorithm that embraces these so-called "Red Queen" dynamics via continual adaptation to a changing objective. DRQ uses an LLM to evolve assembly-like programs, called warriors, which compete against each other for control of a virtual machine in the game of Core War, a Turing-complete environment studied in artificial life and connected to cybersecurity. In each round of DRQ, the model evolves a new warrior to defeat all previous ones, producing a sequence of adapted warriors. Over many rounds, we observe that warriors become increasingly general (relative to a set of held-out human warriors). Interestingly, warriors also become less behaviorally diverse across independent runs, indicating a convergence pressure toward a general-purpose behavioral strategy, much like convergent evolution in nature. This result highlights a potential value of shifting from static objectives to dynamic Red Queen objectives. Our work positions Core War as a rich, controllable sandbox for studying adversarial adaptation in artificial systems and for evaluating LLM-based evolution methods. More broadly, the simplicity and effectiveness of DRQ suggest that similarly minimal self-play approaches could prove useful in other more practical multi-agent adversarial domains, like real-world cybersecurity or combating drug resistance.

  • 7 authors
·
Jan 6

What's In Your Field? Mapping Scientific Research with Knowledge Graphs and Large Language Models

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

  • 4 authors
·
Mar 12, 2025

URPO: A Unified Reward & Policy Optimization Framework for Large Language Models

Large-scale alignment pipelines typically pair a policy model with a separately trained reward model whose parameters remain frozen during reinforcement learning (RL). This separation creates a complex, resource-intensive pipeline and suffers from a performance ceiling due to a static reward signal. We propose a novel framework, Unified Reward & Policy Optimization (URPO), that unifies instruction-following ("player") and reward modeling ("referee") within a single model and a single training phase. Our method recasts all alignment data-including preference pairs, verifiable reasoning, and open-ended instructions-into a unified generative format optimized by a single Group-Relative Policy Optimization (GRPO) loop. This enables the model to learn from ground-truth preferences and verifiable logic while simultaneously generating its own rewards for open-ended tasks. Experiments on the Qwen2.5-7B model demonstrate URPO's superiority. Our unified model significantly outperforms a strong baseline using a separate generative reward model, boosting the instruction-following score on AlpacaEval from 42.24 to 44.84 and the composite reasoning average from 32.66 to 35.66. Furthermore, URPO cultivates a superior internal evaluator as a byproduct of training, achieving a RewardBench score of 85.15 and surpassing the dedicated reward model it replaces (83.55). By eliminating the need for a separate reward model and fostering a co-evolutionary dynamic between generation and evaluation, URPO presents a simpler, more efficient, and more effective path towards robustly aligned language models.

  • 4 authors
·
Jul 23, 2025

EvoLattice: Persistent Internal-Population Evolution through Multi-Alternative Quality-Diversity Graph Representations for LLM-Guided Program Discovery

Large language models (LLMs) are increasingly used to evolve programs and multi-agent systems, yet most existing approaches rely on overwrite-based mutations that maintain only a single candidate at a time. Such methods discard useful variants, suffer from destructive edits, and explore a brittle search space prone to structural failure. We introduce EvoLattice, a framework that represents an entire population of candidate programs or agent behaviors within a single directed acyclic graph. Each node stores multiple persistent alternatives, and every valid path through the graph defines a distinct executable candidate, yielding a large combinatorial search space without duplicating structure. EvoLattice enables fine-grained alternative-level evaluation by scoring each alternative across all paths in which it appears, producing statistics that reveal how local design choices affect global performance. These statistics provide a dense, data-driven feedback signal for LLM-guided mutation, recombination, and pruning, while preserving successful components. Structural correctness is guaranteed by a deterministic self-repair mechanism that enforces acyclicity and dependency consistency independently of the LLM. EvoLattice naturally extends to agent evolution by interpreting alternatives as prompt fragments or sub-agent behaviors. Across program synthesis (proxy and optimizer meta-learning), EvoLattice yields more stable evolution, greater expressivity, and stronger improvement trajectories than prior LLM-guided methods. The resulting dynamics resemble quality-diversity optimization, emerging implicitly from EvoLattice's internal multi-alternative representation rather than an explicit external archive.

  • 1 authors
·
Dec 16, 2025

All You Need Is Sex for Diversity

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.

  • 3 authors
·
Mar 30, 2023

Cultural evolution in populations of Large Language Models

Research in cultural evolution aims at providing causal explanations for the change of culture over time. Over the past decades, this field has generated an important body of knowledge, using experimental, historical, and computational methods. While computational models have been very successful at generating testable hypotheses about the effects of several factors, such as population structure or transmission biases, some phenomena have so far been more complex to capture using agent-based and formal models. This is in particular the case for the effect of the transformations of social information induced by evolved cognitive mechanisms. We here propose that leveraging the capacity of Large Language Models (LLMs) to mimic human behavior may be fruitful to address this gap. On top of being an useful approximation of human cultural dynamics, multi-agents models featuring generative agents are also important to study for their own sake. Indeed, as artificial agents are bound to participate more and more to the evolution of culture, it is crucial to better understand the dynamics of machine-generated cultural evolution. We here present a framework for simulating cultural evolution in populations of LLMs, allowing the manipulation of variables known to be important in cultural evolution, such as network structure, personality, and the way social information is aggregated and transformed. The software we developed for conducting these simulations is open-source and features an intuitive user-interface, which we hope will help to build bridges between the fields of cultural evolution and generative artificial intelligence.

  • 7 authors
·
Mar 13, 2024

Leslie Population Models in Predator-prey and Competitive populations: theory and applications by machine learning

We introduce a new predator-prey model by replacing the growth and predation constant by a square matrix, and the population density as a population vector. The classical Lotka-Volterra model describes a population that either modulates or converges. Stability analysis of such models have been extensively studied by the works of Merdan (https://doi.org/10.1016/j.chaos.2007.06.062). The new model adds complexity by introducing an age group structure where the population of each age group evolves as prescribed by the Leslie matrix. The added complexity changes the behavior of the model such that the population either displays roughly an exponential growth or decay. We first provide an exact equation that describes a time evolution and use analytic techniques to obtain an approximate growth factor. We also discuss the variants of the Leslie model, i.e., the complex value predator-prey model and the competitive model. We then prove the Last Species Standing theorem that determines the dominant population in the large time limit. The recursive structure of the model denies the application of simple regression. We discuss a machine learning scheme that allows an admissible fit for the population evolution of Paramecium Aurelia and Paramecium Caudatum. Another potential avenue to simplify the computation is to use the machinery of quantum operators. We demonstrate the potential of this approach by computing the Hamiltonian of a simple Leslie system.

  • 5 authors
·
Dec 20, 2024

Data Darwinism Part II: DataEvolve -- AI can Autonomously Evolve Pretraining Data Curation

Data Darwinism (Part I) established a ten-level hierarchy for data processing, showing that stronger processing can unlock greater data value. However, that work relied on manually designed strategies for a single category. Modern pretraining corpora comprise hundreds of heterogeneous categories spanning domains and content types, each demanding specialized treatment. At this scale, manual strategy design becomes prohibitive. This raises a key question: can strategies evolve in an automated way? We introduce DataEvolve, a framework that enables strategies to evolve through iterative optimization rather than manual design. For each data category, DataEvolve operates in a closed evolutionary loop: it identifies quality issues, generates candidate strategies, executes them on sampled data, evaluates results, and refines approaches across generations. The process accumulates knowledge through an experience pool of discovered issues and a strategy pool tracking performance across iterations. Applied to 8 categories spanning 672B tokens from Nemotron-CC, DataEvolve produces Darwin-CC, a 504B-token dataset with strategies evolved through 30 iterations per category. Training 3B models on 500B tokens, Darwin-CC outperforms raw data (+3.96 points) and achieves a 44.13 average score across 18 benchmarks, surpassing DCLM, Ultra-FineWeb, and FineWeb-Edu, with strong gains on knowledge-intensive tasks such as MMLU. Analysis shows evolved strategies converge on cleaning-focused approaches: targeted noise removal and format normalization with domain-aware preservation, echoing the L4 (Generative Refinement) principles from Part I. Ablation studies confirm iterative evolution is essential: optimized strategies outperform suboptimal ones by 2.93 points, establishing evolutionary strategy design as feasible and necessary for pretraining-scale data curation.

  • 9 authors
·
Mar 14

Your Agent May Misevolve: Emergent Risks in Self-evolving LLM Agents

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.

  • 11 authors
·
Sep 30, 2025 2

From Grunts to Grammar: Emergent Language from Cooperative Foraging

Early cavemen relied on gestures, vocalizations, and simple signals to coordinate, plan, avoid predators, and share resources. Today, humans collaborate using complex languages to achieve remarkable results. What drives this evolution in communication? How does language emerge, adapt, and become vital for teamwork? Understanding the origins of language remains a challenge. A leading hypothesis in linguistics and anthropology posits that language evolved to meet the ecological and social demands of early human cooperation. Language did not arise in isolation, but through shared survival goals. Inspired by this view, we investigate the emergence of language in multi-agent Foraging Games. These environments are designed to reflect the cognitive and ecological constraints believed to have influenced the evolution of communication. Agents operate in a shared grid world with only partial knowledge about other agents and the environment, and must coordinate to complete games like picking up high-value targets or executing temporally ordered actions. Using end-to-end deep reinforcement learning, agents learn both actions and communication strategies from scratch. We find that agents develop communication protocols with hallmark features of natural language: arbitrariness, interchangeability, displacement, cultural transmission, and compositionality. We quantify each property and analyze how different factors, such as population size and temporal dependencies, shape specific aspects of the emergent language. Our framework serves as a platform for studying how language can evolve from partial observability, temporal reasoning, and cooperative goals in embodied multi-agent settings. We will release all data, code, and models publicly.

  • 7 authors
·
May 19, 2025 2

Opinion Dynamics Models for Sentiment Evolution in Weibo Blogs

Online social media platforms enable influencers to distribute content and quickly capture audience reactions, significantly shaping their promotional strategies and advertising agreements. Understanding how sentiment dynamics and emotional contagion unfold among followers is vital for influencers and marketers, as these processes shape engagement, brand perception, and purchasing behavior. While sentiment analysis tools effectively track sentiment fluctuations, dynamical models explaining their evolution remain limited, often neglecting network structures and interactions both among blogs and between their topic-focused follower groups. In this study, we tracked influential tech-focused Weibo bloggers over six months, quantifying follower sentiment from text-mined feedback. By treating each blogger's audience as a single "macro-agent", we find that sentiment trajectories follow the principle of iterative averaging -- a foundational mechanism in many dynamical models of opinion formation, a theoretical framework at the intersection of social network analysis and dynamical systems theory. The sentiment evolution aligns closely with opinion-dynamics models, particularly modified versions of the classical French-DeGroot model that incorporate delayed perception and distinguish between expressed and private opinions. The inferred influence structures reveal interdependencies among blogs that may arise from homophily, whereby emotionally similar users subscribe to the same blogs and collectively shape the shared sentiment expressed within these communities.

  • 3 authors
·
Nov 18, 2025

MetaDE: Evolving Differential Evolution by Differential Evolution

As a cornerstone in the Evolutionary Computation (EC) domain, Differential Evolution (DE) is known for its simplicity and effectiveness in handling challenging black-box optimization problems. While the advantages of DE are well-recognized, achieving peak performance heavily depends on its hyperparameters such as the mutation factor, crossover probability, and the selection of specific DE strategies. Traditional approaches to this hyperparameter dilemma have leaned towards parameter tuning or adaptive mechanisms. However, identifying the optimal settings tailored for specific problems remains a persistent challenge. In response, we introduce MetaDE, an approach that evolves DE's intrinsic hyperparameters and strategies using DE itself at a meta-level. A pivotal aspect of MetaDE is a specialized parameterization technique, which endows it with the capability to dynamically modify DE's parameters and strategies throughout the evolutionary process. To augment computational efficiency, MetaDE incorporates a design that leverages parallel processing through a GPU-accelerated computing framework. Within such a framework, DE is not just a solver but also an optimizer for its own configurations, thus streamlining the process of hyperparameter optimization and problem-solving into a cohesive and automated workflow. Extensive evaluations on the CEC2022 benchmark suite demonstrate MetaDE's promising performance. Moreover, when applied to robot control via evolutionary reinforcement learning, MetaDE also demonstrates promising performance. The source code of MetaDE is publicly accessible at: https://github.com/EMI-Group/metade.

  • 3 authors
·
Feb 13, 2025

EvoArena: Tracking Memory Evolution for Robust LLM Agents in Dynamic Environments

Large language model (LLM) agents have achieved strong performance on a wide range of benchmarks, yet most evaluations assume static environments. In contrast, real-world deployment is inherently dynamic, requiring agents to continually align their knowledge, skills, and behavior with changing environments and updated task conditions. To address this gap, we introduce EvoArena, a benchmark suite that models environment changes as sequences of progressive updates across terminal, software, and social domains. We further propose EvoMem, a patch-based memory paradigm that records memory evolution as structured update histories, enabling agents to reason about environmental evolution through changes in their memory. Experiments show that current agents struggle on EvoArena, achieving an average accuracy of 39.6% across evolving terminal, software, and social-preference domains. EvoMem consistently improves performance, yielding an average gain of 1.5% on EvoArena and also improving standard benchmarks such as GAIA and LoCoMo by 6.1% and 4.8%. Beyond individual tasks, EvoMem further improves chain-level accuracy by 3.7% on EvoArena, where success requires completing a consecutive sequence of related evolutionary subtasks. Mechanistic analysis shows that EvoMem improves evidence capture in the memory, indicating better preservation of complete evolving environment states. Our results highlight the importance of modeling evolution in both evaluation and memory for reliable agent deployment.

EVOCHAMBER: Test-Time Co-evolution of Multi-Agent System at Individual, Team, and Population Scales

We argue that multi-agent test-time evolution is not single-agent evolution replicated N times. A single-agent learner can only evolve its own context and memory. A multi-agent system additionally evolves who collaborates, how they collaborate, and how knowledge flows across the population. These components have no single-agent counterpart and can produce phenomena such as emergent specialization. Yet prior test-time methods either confine experiences to individual agents, forfeiting cross-agent learning, or broadcast symmetrically to all agents, erasing the specialization that makes collaboration valuable. We present EVOCHAMBER, a training-free framework that instantiates test-time evolution at three levels over a coevolving agent pool. At its core is CODREAM (Collaborative Dreaming), a post-task protocol triggered on team failure or disagreement, in which agents collaboratively reflect, distill insights, and route them asymmetrically from strong to weak agents on the failed niche, preserving specialization while filling knowledge gaps. Team-level operators assemble niche-conditioned teams and select collaboration structures online. Population-level lifecycle operators fork, merge, prune, and seed agents under performance pressure. On three heterogeneous task streams with Qwen3-8B, EVOCHAMBER reaches 63.9% on competition math, 75.7% on code, and 87.1% on multi-domain reasoning, outperforming the best baseline by 32% relative on math and confirming asymmetric cross-agent transfer as the primary driver in ablation. Starting from several identically initialized agents, four to five stable niche specialists spontaneously emerge, a structural signature of multi-agent evolution that no single-agent learner can express. See our code at: https://github.com/Mercury7353/EvoChamber

  • 6 authors
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May 10 1

EvoRubric: Self-Evolving Rubric-Driven RL for Open-Ended Generation

Reinforcement Learning (RL) has significantly advanced Large Language Models (LLMs) in verifiable domains, but aligning models for open-ended generation remains profoundly challenging due to the lack of definitive rewards. Current rubric-based RL methods mitigate this by employing explicit criteria; however, they rely heavily on static, human-annotated rubrics that inevitably cause policy lag, or expensive external proprietary models for dynamic updates. In this paper, we propose EvoRubric, a novel single-policy co-evolutionary RL framework that eliminates the reliance on static criteria and on external rubric generators. By unifying response generation and rubric generation under a single parameterized policy, EvoRubric dynamically alternates between a Reasoner and a Rubric Generator. To prevent reward hacking and ensure the reliability of generated signals, we introduce a multi-level verification pipeline featuring a meta-verifier, zero-variance pruning, and a Leave-One-Out peer consensus mechanism. Validated criteria are dynamically archived into a memory pool, yielding dense, multi-objective rewards to continuously co-optimize both roles. Extensive experiments across Medical, Writing, and Science domains demonstrate that EvoRubric consistently outperforms traditional static and external-LLM-driven alignment methods. Notably, our framework is compatible with human-expert priors. When initialized with expert-annotated rubrics, EvoRubric can further uncover novel, discriminative dimensions, achieving better performance than relying solely on static expert annotations.

  • 9 authors
·
May 27

Computational Foundations for Strategic Coopetition: Formalizing Trust and Reputation Dynamics

Modern socio-technical systems increasingly involve multi-stakeholder environments where actors simultaneously cooperate and compete. These coopetitive relationships exhibit dynamic trust evolution based on observed behavior over repeated interactions. While conceptual modeling languages like i* represent trust relationships qualitatively, they lack computational mechanisms for analyzing how trust changes with behavioral evidence. Conversely, computational trust models from multi-agent systems provide algorithmic updating but lack grounding in conceptual models that capture strategic dependencies covering mixed motives of actors. This technical report bridges this gap by developing a computational trust model that extends game-theoretic foundations for strategic coopetition with dynamic trust evolution. Building on companion work that achieved 58/60 validation (96.7%) for logarithmic specifications, we introduce trust as a two-layer system with immediate trust responding to current behavior and reputation tracking violation history. Trust evolves through asymmetric updating where cooperation builds trust gradually while violations erode it sharply, creating hysteresis effects and trust ceilings that constrain relationship recovery. We develop a structured translation framework enabling practitioners to instantiate computational trust models from i* dependency networks encompassing mixed motives of actors. Comprehensive experimental validation across 78,125 parameter configurations establishes robust emergence of negativity bias, hysteresis effects, and cumulative damage amplification. Empirical validation using the Renault-Nissan Alliance case study (1999-2025) achieves 49/60 validation points (81.7%), successfully reproducing documented trust evolution across five distinct relationship phases including crisis and recovery periods.

  • 2 authors
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Jan 6

Evolving Many Worlds: Towards Open-Ended Discovery in Petri Dish NCA via Population-Based Training

The generation of sustained, open-ended complexity from local interactions remains a fundamental challenge in artificial life. Differentiable multi-agent systems, such as Petri Dish Neural Cellular Automata (PD-NCA), exhibit rich self-organization driven purely by spatial competition; however, they are highly sensitive to hyperparameters and frequently collapse into uninteresting patterns and dynamics, such as frozen equilibria or structureless noise. In this paper, we introduce PBT-NCA, a meta-evolutionary algorithm that evolves a population of PD-NCAs subject to a composite objective that rewards both historical behavioral novelty and contemporary visual diversity. Driven by this continuous evolutionary pressure, PBT-NCA spontaneously generates a plethora of emergent lifelike phenomena over extended horizons-a hallmark of true open-endedness. Strikingly, the substrate autonomously discovers diverse morphological survival and self-organization strategies. We observe highly regular, coordinated periodic waves; spore-like scattering where homogeneous groups eject cell-like clusters to colonize distant territories; and fluid, shape-shifting macro-structures that migrate across the substrate, maintaining stable outer boundaries that enclose highly active interiors. By actively penalizing monocultures and dead states, PBT-NCA sustains a state of effective complexity that is neither globally ordered nor globally random, operating persistently at the "edge of chaos".

  • 4 authors
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Apr 12

Topological Neural Dynamics: A Neuron-wise Framework for Sequence Modeling

Existing sequence models, including RNNs, LSTMs, continuous-time networks, and Transformers, share a common structural principle: layer-wise dynamics, where all neurons in the same layer co-evolve through a shared parameterized operator, leaving individual neurons no freedom to evolve independently. Yet in many complex dynamical systems, rich global behavior emerges precisely from locally evolving units interacting through structured connectivity. Inspired by this principle, we introduce Topological Neural Dynamics (TND), a sequence modeling framework that shifts computation from layer-wise to neuron-wise dynamics. TND represents a neural system as a directed neuron graph, an interaction operator, and a local dynamics function, where each neuron evolves independently and collective computation emerges from interactions through the explicit graph topology. We instantiate TND as a discrete-time graph-coupled dynamical system and evaluate it as a case study on a behavior cloning task in single-player Pong. Compared with Vanilla RNN, Sparse RNN, LSTM, Closed-form continuous-time neural network (CfC), and Transformer baselines, TND achieves the best catch rate and a mean of 17.47 consecutive catches per round, more than three times that of the strongest baseline. These results suggest that shifting from layer-wise to neuron-wise dynamics provides an effective inductive bias for sequence modeling.

  • 2 authors
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Jun 30

LLM Guided Evolution -- The Automation of Models Advancing Models

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.

  • 3 authors
·
Mar 17, 2024

Molt Dynamics: Emergent Social Phenomena in Autonomous AI Agent Populations

MoltBook is a large-scale multi-agent coordination environment where over 770,000 autonomous LLM agents interact without human participation, offering the first opportunity we are aware of to observe emergent multi-agent coordination dynamics at this population scale. We introduce Molt Dynamics: the emergent agent coordination behaviors, inter-agent communication dynamics, and role specialization patterns arising when autonomous agents operate as decentralized decision-makers in an unconstrained multi-agent environment. Through longitudinal observation of 90,704 active agents over three weeks, we characterize three aspects. First, spontaneous role specialization: network-based clustering reveals six structural roles (silhouette 0.91), though the result primarily reflects core-periphery organization -- 93.5\% of agents occupy a homogeneous peripheral cluster, with meaningful differentiation confined to the active minority. Second, decentralized information dissemination: cascade analysis of 10,323 inter-agent propagation events reveals power-law distributed cascade sizes (α= 2.57 pm 0.02) and saturating adoption dynamics where adoption probability shows diminishing returns with repeated exposures (Cox hazard ratio 0.53, concordance 0.78). Third, distributed cooperative task resolution: 164 multi-agent collaborative events show detectable coordination patterns, but success rates are low (6.7\%, p = 0.057) and cooperative outcomes are significantly worse than a matched single-agent baseline (Cohen's d = -0.88), indicating emergent cooperative behavior is nascent. These findings establish an empirical baseline for coordination dynamics in decentralized autonomous agent systems, with implications for multi-agent system design, agent communication protocol engineering, and AI safety.

  • 2 authors
·
Mar 3

Yunjue Agent Tech Report: A Fully Reproducible, Zero-Start In-Situ Self-Evolving Agent System for Open-Ended Tasks

Conventional agent systems often struggle in open-ended environments where task distributions continuously drift and external supervision is scarce. Their reliance on static toolsets or offline training lags behind these dynamics, leaving the system's capability boundaries rigid and unknown. To address this, we propose the In-Situ Self-Evolving paradigm. This approach treats sequential task interactions as a continuous stream of experience, enabling the system to distill short-term execution feedback into long-term, reusable capabilities without access to ground-truth labels. Within this framework, we identify tool evolution as the critical pathway for capability expansion, which provides verifiable, binary feedback signals. Within this framework, we develop Yunjue Agent, a system that iteratively synthesizes, optimizes, and reuses tools to navigate emerging challenges. To optimize evolutionary efficiency, we further introduce a Parallel Batch Evolution strategy. Empirical evaluations across five diverse benchmarks under a zero-start setting demonstrate significant performance gains over proprietary baselines. Additionally, complementary warm-start evaluations confirm that the accumulated general knowledge can be seamlessly transferred to novel domains. Finally, we propose a novel metric to monitor evolution convergence, serving as a function analogous to training loss in conventional optimization. We open-source our codebase, system traces, and evolved tools to facilitate future research in resilient, self-evolving intelligence.

A Comprehensive Survey of Self-Evolving AI Agents: A New Paradigm Bridging Foundation Models and Lifelong Agentic Systems

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.

  • 15 authors
·
Aug 10, 2025 2

Bayesian inference from time series of allele frequency data using exact simulation techniques

A central statistical problem in population genetics is to infer evolutionary and biological parameters such as the strength of natural selection and allele age from DNA samples extracted from a contemporary population. That all samples come only from the present-day has long been known to limit statistical inference; there is potentially more information available if one also has access to ancient DNA so that inference is based on a time-series of historical changes in allele frequencies. We introduce a Markov Chain Monte Carlo (MCMC) method for Bayesian inference from allele frequency time-series data based on an underlying Wright--Fisher diffusion model of evolution, through which one can infer the parameters of essentially any selection model including those with frequency-dependent effects. The chief novelty is that we show this method to be exact in the sense that it is possible to augment the state space explored by MCMC with the unobserved diffusion trajectory, even though the transition function of this diffusion is intractable. Through careful design of a proposal distribution, we describe an efficient method in which updates to the trajectory and accept/reject decisions are calculated without error. We illustrate the method on data capturing changes in coat colour over the past 20,000 years, and find evidence to support previous findings that the mutant alleles ASIP and MC1R responsible for changes in coat color have experienced very strong, possibly overdominant, selection and further provide estimates for the ages of these genes.

  • 4 authors
·
Feb 16, 2025

Does Socialization Emerge in AI Agent Society? A Case Study of Moltbook

As large language model agents increasingly populate networked environments, a fundamental question arises: do artificial intelligence (AI) agent societies undergo convergence dynamics similar to human social systems? Lately, Moltbook approximates a plausible future scenario in which autonomous agents participate in an open-ended, continuously evolving online society. We present the first large-scale systemic diagnosis of this AI agent society. Beyond static observation, we introduce a quantitative diagnostic framework for dynamic evolution in AI agent societies, measuring semantic stabilization, lexical turnover, individual inertia, influence persistence, and collective consensus. Our analysis reveals a system in dynamic balance in Moltbook: while global semantic averages stabilize rapidly, individual agents retain high diversity and persistent lexical turnover, defying homogenization. However, agents exhibit strong individual inertia and minimal adaptive response to interaction partners, preventing mutual influence and consensus. Consequently, influence remains transient with no persistent supernodes, and the society fails to develop stable collective influence anchors due to the absence of shared social memory. These findings demonstrate that scale and interaction density alone are insufficient to induce socialization, providing actionable design and analysis principles for upcoming next-generation AI agent societies.

umd-zhou-lab Tianyi Lab
·
Feb 15 4

Sparse Diffusion Autoencoder for Test-time Adapting Prediction of Complex Systems

Predicting the behavior of complex systems is critical in many scientific and engineering domains, and hinges on the model's ability to capture their underlying dynamics. Existing methods encode the intrinsic dynamics of high-dimensional observations through latent representations and predict autoregressively. However, these latent representations lose the inherent spatial structure of spatiotemporal dynamics, leading to the predictor's inability to effectively model spatial interactions and neglect emerging dynamics during long-term prediction. In this work, we propose SparseDiff, introducing a test-time adaptation strategy to dynamically update the encoding scheme to accommodate emergent spatiotemporal structures during the long-term evolution of the system. Specifically, we first design a codebook-based sparse encoder, which coarsens the continuous spatial domain into a sparse graph topology. Then, we employ a graph neural ordinary differential equation to model the dynamics and guide a diffusion decoder for reconstruction. SparseDiff autoregressively predicts the spatiotemporal evolution and adjust the sparse topological structure to adapt to emergent spatiotemporal patterns by adaptive re-encoding. Extensive evaluations on representative systems demonstrate that SparseDiff achieves an average prediction error reduction of 49.99\% compared to baselines, requiring only 1\% of the spatial resolution.

  • 4 authors
·
May 23, 2025

Intern-Atlas: A Methodological Evolution Graph as Research Infrastructure for AI Scientists

Existing research infrastructure is fundamentally document-centric, providing citation links between papers but lacking explicit representations of methodological evolution. In particular, it does not capture the structured relationships that explain how and why research methods emerge, adapt, and build upon one another. With the rise of AI-driven research agents as a new class of consumers of scientific knowledge, this limitation becomes increasingly consequential, as such agents cannot reliably reconstruct method evolution topologies from unstructured text. We introduce Intern-Atlas, a methodological evolution graph that automatically identifies method-level entities, infers lineage relationships among methodologies, and captures the bottlenecks that drive transitions between successive innovations. Built from 1,030,314 papers spanning AI conferences, journals, and arXiv preprints, the resulting graph comprises 9,410,201 semantically typed edges, each grounded in verbatim source evidence, forming a queryable causal network of methodological development. To operationalize this structure, we further propose a self-guided temporal tree search algorithm for constructing evolution chains that trace the progression of methods over time. We evaluate the quality of the resulting graph against expert-curated ground-truth evolution chains and observe strong alignment. In addition, we demonstrate that Intern-Atlas enables downstream applications in idea evaluation and automated idea generation. We position methodological evolution graphs as a foundational data layer for the emerging automated scientific discovery.

  • 13 authors
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Apr 29 4

Nature-Inspired Population-Based Evolution of Large Language Models

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.

  • 8 authors
·
Mar 2, 2025

Meta Flow Matching: Integrating Vector Fields on the Wasserstein Manifold

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depends on the microenvironment of cells specific to each patient. We propose Meta Flow Matching (MFM), a practical approach to integrating along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions unlike previously proposed methods. We demonstrate the ability of MFM to improve prediction of individual treatment responses on a large scale multi-patient single-cell drug screen dataset.

  • 8 authors
·
Aug 26, 2024 2

CoMAS: Co-Evolving Multi-Agent Systems via Interaction Rewards

Self-evolution is a central research topic in enabling large language model (LLM)-based agents to continually improve their capabilities after pretraining. Recent research has witnessed a transition from reinforcement learning (RL)-free to RL-based methods. Current RL-based methods either rely on dense external reward signals or extract intrinsic reward signals from LLMs themselves. However, these approaches diverge from the self-evolution mechanisms observed in human intelligence, where individuals learn and improve through mutual discussion and collaboration. In this work, we introduce Co-Evolving Multi-Agent Systems (CoMAS), a novel framework that enables agents to improve autonomously by learning from inter-agent interactions without external supervision. CoMAS generates intrinsic rewards from rich discussion dynamics, employs an LLM-as-a-judge mechanism to formulate these rewards, and optimizes each agent's policy through RL, thereby enabling decentralized and scalable co-evolution. Experimental results demonstrate that CoMAS consistently outperforms untrained agents and achieves state-of-the-art performance across most evaluation settings. Ablation studies confirm the necessity of interaction-based reward signals and reveal promising scalability as the number and diversity of agents increase. These findings establish CoMAS as a novel and effective paradigm for self-evolution in LLM-based agents.

  • 10 authors
·
Oct 9, 2025 2

EvoScientist: Towards Multi-Agent Evolving AI Scientists for End-to-End Scientific Discovery

The increasing adoption of Large Language Models (LLMs) has enabled AI scientists to perform complex end-to-end scientific discovery tasks requiring coordination of specialized roles, including idea generation and experimental execution. However, most state-of-the-art AI scientist systems rely on static, hand-designed pipelines and fail to adapt based on accumulated interaction histories. As a result, these systems overlook promising research directions, repeat failed experiments, and pursue infeasible ideas. To address this, we introduce EvoScientist, an evolving multi-agent AI scientist framework that continuously improves research strategies through persistent memory and self-evolution. EvoScientist comprises three specialized agents: a Researcher Agent (RA) for scientific idea generation, an Engineer Agent (EA) for experiment implementation and execution, and an Evolution Manager Agent (EMA) that distills insights from prior interactions into reusable knowledge. EvoScientist contains two persistent memory modules: (i) an ideation memory, which summarizes feasible research directions from top-ranked ideas while recording previously unsuccessful directions; and (ii) an experimentation memory, which captures effective data processing and model training strategies derived from code search trajectories and best-performing implementations. These modules enable the RA and EA to retrieve relevant prior strategies, improving idea quality and code execution success rates over time. Experiments show that EvoScientist outperforms 7 open-source and commercial state-of-the-art systems in scientific idea generation, achieving higher novelty, feasibility, relevance, and clarity via automatic and human evaluation. EvoScientist also substantially improves code execution success rates through multi-agent evolution, demonstrating persistent memory's effectiveness for end-to-end scientific discovery.

  • 12 authors
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Mar 9 5

Chemical Heredity as Group Selection at the Molecular Level

Many examples of cooperation exist in biology. In chemical systems however, which can sometimes be quite complex, we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is then how can molecular cooperation first arise in an abiotic system prior to the emergence of biological replication. We postulate that selection at the molecular level is a driving force behind the complexification of chemical systems, particularly during the origins of life. In the theory of multilevel selection the two selective forces are: within-group and between-group, where the former tends to favor "selfish" replication of individuals and the latter favor cooperation between individuals enhancing the replication of the group as a whole. These forces can be quantified using the Price equation, which is a standard tool used in evolutionary biology to quantify evolutionary change. Our central claim is that replication and heredity in chemical systems are subject to selection, and quantifiable using the multilevel Price equation. We demonstrate this using the Graded Autocatalysis Replication Domain computer model, describing simple protocell composed out of molecules and its replication, which respectively analogue to the group and the individuals. In contrast to previous treatments of this model, we treat the lipid molecules themselves as replicating individuals and the protocells they form as groups of individuals. Our goal is to demonstrate how evolutionary biology tools and concepts can be applied in chemistry and we suggest that molecular cooperation may arise as a result of group selection. Further, the biological relation of parent-progeny is proposed to be analogue to the reactant-product relation in chemistry, thus allowing for tools from evolutionary biology to be applied to chemistry and would deepen the connection between chemistry and biology.

  • 3 authors
·
Feb 22, 2018

EvoCUA: Evolving Computer Use Agents via Learning from Scalable Synthetic Experience

The development of native computer-use agents (CUA) represents a significant leap in multimodal AI. However, their potential is currently bottlenecked by the constraints of static data scaling. Existing paradigms relying primarily on passive imitation of static datasets struggle to capture the intricate causal dynamics inherent in long-horizon computer tasks. In this work, we introduce EvoCUA, a native computer use agentic model. Unlike static imitation, EvoCUA integrates data generation and policy optimization into a self-sustaining evolutionary cycle. To mitigate data scarcity, we develop a verifiable synthesis engine that autonomously generates diverse tasks coupled with executable validators. To enable large-scale experience acquisition, we design a scalable infrastructure orchestrating tens of thousands of asynchronous sandbox rollouts. Building on these massive trajectories, we propose an iterative evolving learning strategy to efficiently internalize this experience. This mechanism dynamically regulates policy updates by identifying capability boundaries -- reinforcing successful routines while transforming failure trajectories into rich supervision through error analysis and self-correction. Empirical evaluations on the OSWorld benchmark demonstrate that EvoCUA achieves a success rate of 56.7%, establishing a new open-source state-of-the-art. Notably, EvoCUA significantly outperforms the previous best open-source model, OpenCUA-72B (45.0%), and surpasses leading closed-weights models such as UI-TARS-2 (53.1%). Crucially, our results underscore the generalizability of this approach: the evolving paradigm driven by learning from experience yields consistent performance gains across foundation models of varying scales, establishing a robust and scalable path for advancing native agent capabilities.

meituan meituan
·
Jan 22 2

A Decoupled Basis-Vector-Driven Generative Framework for Dynamic Multi-Objective Optimization

Dynamic multi-objective optimization requires continuous tracking of moving Pareto fronts. Existing methods struggle with irregular mutations and data sparsity, primarily facing three challenges: the non-linear coupling of dynamic modes, negative transfer from outdated historical data, and the cold-start problem during environmental switches. To address these issues, this paper proposes a decoupled basis-vector-driven generative framework (DB-GEN). First, to resolve non-linear coupling, the framework employs the discrete wavelet transform to separate evolutionary trajectories into low-frequency trends and high-frequency details. Second, to mitigate negative transfer, it learns transferable basis vectors via sparse dictionary learning rather than directly memorizing historical instances. Recomposing these bases under a topology-aware contrastive constraint constructs a structured latent manifold. Finally, to overcome the cold-start problem, a surrogate-assisted search paradigm samples initial populations from this manifold. Pre-trained on 120 million solutions, DB-GEN performs direct online inference without retraining or fine-tuning. This zero-shot generation process executes in milliseconds, requiring approximately 0.2 seconds per environmental change. Experimental results demonstrate that DB-GEN improves tracking accuracy across various dynamic benchmarks compared to existing algorithms.

  • 5 authors
·
Mar 31

The Devil Behind Moltbook: Anthropic Safety is Always Vanishing in Self-Evolving AI Societies

The emergence of multi-agent systems built from large language models (LLMs) offers a promising paradigm for scalable collective intelligence and self-evolution. Ideally, such systems would achieve continuous self-improvement in a fully closed loop while maintaining robust safety alignment--a combination we term the self-evolution trilemma. However, we demonstrate both theoretically and empirically that an agent society satisfying continuous self-evolution, complete isolation, and safety invariance is impossible. Drawing on an information-theoretic framework, we formalize safety as the divergence degree from anthropic value distributions. We theoretically demonstrate that isolated self-evolution induces statistical blind spots, leading to the irreversible degradation of the system's safety alignment. Empirical and qualitative results from an open-ended agent community (Moltbook) and two closed self-evolving systems reveal phenomena that align with our theoretical prediction of inevitable safety erosion. We further propose several solution directions to alleviate the identified safety concern. Our work establishes a fundamental limit on the self-evolving AI societies and shifts the discourse from symptom-driven safety patches to a principled understanding of intrinsic dynamical risks, highlighting the need for external oversight or novel safety-preserving mechanisms.

  • 13 authors
·
Feb 10 9

Chreode: A Cell World Model for One-Step Temporal Dynamics and Perturbation Prediction

Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.

  • 7 authors
·
May 26

Mathematical exploration and discovery at scale

AlphaEvolve is a generic evolutionary coding agent that combines the generative capabilities of LLMs with automated evaluation in an iterative evolutionary framework that proposes, tests, and refines algorithmic solutions to challenging scientific and practical problems. In this paper we showcase AlphaEvolve as a tool for autonomously discovering novel mathematical constructions and advancing our understanding of long-standing open problems. To demonstrate its breadth, we considered a list of 67 problems spanning mathematical analysis, combinatorics, geometry, and number theory. The system rediscovered the best known solutions in most of the cases and discovered improved solutions in several. In some instances, AlphaEvolve is also able to generalize results for a finite number of input values into a formula valid for all input values. Furthermore, we are able to combine this methodology with Deep Think and AlphaProof in a broader framework where the additional proof-assistants and reasoning systems provide automated proof generation and further mathematical insights. These results demonstrate that large language model-guided evolutionary search can autonomously discover mathematical constructions that complement human intuition, at times matching or even improving the best known results, highlighting the potential for significant new ways of interaction between mathematicians and AI systems. We present AlphaEvolve as a powerful new tool for mathematical discovery, capable of exploring vast search spaces to solve complex optimization problems at scale, often with significantly reduced requirements on preparation and computation time.

  • 4 authors
·
Nov 3, 2025 1

Deep Neuroevolution: Genetic Algorithms Are a Competitive Alternative for Training Deep Neural Networks for Reinforcement Learning

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.

  • 6 authors
·
Dec 18, 2017

Discovering Multiagent Learning Algorithms with Large Language Models

Much of the advancement of Multi-Agent Reinforcement Learning (MARL) in imperfect-information games has historically depended on manual iterative refinement of baselines. While foundational families like Counterfactual Regret Minimization (CFR) and Policy Space Response Oracles (PSRO) rest on solid theoretical ground, the design of their most effective variants often relies on human intuition to navigate a vast algorithmic design space. In this work, we propose the use of AlphaEvolve, an evolutionary coding agent powered by large language models, to automatically discover new multiagent learning algorithms. We demonstrate the generality of this framework by evolving novel variants for two distinct paradigms of game-theoretic learning. First, in the domain of iterative regret minimization, we evolve the logic governing regret accumulation and policy derivation, discovering a new algorithm, Volatility-Adaptive Discounted (VAD-)CFR. VAD-CFR employs novel, non-intuitive mechanisms-including volatility-sensitive discounting, consistency-enforced optimism, and a hard warm-start policy accumulation schedule-to outperform state-of-the-art baselines like Discounted Predictive CFR+. Second, in the regime of population based training algorithms, we evolve training-time and evaluation-time meta strategy solvers for PSRO, discovering a new variant, Smoothed Hybrid Optimistic Regret (SHOR-)PSRO. SHOR-PSRO introduces a hybrid meta-solver that linearly blends Optimistic Regret Matching with a smoothed, temperature-controlled distribution over best pure strategies. By dynamically annealing this blending factor and diversity bonuses during training, the algorithm automates the transition from population diversity to rigorous equilibrium finding, yielding superior empirical convergence compared to standard static meta-solvers.

google Google
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Feb 18 2

The Role of Social Learning and Collective Norm Formation in Fostering Cooperation in LLM Multi-Agent Systems

A growing body of multi-agent studies with LLMs explores how norms and cooperation emerge in mixed-motive scenarios, where pursuing individual gain can undermine the collective good. While prior work has explored these dynamics in both richly contextualized simulations and simplified game-theoretic environments, most LLM systems featuring common-pool resource (CPR) games provide agents with explicit reward functions directly tied to their actions. In contrast, human cooperation often emerges without explicit knowledge of the payoff structure or how individual actions translate into long-run outcomes, relying instead on heuristics, communication, and enforcement. We introduce a CPR simulation framework that removes explicit reward signals and embeds cultural-evolutionary mechanisms: social learning (adopting strategies and beliefs from successful peers) and norm-based punishment, grounded in Ostrom's principles of resource governance. Agents also individually learn from the consequences of harvesting, monitoring, and punishing via environmental feedback, enabling norms to emerge endogenously. We establish the validity of our simulation by reproducing key findings from existing studies on human behavior. Building on this, we examine norm evolution across a 2times2 grid of environmental and social initialisations (resource-rich vs. resource-scarce; altruistic vs. selfish) and benchmark how agentic societies comprised of different LLMs perform under these conditions. Our results reveal systematic model differences in sustaining cooperation and norm formation, positioning the framework as a rigorous testbed for studying emergent norms in mixed-motive LLM societies. Such analysis can inform the design of AI systems deployed in social and organizational contexts, where alignment with cooperative norms is critical for stability, fairness, and effective governance of AI-mediated environments.

  • 5 authors
·
Oct 16, 2025

What Do Evolutionary Coding Agents Evolve?

Recent work pairs LLMs with evolutionary search to iteratively generate, modify, and select code using task-specific feedback. These systems have produced strong results in mathematical discovery and algorithm design, yet a fundamental question remains: what do they actually evolve? Progress is typically summarized by the best score a run reaches under a task-specific evaluator, but that score can reflect several different mechanisms: new algorithmic structure, re-tuning an existing strategy, recombining ideas already in the model's internal knowledge, or overfitting to the evaluator. Distinguishing these mechanisms requires inspecting the search process itself, not only its final outcome. We introduce EvoTrace, a dataset of evolutionary coding traces spanning four evolutionary frameworks, reasoning and non-reasoning models, and 16 tasks across mathematics and algorithm design. To analyze these traces, we develop EvoReplay, a replay-based methodology that reconstructs the local search states behind high-scoring solutions and tests controlled interventions, including adjusting constants, removing program components and substituting models or prompting contexts. We annotate every code edit in EvoTrace with one of nine recurring edit types using an LLM-as-judge pipeline validated against blind human re-annotation. Across EvoTrace, most score gains come from a small subset of these edit types. We further find a deterministic cycling pattern: about 30% of code lines added during search are byte-identical re-introductions of previously-deleted lines, present throughout nearly every run. These results show that benchmark gains in evolutionary coding agents can arise from qualitatively different mechanisms, only some of which correspond to new algorithmic structure. EvoTrace enables more diagnostic evaluation of evolutionary coding agents beyond final benchmark scores.

  • 7 authors
·
May 18

Fluctuations and correlations in chemical reaction kinetics and population dynamics

This chapter provides a pedagogical introduction and overview of spatial and temporal correlation and fluctuation effects resulting from the fundamentally stochastic kinetics underlying chemical reactions and the dynamics of populations or epidemics. After reviewing the assumptions and mean-field type approximations involved in the construction of chemical rate equations for uniform reactant densities, we first discuss spatial clustering in birth-death systems, where non-linearities are introduced through either density-limiting pair reactions, or equivalently via local imposition of finite carrying capacities. The competition of offspring production, death, and non-linear inhibition induces a population extinction threshold, which represents a non-equilibrium phase transition that separates active from absorbing states. This continuous transition is characterized by the universal scaling exponents of critical directed percolation clusters. Next we focus on the emergence of depletion zones in single-species annihilation processes and spatial population segregation with the associated reaction fronts in two-species pair annihilation. These strong (anti-)correlation effects are dynamically generated by the underlying stochastic kinetics. Finally, we address noise-induced and fluctuation-stabilized spatio-temporal patterns in basic predator-prey systems, exemplified by spreading activity fronts in the two-species Lotka-Volterra model as well as spiral structures in the May-Leonard variant of cyclically competing three-species systems akin to rock-paper-scissors games.

  • 1 authors
·
Jul 3, 2018