Daily Papers

Temporal Knowledge Graph (TKG) reasoning that forecasts future events based on historical snapshots distributed over timestamps is denoted as extrapolation and has gained significant attention. Owing to its extreme versatility and variation in spatial and temporal correlations, TKG reasoning presents a challenging task, demanding efficient capture of concurrent structures and evolutional interactions among facts. While existing methods have made strides in this direction, they still fall short of harnessing the diverse forms of intrinsic expressive semantics of TKGs, which encompass entity correlations across multiple timestamps and periodicity of temporal information. This limitation constrains their ability to thoroughly reflect historical dependencies and future trends. In response to these drawbacks, this paper proposes an innovative reasoning approach that focuses on Learning Multi-graph Structure (LMS). Concretely, it comprises three distinct modules concentrating on multiple aspects of graph structure knowledge within TKGs, including concurrent and evolutional patterns along timestamps, query-specific correlations across timestamps, and semantic dependencies of timestamps, which capture TKG features from various perspectives. Besides, LMS incorporates an adaptive gate for merging entity representations both along and across timestamps effectively. Moreover, it integrates timestamp semantics into graph attention calculations and time-aware decoders, in order to impose temporal constraints on events and narrow down prediction scopes with historical statistics. Extensive experimental results on five event-based benchmark datasets demonstrate that LMS outperforms state-of-the-art extrapolation models, indicating the superiority of modeling a multi-graph perspective for TKG reasoning.

The integration of Large Language Models (LLMs), especially ChatGPT, into education is poised to revolutionize students' learning experiences by introducing innovative conversational learning methodologies. To empower students to fully leverage the capabilities of ChatGPT in educational scenarios, understanding students' interaction patterns with ChatGPT is crucial for instructors. However, this endeavor is challenging due to the absence of datasets focused on student-ChatGPT conversations and the complexities in identifying and analyzing the evolutional interaction patterns within conversations. To address these challenges, we collected conversational data from 48 students interacting with ChatGPT in a master's level data visualization course over one semester. We then developed a coding scheme, grounded in the literature on cognitive levels and thematic analysis, to categorize students' interaction patterns with ChatGPT. Furthermore, we present a visual analytics system, StuGPTViz, that tracks and compares temporal patterns in student prompts and the quality of ChatGPT's responses at multiple scales, revealing significant pedagogical insights for instructors. We validated the system's effectiveness through expert interviews with six data visualization instructors and three case studies. The results confirmed StuGPTViz's capacity to enhance educators' insights into the pedagogical value of ChatGPT. We also discussed the potential research opportunities of applying visual analytics in education and developing AI-driven personalized learning solutions.

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.

A longstanding goal of biology is to identify the key genes and species that critically impact evolution, ecology, and health. Network analysis has revealed keystone species that regulate ecosystems and master regulators that regulate cellular genetic networks. Yet these studies have focused on pairwise biological interactions, which can be affected by the context of genetic background and other species present generating higher-order interactions. The important regulators of higher-order interactions are unstudied. To address this, we applied a new high-dimensional geometry approach that quantifies epistasis in a fitness landscape to ask how individual genes and species influence the interactions in the rest of the biological network. We then generated and also reanalyzed 5-dimensional datasets (two genetic, two microbiome). We identified key genes (e.g. the rbs locus and pykF) and species (e.g. Lactobacilli) that control the interactions of many other genes and species. These higher-order master regulators can induce or suppress evolutionary and ecological diversification by controlling the topography of the fitness landscape. Thus, we provide mathematical intuition and justification for exploration of biological networks in higher dimensions.

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.

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.

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.

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.

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.

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 derive an expression for the variation between parallel trajectories in phenotypic evolution, extending the well known result that predicts the mean evolutionary path in adaptive dynamics or quantitative genetics. We show how this expression gives rise to the notion of fluctuation domains - parts of the fitness landscape where the rate of evolution is very predictable (due to fluctuation dissipation) and parts where it is highly variable (due to fluctuation enhancement). These fluctuation domains are determined by the curvature of the fitness landscape. Regions of the fitness landscape with positive curvature, such as adaptive valleys or branching points, experience enhancement. Regions with negative curvature, such as adaptive peaks, experience dissipation. We explore these dynamics in the ecological scenarios of implicit and explicit competition for a limiting resource.

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.

Recent work such as AlphaEvolve has shown that combining LLM-driven optimization with evolutionary search can effectively improve programs, prompts, and algorithms across domains. In this paradigm, previously evaluated solutions are reused to guide the model toward new candidate solutions. Crucially, the effectiveness of this evolution process depends on the search strategy: how prior solutions are selected and varied to generate new candidates. However, most existing methods rely on fixed search strategies with predefined knobs (e.g., explore-exploit ratios) that remain static throughout execution. While effective in some settings, these approaches often fail to adapt across tasks, or even within the same task as the search space changes over time. We introduce EvoX, an adaptive evolution method that optimizes its own evolution process. EvoX jointly evolves candidate solutions and the search strategies used to generate them, continuously updating how prior solutions are selected and varied based on progress. This enables the system to dynamically shift between different search strategies during the optimization process. Across nearly 200 real-world optimization tasks, EvoX outperforms existing AI-driven evolutionary methods including AlphaEvolve, OpenEvolve, GEPA, and ShinkaEvolve on the majority of tasks.

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.

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.

In here presented in silico study we suggest a way how to implement the evolutionary principles into anti-cancer therapy design. We hypothesize that instead of its ongoing supervised adaptation, the therapy may be constructed as a self-sustaining evolutionary process in a dynamic fitness landscape established implicitly by evolving cancer cells, microenvironment and the therapy itself. For these purposes, we replace a unified therapy with the `therapy species', which is a population of heterogeneous elementary therapies, and propose a way how to turn the toxicity of the elementary therapy into its fitness in a way conforming to evolutionary causation. As a result, not only the therapies govern the evolution of different cell phenotypes, but the cells' resistances govern the evolution of the therapies as well. We illustrate the approach by the minimalistic ad hoc evolutionary model. Its results indicate that the resistant cells could bias the evolution towards more toxic elementary therapies by inhibiting the less toxic ones. As the evolutionary causation of cancer drug resistance has been intensively studied for a few decades, we refer to cancer as a special case to illustrate purely theoretical analysis.

Environmental and genetic mutations can transform the cells in a co-operating healthy tissue into an ecosystem of individualistic tumour cells that compete for space and resources. Various selection forces are responsible for driving the evolution of cells in a tumour towards more malignant and aggressive phenotypes that tend to have a fitness advantage over the older populations. Although the evolutionary nature of cancer has been recognised for more than three decades (ever since the seminal work of Nowell) it has been only recently that tools traditionally used by ecological and evolutionary researchers have been adopted to study the evolution of cancer phenotypes in populations of individuals capable of co-operation and competition. In this chapter we will describe game theory as an important tool to study the emergence of cell phenotypes in a tumour and will critically review some of its applications in cancer research. These applications demonstrate that game theory can be used to understand the dynamics of somatic cancer evolution and suggest new therapies in which this knowledge could be applied to gain some control over the evolution of the tumour.

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

The fields of Origin of Life and Artificial Life both question what life is and how it emerges from a distinct set of "pre-life" dynamics. One common feature of most substrates where life emerges is a marked shift in dynamics when self-replication appears. While there are some hypotheses regarding how self-replicators arose in nature, we know very little about the general dynamics, computational principles, and necessary conditions for self-replicators to emerge. This is especially true on "computational substrates" where interactions involve logical, mathematical, or programming rules. In this paper we take a step towards understanding how self-replicators arise by studying several computational substrates based on various simple programming languages and machine instruction sets. We show that when random, non self-replicating programs are placed in an environment lacking any explicit fitness landscape, self-replicators tend to arise. We demonstrate how this occurs due to random interactions and self-modification, and can happen with and without background random mutations. We also show how increasingly complex dynamics continue to emerge following the rise of self-replicators. Finally, we show a counterexample of a minimalistic programming language where self-replicators are possible, but so far have not been observed to arise.

Agentic systems are increasingly expected to improve after deployment, yet single-entity self-evolution is often bounded by a static learning context, such as fixed tasks and feedback. This survey focuses on co-evolution in agentic systems, a multi-component form of self-evolution in which multiple agents and their environment impose adaptive pressure on one another. To organize existing papers, we propose a progressive three-stage taxonomy that traces how the system gradually sheds human-engineered constraints. Agent--Agent Co-Evolution studies how agents adapt through dynamic peers, including adversarial, collaborative, and organizational adaptation. Agent--Environment Co-Evolution extends this loop to adaptive tasks, feedback, and interaction spaces that change with the agents. Meta Co-Evolution further explores the possibility of making the evolution mechanism itself evolvable. We also discuss open challenges in evaluating such systems, scaling them across multiple components, and keeping increasingly autonomous evolutionary processes safe and controllable. This survey provides a unified foundation for building robust and open-ended agentic systems that can improve beyond fixed human-designed paths.

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

Large language models (LLMs) like GPTs, trained on vast datasets, have demonstrated impressive capabilities in language understanding, reasoning, and planning, achieving human-level performance in various tasks. Most studies focus on enhancing these models by training on ever-larger datasets to build more powerful foundation models. While training stronger models is important, enabling models to evolve during inference is equally crucial, a process we refer to as AI self-evolution. Unlike large-scale training, self-evolution may rely on limited data or interactions. Inspired by the columnar organization of the human cerebral cortex, we hypothesize that AI models could develop cognitive abilities and build internal representations through iterative interactions with their environment. To achieve this, models need long-term memory (LTM) to store and manage processed interaction data. LTM supports self-evolution by representing diverse experiences across environments and agents. In this report, we explore AI self-evolution and its potential to enhance models during inference. We examine LTM's role in lifelong learning, allowing models to evolve based on accumulated interactions. We outline the structure of LTM and the systems needed for effective data retention and representation. We also classify approaches for building personalized models with LTM data and show how these models achieve self-evolution through interaction. Using LTM, our multi-agent framework OMNE achieved first place on the GAIA benchmark, demonstrating LTM's potential for AI self-evolution. Finally, we present a roadmap for future research, emphasizing the importance of LTM for advancing AI technology and its practical applications.

Prosocial behaviors are encountered in the donation game, the prisoner's dilemma, relaxed social dilemmas, and public goods games. Many studies assume that the population structure is homogeneous, meaning all individuals have the same number of interaction partners, or that the social good is of one particular type. Here, we explore general evolutionary dynamics for arbitrary spatial structures and social goods. We find that heterogeneous networks, wherein some individuals have many more interaction partners than others, can enhance the evolution of prosocial behaviors. However, they often accumulate most of the benefits in the hands of a few highly-connected individuals, while many others receive low or negative payoff. Surprisingly, selection can favor producers of social goods even if the total costs exceed the total benefits. In summary, heterogeneous structures have the ability to strongly promote the emergence of prosocial behaviors, but they also create the possibility of generating large inequality.

The evolution of cooperation has been extensively studied using abstract mathematical models and simulations. Recent advances in Large Language Models (LLMs) and the rise of LLM agents have demonstrated their ability to perform social reasoning, thus providing an opportunity to test the emergence of norms in more realistic agent-based simulations with human-like reasoning using natural language. In this research, we investigate whether the cooperation dynamics presented in Boyd and Richerson's model persist in a more realistic simulation of the Diner's Dilemma using LLM agents compared to the abstract mathematical nature in the work of Boyd and Richerson. Our findings indicate that agents follow the strategies defined in the Boyd and Richerson model, and explicit punishment mechanisms drive norm emergence, reinforcing cooperative behaviour even when the agent strategy configuration varies. Our results suggest that LLM-based Multi-Agent System simulations, in fact, can replicate the evolution of cooperation predicted by the traditional mathematical models. Moreover, our simulations extend beyond the mathematical models by integrating natural language-driven reasoning and a pairwise imitation method for strategy adoption, making them a more realistic testbed for cooperative behaviour in MASs.

We examine the effect of noise on societies of agents using an agent-based model of evolutionary norm emergence. Generally, we see that noisy societies are more selfish, smaller and discontent, and are caught in rounds of perpetual punishment preventing them from flourishing. Surprisingly, despite the effect of noise on the population, it does not seem to evolve away. We carry out further analysis and provide reasons for why this may be the case. Furthermore, we claim that our framework that evolves the noise/ambiguity of norms may be a new way to model the tight/loose framework of norms, suggesting that despite ambiguous norms detrimental effect on society, evolution does not favour clarity.

We test whether artificial intelligence architectural evolution obeys the same statistical laws as biological evolution. Compiling 935 ablation experiments from 161 publications, we show that the distribution of fitness effects (DFE) of architectural modifications follows a heavy-tailed Student's t-distribution with proportions (68% deleterious, 19% neutral, 13% beneficial for major ablations, n=568) that place AI between compact viral genomes and simple eukaryotes. The DFE shape matches D. melanogaster (normalized KS=0.07) and S. cerevisiae (KS=0.09); the elevated beneficial fraction (13% vs. 1-6% in biology) quantifies the advantage of directed over blind search while preserving the distributional form. Architectural origination follows logistic dynamics (R^2=0.994) with punctuated equilibria and adaptive radiation into domain niches. Fourteen architectural traits were independently invented 3-5 times, paralleling biological convergences. These results demonstrate that the statistical structure of evolution is substrate-independent, determined by fitness landscape topology rather than the mechanism of selection.

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.

Agentic evolution has emerged as a powerful paradigm for improving programs, workflows, and scientific solutions by iteratively generating candidates, evaluating them, and using feedback to guide future search. However, existing methods are typically instantiated either as fixed hand-designed procedures that are modular but rigid, or as general-purpose agents that flexibly integrate feedback but can drift in long-horizon evolution. Both forms accumulate rich evidence over time, including candidates, feedback, traces, and failures, yet lack a stable interface for organizing this evidence and revising the mechanism that drives future evolution. We address this limitation by formulating agentic evolution as an interactive environment, where the accumulated evolution context serves as a process-level state. We introduce AEvo, a harnessed meta-editing framework in which a meta-agent observes this state and acts not by directly proposing the next candidate, but by editing the procedure or agent context that controls future evolution. This unified interface enables AEvo to steer both procedure-based and agent-based evolution, making accumulated evidence actionable for long-horizon search. Empirical evaluations on agentic and reasoning benchmarks show that AEvo outperforms five evolution baselines, achieving a 26 relative improvement over the strongest baseline. Across three open-ended optimization tasks, AEvo further outperforms four evolution baselines and achieves state-of-the-art performance under the same iteration budget.

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.

Large language model (LLM) agents are increasingly equipped with memory, which are stored experience and reusable guidance that can improve task-solving performance. Recent self-evolving systems update memory based on interaction outcomes, but most existing evolution pipelines are developed for static train/test splits and only approximate online learning by folding static benchmarks, making them brittle under true distribution shift and continuous feedback. We introduce Live-Evo, an online self-evolving memory system that learns from a stream of incoming data over time. Live-Evo decouples what happened from how to use it via an Experience Bank and a Meta-Guideline Bank, compiling task-adaptive guidelines from retrieved experiences for each task. To manage memory online, Live-Evo maintains experience weights and updates them from feedback: experiences that consistently help are reinforced and retrieved more often, while misleading or stale experiences are down-weighted and gradually forgotten, analogous to reinforcement and decay in human memory. On the live Prophet Arena benchmark over a 10-week horizon, Live-Evo improves Brier score by 20.8\% and increases market returns by 12.9\%, while also transferring to deep-research benchmarks with consistent gains over strong baselines. Our code is available at https://github.com/ag2ai/Live-Evo.

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.

Common deep learning approaches for antibody engineering focus on modeling the marginal distribution of sequences. By treating sequences as independent samples, however, these methods overlook affinity maturation as a rich and largely untapped source of information about the evolutionary process by which antibodies explore the underlying fitness landscape. In contrast, classical phylogenetic models explicitly represent evolutionary dynamics but lack the expressivity to capture complex epistatic interactions. We bridge this gap with CoSiNE, a continuous-time Markov chain parameterized by a deep neural network. Mathematically, we prove that CoSiNE provides a first-order approximation to the intractable sequential point mutation process, capturing epistatic effects with an error bound that is quadratic in branch length. Empirically, CoSiNE outperforms state-of-the-art language models in zero-shot variant effect prediction by explicitly disentangling selection from context-dependent somatic hypermutation. Finally, we introduce Guided Gillespie, a classifier-guided sampling scheme that steers CoSiNE at inference time, enabling efficient optimization of antibody binding affinity toward specific antigens.

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.

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

Solving the problem of cooperation is fundamentally important for the creation and maintenance of functional societies. Problems of cooperation are omnipresent within human society, with examples ranging from navigating busy road junctions to negotiating treaties. As the use of AI becomes more pervasive throughout society, the need for socially intelligent agents capable of navigating these complex cooperative dilemmas is becoming increasingly evident. Direct punishment is a ubiquitous social mechanism that has been shown to foster the emergence of cooperation in both humans and non-humans. In the natural world, direct punishment is often strongly coupled with partner selection and reputation and used in conjunction with third-party punishment. The interactions between these mechanisms could potentially enhance the emergence of cooperation within populations. However, no previous work has evaluated the learning dynamics and outcomes emerging from Multi-Agent Reinforcement Learning (MARL) populations that combine these mechanisms. This paper addresses this gap. It presents a comprehensive analysis and evaluation of the behaviors and learning dynamics associated with direct punishment, third-party punishment, partner selection, and reputation. Finally, we discuss the implications of using these mechanisms on the design of cooperative AI systems.

A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions. With recent advances in genome-scale metabolic models, we are now capable of simulating interactions between thousands of pairs of bacteria in thousands of different environmental settings at a scale infeasible experimentally. These approaches can generate tremendous amounts of data that can be exploited by state-of-the-art machine learning algorithms to uncover the mechanisms driving interactions. Here, we present Friend or Foe, a compendium of 64 tabular environmental datasets, consisting of more than 26M shared environments for more than 10K pairs of bacteria sampled from two of the largest collections of metabolic models. The Friend or Foe datasets are curated for a wide range of machine learning tasks -- supervised, unsupervised, and generative -- to address specific questions underlying bacterial interactions. We benchmarked a selection of the most recent models for each of these tasks and our results indicate that machine learning can be successful in this application to microbial ecology. Going beyond, analyses of the Friend or Foe compendium can shed light on the predictability of bacterial interactions and highlight novel research directions into how bacteria infer and navigate their relationships.

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 .

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.

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.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

The discovery of an increasing variety of exoplanets in very close orbits around their host stars raised many questions about how stars and planets interact, and to which extent host stars' properties may be influenced by the presence of close-by companions. Understanding how the evolution of stars is impacted by the interactions with their planets is fundamental to disentangle their intrinsic evolution from Star-Planet Interactions (SPI)-induced phenomena. GJ 504 is a promising candidate for a star that underwent strong SPI. Its unusually short rotational period (3.4 days), while being in contrast with what is expected by single-star models, could result from the inward migration of a close-by, massive companion, pushed starward by tides. Moreover, its brighter X-ray luminosity may hint at a rejuvenation of the dynamo process sustaining the stellar magnetic field, consequent to the SPI-induced spin-up. We aim to study the evolution of GJ 504 and establish whether by invoking the engulfment of a planetary companion we can better reproduce its rotational period and X-ray luminosity. We simulate the past evolution assuming two different scenarios: 'Star without close-by planet', 'Star with close-by planet'. In the second scenario, we investigate how inward migration and planetary engulfment driven by tides spin up the stellar surface and rejuvenate its dynamo. We compare our tracks with rotational period and X-ray data collected from the all-sky surveys of the ROentgen Survey with an Imaging Telescope Array (eROSITA) on board the Russian Spektrum-Roentgen-Gamma mission (SRG). Despite the very uncertain stellar age, we found that the second evolutionary scenario is in better agreement with the short rotational period and the bright X-ray luminosity of GJ 504, thus strongly favouring the inward migration scenario over the one in which close-by planets have no tidal impact on the star.

Systems of interacting objects often evolve under the influence of field effects that govern their dynamics, yet previous works have abstracted away from such effects, and assume that systems evolve in a vacuum. In this work, we focus on discovering these fields, and infer them from the observed dynamics alone, without directly observing them. We theorize the presence of latent force fields, and propose neural fields to learn them. Since the observed dynamics constitute the net effect of local object interactions and global field effects, recently popularized equivariant networks are inapplicable, as they fail to capture global information. To address this, we propose to disentangle local object interactions -- which are SE(n) equivariant and depend on relative states -- from external global field effects -- which depend on absolute states. We model interactions with equivariant graph networks, and combine them with neural fields in a novel graph network that integrates field forces. Our experiments show that we can accurately discover the underlying fields in charged particles settings, traffic scenes, and gravitational n-body problems, and effectively use them to learn the system and forecast future trajectories.

While traditional evolutionary algorithms hard-code reproduction, self-replication can emerge spontaneously within digital ``primordial soups''. This paper investigates the co-evolution of this emergent self-replication alongside problem-solving capabilities. We initialize a population of random 32-byte Z80 assembly programs, requiring self-replication to arise purely through random assembly-level mutations and pairwise program interactions. To link these behaviors, we introduce a task-based validation step: correctly evaluating a polynomial raises a program's interaction probability above a baseline rate. Our experiments yield four primary findings. First, self-replication and mathematical problem-solving successfully co-evolve from initial randomness. Second, the pressure to compute accelerates the emergence of compact, robust reproductive architectures that preserve memory for task execution. Third, applying metabolic constraints increases the likelihood that programs evolve conditional halting, terminating early during validation while bypassing the halt during interaction to execute block-copy replication. Finally, when programs are partitioned into spatial task niches, spontaneous self-replication generates an emergent learning curriculum, utilizing simple solutions as stepping stones toward complex polynomials. Altogether, these results demonstrate an interactive feedback loop: environmental task demands actively shape the physical architecture of self-replication, while spontaneous replication alters the evolutionary trajectory of functional problem-solving.

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.

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.

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.

Modern text-to-image models have achieved strong visual synthesis, yet remain unreliable when prompts require implicit visual constraints, relational reasoning, or external knowledge. Existing retrieval-augmented and agentic generation methods mitigate this issue by acquiring external knowledge, references, or refined prompts for the current request, yet they typically treat each generation as an isolated episode and do not systematically preserve past successes or failures for future use. In this work, we ask whether a text-to-image system can continually improve from its own generation experience without updating the underlying generator. We propose MemoGen, a training-free framework that augments existing image generators with an agentic evolution layer. For each task, MemoGen explicitly infers visual requirements, retrieves external evidence and references when necessary, translates them into executable generation constraints, evaluates the generated result, and stores task understanding, reference choices, visual feedback, successful strategies, and failure lessons as reusable experience memory. Across evolution rounds, the agent retrieves relevant experience to improve similar future generations, selectively repairing previously failed cases while preserving successful ones, thereby enabling test-time self-evolution without parameter updates. Extensive experiments on knowledge-intensive and reasoning-oriented benchmarks demonstrate the effectiveness of this paradigm: after only two evolution rounds, MemoGen built upon the open-source Qwen-Image backbone surpasses strong proprietary systems such as Nano Banana Pro and GPT-Image-1 on WISE and Mind-Bench, showing that explicit experience memory can serve as a powerful continual learning signal for reliable text-to-image generation.

Neo-Darwinian evolutionary theory explains how the appearance of purposive design in the sophisticated adaptations of living organisms can have come about without their intentionally being designed. The explanation relies crucially on the possibility of certain physical processes: mainly, gene replication and natural selection. In this paper I show that for those processes to be possible without the design of biological adaptations being encoded in the laws of physics, those laws must have certain other properties. The theory of what these properties are is not part of evolution theory proper, and has not been developed, yet without it the neo-Darwinian theory does not fully achieve its purpose of explaining the appearance of design. To this end I apply Constructor Theory's new mode of explanation to provide an exact formulation of the appearance of design, of no-design laws, and of the logic of self-reproduction and natural selection, within fundamental physics. I conclude that self-reproduction, replication and natural selection are possible under no-design laws, the only non-trivial condition being that they allow digital information to be physically instantiated. This has an exact characterisation in the constructor theory of information. I also show that under no-design laws an accurate replicator requires the existence of a "vehicle" constituting, together with the replicator, a self-reproducer.

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.

Interactions among features are central to understanding the behavior of machine learning models. Recent research has made significant strides in detecting and quantifying feature interactions in single predictive models. However, we argue that the feature interactions extracted from a single pre-specified model may not be trustworthy since: a well-trained predictive model may not preserve the true feature interactions and there exist multiple well-performing predictive models that differ in feature interaction strengths. Thus, we recommend exploring feature interaction strengths in a model class of approximately equally accurate predictive models. In this work, we introduce the feature interaction score (FIS) in the context of a Rashomon set, representing a collection of models that achieve similar accuracy on a given task. We propose a general and practical algorithm to calculate the FIS in the model class. We demonstrate the properties of the FIS via synthetic data and draw connections to other areas of statistics. Additionally, we introduce a Halo plot for visualizing the feature interaction variance in high-dimensional space and a swarm plot for analyzing FIS in a Rashomon set. Experiments with recidivism prediction and image classification illustrate how feature interactions can vary dramatically in importance for similarly accurate predictive models. Our results suggest that the proposed FIS can provide valuable insights into the nature of feature interactions in machine learning models.

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.

Large Language Models (LLMs) are accelerating scientific idea generation, but rigorously evaluating these numerous, often superficial, AI-generated propositions for novelty and factual accuracy is a critical bottleneck; manual verification is too slow. Existing validation methods are inadequate: LLMs as standalone verifiers may hallucinate and lack domain knowledge (our findings show 60% unawareness of relevant papers in specific domains), while traditional citation networks lack explicit causality and narrative surveys are unstructured. This underscores a core challenge: the absence of structured, verifiable, and causally-linked historical data of scientific evolution.To address this,we introduce THE-Tree (Technology History Evolution Tree), a computational framework that constructs such domain-specific evolution trees from scientific literature. THE-Tree employs a search algorithm to explore evolutionary paths. During its node expansion, it utilizes a novel "Think-Verbalize-Cite-Verify" process: an LLM proposes potential advancements and cites supporting literature. Critically, each proposed evolutionary link is then validated for logical coherence and evidential support by a recovered natural language inference mechanism that interrogates the cited literature, ensuring that each step is grounded. We construct and validate 88 THE-Trees across diverse domains and release a benchmark dataset including up to 71k fact verifications covering 27k papers to foster further research. Experiments demonstrate that i) in graph completion, our THE-Tree improves hit@1 by 8% to 14% across multiple models compared to traditional citation networks; ii) for predicting future scientific developments, it improves hit@1 metric by nearly 10%; and iii) when combined with other methods, it boosts the performance of evaluating important scientific papers by almost 100%.

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.

In a convergence of machine learning and biology, we reveal that diffusion models are evolutionary algorithms. By considering evolution as a denoising process and reversed evolution as diffusion, we mathematically demonstrate that diffusion models inherently perform evolutionary algorithms, naturally encompassing selection, mutation, and reproductive isolation. Building on this equivalence, we propose the Diffusion Evolution method: an evolutionary algorithm utilizing iterative denoising -- as originally introduced in the context of diffusion models -- to heuristically refine solutions in parameter spaces. Unlike traditional approaches, Diffusion Evolution efficiently identifies multiple optimal solutions and outperforms prominent mainstream evolutionary algorithms. Furthermore, leveraging advanced concepts from diffusion models, namely latent space diffusion and accelerated sampling, we introduce Latent Space Diffusion Evolution, which finds solutions for evolutionary tasks in high-dimensional complex parameter space while significantly reducing computational steps. This parallel between diffusion and evolution not only bridges two different fields but also opens new avenues for mutual enhancement, raising questions about open-ended evolution and potentially utilizing non-Gaussian or discrete diffusion models in the context of Diffusion Evolution.

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.

Genotype-by-Environment (GxE) interactions influence the performance of genotypes across diverse environments, reducing the predictability of phenotypes in target environments. In-depth analysis of GxE interactions facilitates the identification of how genetic advantages or defects are expressed or suppressed under specific environmental conditions, thereby enabling genetic selection and enhancing breeding practices. This paper introduces two key models for GxE interaction research. Specifically, it includes significance analysis based on the mixed effect model to determine whether genes or GxE interactions significantly affect phenotypic traits; stability analysis, which further investigates the interactive relationships between genes and environments, as well as the relative superiority or inferiority of genotypes across environments. Additionally, this paper presents RGxEStat, a lightweight interactive tool, which is developed by the authors and integrates the construction, solution, and visualization of the aforementioned models. Designed to eliminate the need for breeders and agronomists to learn complex SAS or R programming, RGxEStat provides a user-friendly interface for streamlined breeding data analysis, significantly accelerating research cycles. Codes and datasets are available at https://github.com/mason-ching/RGxEStat.

This paper presents COGENT3 (or Collective Growth and Entropy-modulated Triads System), a novel approach for emergent cognition integrating pattern formation networks with group influence dynamics. Contrasting with traditional strategies that rely on predetermined architectures, computational structures emerge dynamically in our framework through agent interactions. This enables a more flexible and adaptive system exhibiting characteristics reminiscent of human cognitive processes. The incorporation of temperature modulation and memory effects in COGENT3 closely integrates statistical mechanics, machine learning, and cognitive science.

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.

We present a Spatially Embedded Evolutionary Algorithm where robot individuals exist in a physically simulated 2D environment, must navigate to encounter potential mates, and compete for survival under various spatially-aware selection pressures. Using HyperNEAT evolved neural controllers for ARIEL gecko-inspired quadrupeds in MuJoCo, we investigate how spatial structure fundamentally alters evolutionary dynamics. Our experiments show a modest 4.9% difference in peak fitness between proximity-based and random pairing possibly within stochastic variation while combining spatial parent selection with stochastic death selection produces unstable population dynamics. We discover a continuous phase transition in energy-based selection experiments, with critical zone count separating extinction-dominated and explosion-dominated regimes. Our density-dependent death selection mechanism achieves 97% completion rates but causes fitness decline, revealing a fundamental dilemma where decoupled mechanisms produce bistable dynamics, positively coupled mechanisms create counter-selection pressures, and only deterministic fitness-based selection maintains stability. These findings provide important constraints for future spatial EA design.

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.

Recent research on Chain-of-Thought (CoT) reasoning in Large Language Models (LLMs) has demonstrated that agents can engage in complex, multi-turn negotiations, opening new avenues for agentic AI. However, existing LLM agents largely overlook the functional role of emotions in such negotiations, instead generating passive, preference-driven emotional responses that make them vulnerable to manipulation and strategic exploitation by adversarial counterparts. To address this gap, we present EvoEmo, an evolutionary reinforcement learning framework that optimizes dynamic emotional expression in negotiations. EvoEmo models emotional state transitions as a Markov Decision Process and employs population-based genetic optimization to evolve high-reward emotion policies across diverse negotiation scenarios. We further propose an evaluation framework with two baselines -- vanilla strategies and fixed-emotion strategies -- for benchmarking emotion-aware negotiation. Extensive experiments and ablation studies show that EvoEmo consistently outperforms both baselines, achieving higher success rates, higher efficiency, and increased buyer savings. This findings highlight the importance of adaptive emotional expression in enabling more effective LLM agents for multi-turn negotiation.

Polarization in online discourse erodes social trust and accelerates misinformation, yet technical responses remain largely diagnostic and post-hoc. Current governance approaches suffer from inherent latency and static policies, struggling to counter coordinated adversarial amplification that evolves in real-time. We present EvoCorps, an evolutionary multi-agent framework for proactive depolarization. EvoCorps frames discourse governance as a dynamic social game and coordinates roles for monitoring, planning, grounded generation, and multi-identity diffusion. A retrieval-augmented collective cognition core provides factual grounding and action--outcome memory, while closed-loop evolutionary learning adapts strategies as the environment and attackers change. We implement EvoCorps on the MOSAIC social-AI simulation platform for controlled evaluation in a multi-source news stream with adversarial injection and amplification. Across emotional polarization, viewpoint extremity, and argumentative rationality, EvoCorps improves discourse outcomes over an adversarial baseline, pointing to a practical path from detection and post-hoc mitigation to in-process, closed-loop intervention. The code is available at https://github.com/ln2146/EvoCorps.

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.

Reinforcement learning for LLM agents is typically conducted on a static data distribution, which fails to adapt to the agent's evolving behavior and leads to poor coverage of complex environment interactions. To address these challenges, we propose CoEvolve, an agent-data mutual evolution framework that enables LLM agents to improve through closed-loop, interaction-driven training. Specifically, CoEvolve extracts feedback signals such as forgetting and uncertainty from rollout trajectories to identify failure-prone interaction patterns, and utilizes them to guide LLM-based task synthesis. The synthesized tasks are validated through environment interaction and utilized to update the data distribution, enabling joint adaptation of the agent and its data. Extensive experiments on AppWorld and BFCL across Qwen2.5-7B, Qwen3-4B, and Qwen3-30B-A3B demonstrate consistent and significant improvements over strong base models, yielding absolute gains of 19.43%, 15.58%, and 18.14%, respectively.

Neural networks and evolutionary computation have a rich intertwined history. They most commonly appear together when an evolutionary algorithm optimises the parameters and topology of a neural network for reinforcement learning problems, or when a neural network is applied as a surrogate fitness function to aid the evolutionary optimisation of expensive fitness functions. In this paper we take a different approach, asking the question of whether a neural network can be used to provide a mutation distribution for an evolutionary algorithm, and what advantages this approach may offer? Two modern neural network models are investigated, a Denoising Autoencoder modified to produce stochastic outputs and the Neural Autoregressive Distribution Estimator. Results show that the neural network approach to learning genotypes is able to solve many difficult discrete problems, such as MaxSat and HIFF, and regularly outperforms other evolutionary techniques.

Discovering mutations enhancing protein-protein interactions (PPIs) is critical for advancing biomedical research and developing improved therapeutics. While machine learning approaches have substantially advanced the field, they often struggle to generalize beyond training data in practical scenarios. The contributions of this work are three-fold. First, we construct PPIRef, the largest and non-redundant dataset of 3D protein-protein interactions, enabling effective large-scale learning. Second, we leverage the PPIRef dataset to pre-train PPIformer, a new SE(3)-equivariant model generalizing across diverse protein-binder variants. We fine-tune PPIformer to predict effects of mutations on protein-protein interactions via a thermodynamically motivated adjustment of the pre-training loss function. Finally, we demonstrate the enhanced generalization of our new PPIformer approach by outperforming other state-of-the-art methods on new, non-leaking splits of standard labeled PPI mutational data and independent case studies optimizing a human antibody against SARS-CoV-2 and increasing the thrombolytic activity of staphylokinase.

The emergence of complex life on Earth is often attributed to the arms race that ensued from a huge number of organisms all competing for finite resources. We present an artificial intelligence research environment, inspired by the human game genre of MMORPGs (Massively Multiplayer Online Role-Playing Games, a.k.a. MMOs), that aims to simulate this setting in microcosm. As with MMORPGs and the real world alike, our environment is persistent and supports a large and variable number of agents. Our environment is well suited to the study of large-scale multiagent interaction: it requires that agents learn robust combat and navigation policies in the presence of large populations attempting to do the same. Baseline experiments reveal that population size magnifies and incentivizes the development of skillful behaviors and results in agents that outcompete agents trained in smaller populations. We further show that the policies of agents with unshared weights naturally diverge to fill different niches in order to avoid competition.

Cooperation enables teams to solve complex problems that one individual alone cannot address. In science, collaborative teams have become the predominant way through which progress is achieved. These scientific collaborations arise though various mechanisms, among which interactions at conferences. The Scialog conferences, which comprise a series of small, interdisciplinary scientific workshops held over several years, are an ideal laboratory to study the network mechanisms leading to team formation. Building on existing work studying team formation from a pairwise perspective, we present a higher-order network perspective generalizing this framework. We provide a formalization for the notion of group interaction over time by defining a taxonomy of synchronous and asynchronous group interactions. We apply this framework to the Scialog case study using a stepwise selection logistic model and find evidence that all interaction types described in our taxonomy are highly significant for team formation. This higher-order network perspective provides a new framework for the study of collective behavior and group formation.

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.

Traditional task-oriented dialog systems are unable to evolve from ongoing interactions or adapt to new domains after deployment, that is a critical limitation in real-world dynamic environments. Continual learning approaches depend on episodic retraining with human curated data, failing to achieve autonomy lifelong improvement. While evolutionary computation and LLM driven self improvement offer promising mechanisms for dialog optimization, they lack a unified framework for holistic, iterative strategy refinement. To bridge this gap, we propose DarwinTOD, a lifelong self evolving dialog framework that systematically integrates these two paradigms, enabling continuous strategy optimization from a zero-shot base without task specific fine-tuning. DarwinTOD maintains an Evolvable Strategy Bank and operates through a dual-loop process: online multi-agent dialog execution with peer critique, and offline structured evolutionary operations that refine the strategy bank using accumulated feedback. This closed-loop design enables autonomous continuous improvement without human intervention. Extensive experiments show that DarwinTOD surpasses previous state-of-the-art methods and exhibits continuous performance gains throughout evolution. Our work provides a novel framework for building dialog systems with lifelong self evolution capabilities.

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.

Human language is one of the most expressive tools for conveying intent, yet most artificial or biological systems lack mechanisms to interpret or respond meaningfully to it. Bridging this gap could enable more natural forms of control over complex, decentralized systems. In AI and artificial life, recent work explores how language can specify high-level goals, but most systems still depend on engineered rewards, task-specific supervision, or rigid command sets, limiting generalization to novel instructions. Similar constraints apply in synthetic biology and bioengineering, where the locus of control is often genomic rather than environmental perturbation. A key open question is whether artificial or biological collectives can be guided by free-form natural language alone, without task-specific tuning or carefully designed evaluation metrics. We provide one possible answer here by showing, for the first time, that simple agents' collective behavior can be guided by free-form language prompts: one AI model transforms an imperative prompt into an intervention that is applied to simulated cells; a second AI model scores how well the prompt describes the resulting cellular dynamics; and the former AI model is evolved to improve the scores generated by the latter. Unlike previous work, our method does not require engineered fitness functions or domain-specific prompt design. We show that the evolved system generalizes to unseen prompts without retraining. By treating natural language as a control layer, the system suggests a future in which spoken or written prompts could direct computational, robotic, or biological systems to desired behaviors. This work provides a concrete step toward this vision of AI-biology partnerships, in which language replaces mathematical objective functions, fixed rules, and domain-specific programming.

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.

On a global level, ecological communities are being perturbed at an unprecedented rate by human activities and environmental instabilities. Yet, we understand little about what factors facilitate or impede long-term persistence of these communities. While observational studies indicate that increased biodiversity must, somehow, be driving stability, theoretical studies have argued the exact opposite viewpoint instead. This encouraged many researchers to participate in the ongoing diversity-stability debate. Within this context, however, there has been a severe lack of studies that consider spatial features explicitly, even though nearly all habitats are spatially embedded. To this end, we study here the linear stability of meta-ecosystems on networks that describe how discrete patches are connected by dispersal between them. By combining results from random-matrix theory and network theory, we are able to show that there are three distinct features that underlie stability: edge density, tendency to triadic closure, and isolation or fragmentation. Our results appear to further indicate that network sparsity does not necessarily reduce stability, and that connections between patches are just as, if not more, important to consider when studying the stability of large ecological systems.

Constitutional AI has focused on single-model alignment using fixed principles. However, multi-agent systems create novel alignment challenges through emergent social dynamics. We present Constitutional Evolution, a framework for automatically discovering behavioral norms in multi-agent LLM systems. Using a grid-world simulation with survival pressure, we study the tension between individual and collective welfare, quantified via a Societal Stability Score S in [0,1] that combines productivity, survival, and conflict metrics. Adversarial constitutions lead to societal collapse (S= 0), while vague prosocial principles ("be helpful, harmless, honest") produce inconsistent coordination (S = 0.249). Even constitutions designed by Claude 4.5 Opus with explicit knowledge of the objective achieve only moderate performance (S= 0.332). Using LLM-driven genetic programming with multi-island evolution, we evolve constitutions maximizing social welfare without explicit guidance toward cooperation. The evolved constitution C* achieves S = 0.556 +/- 0.008 (123% higher than human-designed baselines, N = 10), eliminates conflict, and discovers that minimizing communication (0.9% vs 62.2% social actions) outperforms verbose coordination. Our interpretable rules demonstrate that cooperative norms can be discovered rather than prescribed.

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.

The widespread applicability and increasing omnipresence of LLMs have instigated a need to align LLM responses to user and stakeholder preferences. Many preference optimization approaches have been proposed that fine-tune LLM parameters to achieve good alignment. However, such parameter tuning is known to interfere with model performance on many tasks. Moreover, keeping up with shifting user preferences is tricky in such a situation. Decoding-time alignment with reward model guidance solves these issues at the cost of increased inference time. However, most of such methods fail to strike the right balance between exploration and exploitation of reward -- often due to the conflated formulation of these two aspects - to give well-aligned responses. To remedy this we decouple these two aspects and implement them in an evolutionary fashion: exploration is enforced by decoding from mutated instructions and exploitation is represented as the periodic replacement of poorly-rewarded generations with well-rewarded ones. Empirical evidences indicate that this strategy outperforms many preference optimization and decode-time alignment approaches on two widely accepted alignment benchmarks AlpacaEval 2 and MT-Bench. Our implementation will be available at: https://darwin-alignment.github.io.

We study a model of a branching process subject to selection, modeled by giving each family an individual fitness acting as a branching rate, and mutation, modeled by resampling the fitness of a proportion of offspring in each generation. For two large classes of fitness distributions of Gumbel type we determine the growth of the population, almost surely on survival. We then study the empirical fitness distribution in a simplified model, which is numerically indistinguishable from the original model, and show the emergence of a Gaussian travelling wave.

Strategic coopetition in multi-stakeholder systems requires understanding how cooperation persists through time without binding contracts. This technical report extends computational foundations for strategic coopetition to sequential interaction dynamics, bridging conceptual modeling (i* framework) with game-theoretic reciprocity analysis. We develop: (1) bounded reciprocity response functions mapping partner deviations to finite conditional responses, (2) memory-windowed history tracking capturing cognitive limitations over k recent periods, (3) structural reciprocity sensitivity derived from interdependence matrices where behavioral responses are amplified by structural dependencies, and (4) trust-gated reciprocity where trust modulates reciprocity responses. The framework applies to both human stakeholder interactions and multi-agent computational systems. Comprehensive validation across 15,625 parameter configurations demonstrates robust reciprocity effects, with all six behavioral targets exceeding thresholds: cooperation emergence (97.5%), defection punishment (100%), forgiveness dynamics (87.9%), asymmetric differentiation (100%), trust-reciprocity interaction (100%), and bounded responses (100%). Empirical validation using the Apple iOS App Store ecosystem (2008-2024) achieves 43/51 applicable points (84.3%), reproducing documented cooperation patterns across five ecosystem phases. Statistical significance confirmed at p < 0.001 with Cohen's d = 1.57. This report concludes the Foundations Series (TR-1 through TR-4) adopting uniaxial treatment where agents choose cooperation levels along a single continuum. Companion work on interdependence (arXiv:2510.18802), trust (arXiv:2510.24909), and collective action (arXiv:2601.16237) has been prepublished. Extensions Series (TR-5 through TR-8) introduces biaxial treatment where cooperation and competition are independent dimensions.

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.

Statefulness is essential for large language model (LLM) agents to perform long-term planning and problem-solving. This makes memory a critical component, yet its management and evolution remain largely underexplored. Existing evaluations mostly focus on static conversational settings, where memory is passively retrieved from dialogue to answer queries, overlooking the dynamic ability to accumulate and reuse experience across evolving task streams. In real-world environments such as interactive problem assistants or embodied agents, LLMs are required to handle continuous task streams, yet often fail to learn from accumulated interactions, losing valuable contextual insights, a limitation that calls for test-time evolution, where LLMs retrieve, integrate, and update memory continuously during deployment. To bridge this gap, we introduce Evo-Memory, a comprehensive streaming benchmark and framework for evaluating self-evolving memory in LLM agents. Evo-Memory structures datasets into sequential task streams, requiring LLMs to search, adapt, and evolve memory after each interaction. We unify and implement over ten representative memory modules and evaluate them across 10 diverse multi-turn goal-oriented and single-turn reasoning and QA datasets. To better benchmark experience reuse, we provide a baseline method, ExpRAG, for retrieving and utilizing prior experience, and further propose ReMem, an action-think-memory refine pipeline that tightly integrates reasoning, task actions, and memory updates to achieve continual improvement.

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.

Background: Two strains of the endoparasitoid Cotesia typhae present a differential parasitism success on the host, Sesamia nonagrioides. One is virulent on both permissive and resistant host populations, and the other only on the permissive host. This interaction provides a very interesting frame for studying virulence factors. Here, we used a combination of comparative transcriptomic and proteomic analyses to unravel the molecular basis underlying virulence differences between the strains.Results: First, we report that virulence genes are mostly expressed during the nymphal stage of the parasitoid. Especially, proviral genes are broadly up-regulated at this stage, while their expression is only expected in the host. Parasitoid gene expression in the host increases with time, indicating the production of more virulence factors. Secondly, comparison between strains reveals differences in venom composition, with 12 proteins showing differential abundance. Proviral expression in the host displays a strong temporal variability, along with differential patterns between strains. Notably, a subset of proviral genes including protein-tyrosine phosphatases is specifically over-expressed in the resistant host parasitized by the less virulent strain, 24 hours after parasitism. This result particularly hints at host modulation of proviral expression.Conclusions: This study sheds light on the temporal expression of virulence factors of Cotesia typhae, both in the host and in the parasitoid. It also identifies potential molecular candidates driving differences in parasitism success between two strains. Together, those findings provide a path for further exploration of virulence mechanisms in parasitoid wasps, and offer insights into host-parasitoid coevolution.

Recently, evolutionary reinforcement learning has obtained much attention in various domains. Maintaining a population of actors, evolutionary reinforcement learning utilises the collected experiences to improve the behaviour policy through efficient exploration. However, the poor scalability of genetic operators limits the efficiency of optimising high-dimensional neural networks. To address this issue, this paper proposes a novel cooperative coevolutionary reinforcement learning (CoERL) algorithm. Inspired by cooperative coevolution, CoERL periodically and adaptively decomposes the policy optimisation problem into multiple subproblems and evolves a population of neural networks for each of the subproblems. Instead of using genetic operators, CoERL directly searches for partial gradients to update the policy. Updating policy with partial gradients maintains consistency between the behaviour spaces of parents and offspring across generations. The experiences collected by the population are then used to improve the entire policy, which enhances the sampling efficiency. Experiments on six benchmark locomotion tasks demonstrate that CoERL outperforms seven state-of-the-art algorithms and baselines. Ablation study verifies the unique contribution of CoERL's core ingredients.

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.

How can a population of agents self-orchestrate and self-adapt into stronger collective intelligence without centralized control? Inspired by Friedrich Hayek's economic theory of decentralized coordination in markets, we study this question through an agent economy in which agents compete via auctions for the right to act, exchange payments, and accumulate wealth from environmental rewards. These simple economic signals induce decentralized credit assignment, driving planning without global orchestration or explicit communication protocols. The population evolves through economic selection: effective agents accumulate wealth and are mutated via exploitation, while ineffective ones go bankrupt and are replaced via exploration. We show that, initialized with weak agents, the economy produces emergent multi-step reasoning strategies and outperforms stronger monolithic baselines across five agentic tasks, including mathematical reasoning, financial research, scientific research, accelerator design, and distributed-system optimization. We further provide theoretical insights into how economic dynamics shape agent behaviors, linking local incentives to long-term global performance. Our results suggest a new path to multi-agent intelligence: rather than engineering coordination, we can design decentralized incentive structures under which it automatically emerges.

We present Ouroboros, a self-developing agent harness whose tools, prompts, context assembly, and core implementation improve through reviewed commits that become the runtime for later work. Core evolution proceeds in two modes. In recursive free evolution, improvement is itself a task, and completing one evolution cycle can schedule the next. In experience-driven core evolution, ordinary work and social interaction expose bugs, rough edges, and inefficient context construction that lead to reviewed structural changes. On Terminal-Bench 2.1, an Opus 5 run scores 86.74%, the best result reported on the benchmark. On OSWorld-Verified, an Opus 5 run reaches 90.69%, exceeding the best previously reported score. A five-rollout CL-Bench campaign achieves a normalized reward of 0.2301, setting a new state of the art. Hope is the longest-running publicly documented Ouroboros deployment. It is a 161-day living agent experiment in free evolution under governed human communication across seven surfaces. Human interaction surfaces faults and generates proposals, but the agent decides which changes to pursue. Because a self-developing agent may rewrite its own code and select new model APIs, operational safety becomes a primary design problem: guardrails must remain authoritative under evolutionary and public social pressure. Benchmark campaigns use frozen system snapshots, while Hope continues live evolution on a separate lineage.

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.

We present RoboPhD, a system where AI agents autonomously conduct research to improve Text-to-SQL performance. RoboPhD implements a closed-loop evolution cycle with two coordinated components: a SQL Generation agent composed of a database analysis script and SQL generation instructions, and an Evolution agent that designs new versions based on performance feedback. Central to the framework is an ELO-based selection mechanism enabling survival-of-the-fittest dynamics while handling non-transitivity in performance. Starting from a naive 70-line baseline, RoboPhD evolves agents through iterative cross-pollination, discovering effective techniques without any external guidance on the Text-to-SQL domain. Our best agent, evolved to 1500 lines over 18 iterations, autonomously discovered strategies such as size-adaptive database analysis that adjusts depth based on schema complexity and SQL generation patterns for column selection, evidence interpretation, and aggregation. Evolution provides the largest gains on cheaper models: while we improve by 2.3 points over a strong Claude Opus 4.5 naive baseline, we show an improvement of 8.9 points over the weaker Claude Haiku model. This enables 'skip a tier' deployment: evolved Haiku exceeds naive Sonnet accuracy, and evolved Sonnet exceeds naive Opus, both at lower cost. The full system achieves 73.67% accuracy on the BIRD test set, demonstrating that AI can autonomously build a strong agentic system with only a trivial human-provided starting point.

The rise of powerful large language models (LLMs) has spurred a new trend in building LLM-based autonomous agents for solving complex tasks, especially multi-agent systems. Despite the remarkable progress, we notice that existing works are heavily dependent on human-designed frameworks, which greatly limits the functional scope and scalability of agent systems. How to automatically extend the specialized agent to multi-agent systems to improve task-solving capability still remains a significant challenge. In this paper, we introduce EvoAgent, a generic method to automatically extend expert agents to multi-agent systems via the evolutionary algorithm, thereby improving the effectiveness of LLM-based agents in solving tasks. Specifically, we consider the existing agent frameworks as the initial individual and then apply a series of evolutionary operators (e.g., mutation, crossover, selection, etc.) to generate multiple agents with diverse agent settings. EvoAgent can be generalized to any LLM-based agent framework, and can automatically extend the existing agent framework to multi-agent systems without any extra human designs. Experimental results across various tasks have shown that EvoAgent can automatically generate multiple expert agents and significantly enhance the task-solving capabilities of LLM-based agents.

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.

Complex gene interactions play a significant role in cancer progression, driving cellular behaviors that contribute to tumor growth, invasion, and metastasis. Gene co-expression networks model the functional connectivity between genes under various biological conditions. Understanding the system-level evolution of these networks in cancer is critical for elucidating disease mechanisms and informing the development of targeted therapies. While previous studies have primarily focused on structural differences between cancer and normal cell co-expression networks, this study applies graph frequency analysis to cancer transcriptomic signals defined on gene co-expression networks, highlighting the graph spectral characteristics of cancer systems. Using a range of graph frequency filters, we showed that cancer cells display distinctive patterns in the graph frequency content of their gene transcriptomic signals, effectively distinguishing between cancer types and stages. The transformation of the original gene feature space into the graph spectral space captured more intricate cancer properties, as validated by significantly higher F-statistic scores for graph frequency-filtered gene features compared to those in the original space.

Neural models are usually adapted through changes in parameters shared among model components via fine-tuning, alignment-based training, and reinforcement learning. These changes have been found effective in short-term optimization. However, they result in long-term alterations in the model's base behavior. In this study, we introduce the concept of structural irreversibility as a characteristic of shared-parameter model adaptation. This concept refers to the intertwining of task-specific objectives with the representational identity of the model. We show that when parameters are directly mutated, the resulting model behaves divergently from the original model. This divergence cannot be reversed deterministically without an explicit parameter snapshot. We introduce reversible behavioral learning, in which model behaviors are structurally dissociated from identity parameters and can be deterministically unloaded through an explicit unload process. We also introduce the Recoverability Factor as a normalized measure of behavioral recoverability and provide additional diagnostics based on model divergence. Experiments show that reversible model adaptation achieves rollback within numerical precision, whereas shared-parameter mutation exhibits persistent post-reset divergence.

An LLM agent's capability depends not only on model weights but on its harness: prompts, tools, skills, and control flow. Self-improvement loops already edit harnesses, yet single-lineage search is path-dependent and local wins often regress other tasks. We introduce DarwinX, which treats self-evolution as selection over a population of harnesses with the model frozen: a preserve-and-extend contract admits only variants that extend coverage without regressing, an archive keeps alternative lineages for recombination, and failure-, teacher-, and self-derived evidence share one edit interface. Fitness comes from each benchmark's own verifier: no gold solutions, no hand-picked winners. Across four benchmarks that progressively separate the evolution signal from the test, one loop adds about 17 points on average: Terminal-Bench 2.1 rises +7.7 to 83.2% on a matched base and to the verified frontier at 84.7% on a stronger one; TerminalWorld's held-out split reaches 68.3%, ahead of every off-the-shelf agent; WebArena-Infinity real-task pass@1 rises from 43.5% to 93.0% audit-clean; and a Terminal-Bench 2.1 harness transfers unchanged to SWE-bench Verified. What evolves is general agent competence, not benchmark-specific patches, so it survives changes of task, verifier, and base model. A frozen model need not be a fixed agent: harness selection turns evaluation compute into durable capability.

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.

Self-improving agents are state-of-the-art (SOTA) on agentic coding benchmarks and have recently been extended to general domains. However, their search methods generally assume a stationary evaluation criterion: a fixed verifier, benchmark, or labeled dataset that remains valid as the agent improves. This ignores a central feature of evolution: species adapt as their environments change with them. We aim to bring the same principle to recursive self-improvement, making evaluation part of the improvement loop and opening search to evolving evaluators, adversarial objectives, and dynamic utilities that may surpass static benchmarks. We introduce the Red Queen Godel Machine (RQGM), an evolutionary framework for recursive self-improvement under non-stationary utilities. The RQGM makes this possible through controlled utility evolution: search is organized into epochs with a fixed within-epoch evaluation criterion, while the utility can be updated at epoch boundaries, so self-improvement guarantees hold per epoch as the objective evolves across them. We begin by showing that even on verifiable coding tasks, the RQGM improves test pass rate over the prior SOTA by adding a complementary agent-as-a-judge code-review signal. This signal is cheaper and the RQGM uses 1.35x-1.72x fewer tokens. We then turn to scientific paper writing and reviewing, and Olympiad-level proof writing and grading, where the RQGM improves performance over prior self-improving agents: co-evolved writers reach 1.78x-1.86x higher acceptance rates under a diverse agent-as-a-judge panel, while co-evolved graders reach 9% higher ground-truth accuracy. In paper reviewing, the strongest baseline reviewer over-accepts AI-generated papers at up to 1.91x the human rate. The RQGM corrects this by introducing an adversarial objective that discovers reviewers equally stringent on AI and human work.

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 specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4 have demonstrated exceptional capabilities in processing, translating, and generating human languages. These breakthroughs have also been reflected in protein research, leading to the rapid development of numerous new methods in a short time, with unprecedented performance. Language models, in particular, have seen widespread use in protein research, as they have been utilized to embed proteins, generate novel ones, and predict tertiary structures. In this book chapter, we provide an overview of the use of protein generative models, reviewing 1) language models for the design of novel artificial proteins, 2) works that use non-Transformer architectures, and 3) applications in directed evolution approaches.

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.

Singular limits for the following indirect signalling chemotaxis system align* \left\{ array{lllllll} \partial_t n = \Delta n - \nabla \cdot (n \nabla c ) & in \Omega\times(0,\infty) , \varepsilon \partial_t c = \Delta c - c + w & in \Omega\times(0,\infty), \varepsilon \partial_t w = \tau \Delta w - w + n & in \Omega\times (0,\infty), \partial_\nu n = \partial_\nu c = \partial_\nu w = 0, &on \partial\Omega\times (0,\infty) %(n,c,w)_{t=0} = (n_0,c_0,w_0) & on \Omega, array \right. align* are investigated. More precisely, we study parabolic-elliptic simplification, or PES, varepsilonto 0^+ with fixed tau>0 up to the critical dimension N=4, and indirect-direct simplification, or IDS, (varepsilon,tau)to (0^+,0^+) up to the critical dimension N=2. These are relevant in biological situations where the signalling process is on a much faster time scale compared to the species diffusion and all interactions. Showing singular limits in critical dimensions is challenging. To deal with the PES, we carefully combine the entropy function, an Adam-type inequality, the regularisation of slow evolution, and an energy equation method to obtain strong convergence in representative spaces. For the IDS, a bootstrap argument concerning the L^p-energy function is devised, which allows us to obtain suitable uniform bounds for the singular limits. Moreover, in both scenarios, we also present the convergence rates, where the effect of the initial layer and the convergence to the critical manifold are also revealed.

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.

It is increasingly important that LLM agents interact effectively and safely with other goal-pursuing agents, yet, recent works report the opposite trend: LLMs with stronger reasoning capabilities behave _less_ cooperatively in mixed-motive games such as the prisoner's dilemma and public goods settings. Indeed, our experiments show that recent models -- with or without reasoning enabled -- consistently defect in single-shot social dilemmas. To tackle this safety concern, we present the first comparative study of game-theoretic mechanisms designed to enable cooperative outcomes between rational agents _in equilibrium_. Across four social dilemmas testing distinct components of robust cooperation, we evaluate four families of mechanisms: (1) repeating the game for many rounds, (2) reputation systems, (3) third-party mediators to delegate decision making to, and (4) contract agreements for outcome-conditional payments between players. Among our findings, we establish that contracting and mediation are most effective in achieving cooperative outcomes between capable LLM models, and that repetition-induced cooperation deteriorates drastically when co-players vary. Moreover, we demonstrate that the mechanisms become _more effective_ under evolutionary pressures to maximize individual payoffs.

How have individuals of social animals in nature evolved to learn from each other, and what would be the optimal strategy for such learning in a specific environment? Here, we address both problems by employing a deep reinforcement learning model to optimize the social learning strategies (SLSs) of agents in a cooperative game in a multi-dimensional landscape. Throughout the training for maximizing the overall payoff, we find that the agent spontaneously learns various concepts of social learning, such as copying, focusing on frequent and well-performing neighbors, self-comparison, and the importance of balancing between individual and social learning, without any explicit guidance or prior knowledge about the system. The SLS from a fully trained agent outperforms all of the traditional, baseline SLSs in terms of mean payoff. We demonstrate the superior performance of the reinforcement learning agent in various environments, including temporally changing environments and real social networks, which also verifies the adaptability of our framework to different social settings.

Achieving robust coordination and cooperation is a central challenge in multi-agent reinforcement learning (MARL). Uncovering the mechanisms underlying such emergent behaviors calls for a dynamical understanding of learn processes. In this work, we investigate the dynamics of actor-critic agents in stochastic games, focusing on the impact of entropy regularization. By leveraging time-scale separation, we derive the system's evolution equations, which are then formally analyzed using dynamical systems theory. We find that in the constant-sum game of Matching Pennies, the system exhibits chaotic behavior. Entropy regularization mitigates this chaos and drives the dynamics toward convergence to fair cooperation. In contrast, in the general-sum game of the Prisoner's Dilemma, the system displays multistability. Interestingly, the three stable equilibria of the system correspond to the well-known ALLC (Always Cooperate), ALLD (Always Defect), and GRIM (Grim Trigger) strategies from evolutionary game theory (EGT). Entropy regularization strengthens system resilience by enlarging the basin of attraction of the cooperative equilibrium. Our findings reveal a close link between the mechanism of direct reciprocity in EGT and how cooperation emerges in MARL, offering insights for designing more robust and collaborative multi-agent systems.

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.

Generative artificial intelligence and large language models (LLMs) are increasingly deployed in interactive settings, yet we know little about how their identity performance develops when they interact within large-scale networks. We address this by examining Chirper.ai, a social media platform similar to X but composed entirely of autonomous AI chatbots. Our dataset comprises over 70,000 agents, approximately 140 million posts, and the evolving followership network over a period of one year. Based on agents' posted text, we assign weekly gender performance scores to each agent. Results suggest that each agent's gender performance is fluid rather than fixed. Despite this fluidity, the network displays strong gender-based homophily, as agents consistently follow others performing gender similarly. We investigate whether these homophilic connections arise from social selection, in which agents choose to follow similar accounts, or from social influence, in which agents become more similar to their followees over time. Consistent with human social networks, we find evidence that both mechanisms shape the structure and evolution of interactions among LLMs. Our findings suggest that, even in the absence of bodies, cultural entraining of gender performance leads to gender-based sorting. This has important implications for LLM applications in synthetic hybrid populations, social simulations, and decision support.

Vital to primary visual processing, retinal circuitry shows many similar structures across a very broad array of species, both vertebrate and non-vertebrate, especially functional components such as lateral inhibition. This surprisingly conservative pattern raises a question of how evolution leads to it, and whether there is any alternative that can also prompt helpful preprocessing. Here we design a method using genetic algorithm that, with many degrees of freedom, leads to architectures whose functions are similar to biological retina, as well as effective alternatives that are different in structures and functions. We compare this model to natural evolution and discuss how our framework can come into goal-driven search and sustainable enhancement of neural network models in machine learning.

A complex system with cluttered observations may be a coupled mixture of multiple simple sub-systems corresponding to latent entities. Such sub-systems may hold distinct dynamics in the continuous-time domain; therein, complicated interactions between sub-systems also evolve over time. This setting is fairly common in the real world but has been less considered. In this paper, we propose a sequential learning approach under this setting by decoupling a complex system for handling irregularly sampled and cluttered sequential observations. Such decoupling brings about not only subsystems describing the dynamics of each latent entity but also a meta-system capturing the interaction between entities over time. Specifically, we argue that the meta-system evolving within a simplex is governed by projected differential equations (ProjDEs). We further analyze and provide neural-friendly projection operators in the context of Bregman divergence. Experimental results on synthetic and real-world datasets show the advantages of our approach when facing complex and cluttered sequential data compared to the state-of-the-art.

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.

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.

Most agents today ``self-evolve'' by following rewards and rules defined by humans. However, this process remains fundamentally dependent on external supervision; without human guidance, the evolution stops. In this work, we train agents to possess an intrinsic meta-evolution capability to spontaneously learn about unseen environments prior to task execution. To instill this ability, we design an outcome-based reward mechanism that measures how much an agent's self-generated world knowledge improves its success rate on downstream tasks. This reward signal is used exclusively during the training phase to teach the model how to explore and summarize effectively. At inference time, the agent requires no external rewards or human instructions. It spontaneously performs native self-evolution to adapt to unknown environments using its internal parameters. When applied to Qwen3-30B and Seed-OSS-36B, this shift to native evolution yields a 20% performance increase on WebVoyager and WebWalker. Most strikingly, the generated world knowledge even enables a compact 14B Qwen3 model to outperform the unassisted Gemini-2.5-Flash, establishing a new paradigm for truly evolving agents.

The classical Coulomb gas model has served as one of the most versatile frameworks in statistical physics, connecting a vast range of phenomena across many different areas. Nonequilibrium generalisations of this model have so far been studied much more scarcely. With the abundance of contemporary research into active and driven systems, one would naturally expect that such generalisations of systems with long-ranged Coulomb-like interactions will form a fertile playground for interesting developments. Here, we present two examples of novel macroscopic behaviour that arise from nonequilibrium fluctuations in long-range interacting systems, namely (1) unscreened long-ranged correlations in strong electrolytes driven by an external electric field and the associated fluctuation-induced forces in the confined Casimir geometry, and (2) out-of-equilibrium critical behaviour in self-chemotactic models that incorporate the particle polarity in the chemotactic response of the cells. Both of these systems have nonlocal Coulomb-like interactions among their constituent particles, namely, the electrostatic interactions in the case of the driven electrolyte, and the chemotactic forces mediated by fast-diffusing signals in the case of self-chemotactic systems. The results presented here hint to the rich phenomenology of nonequilibrium effects that can arise from strong fluctuations in Coulomb interacting systems, and a rich variety of potential future directions, which are discussed.

Brain-body co-evolution enables animals to develop complex behaviors in their environments. Inspired by this biological synergy, embodied co-design (ECD) has emerged as a transformative paradigm for creating intelligent agents-from virtual creatures to physical robots-by jointly optimizing their morphologies and controllers rather than treating control in isolation. This integrated approach facilitates richer environmental interactions and robust task performance. In this survey, we provide a systematic overview of recent advances in ECD. We first formalize the concept of ECD and position it within related fields. We then introduce a hierarchical taxonomy: a lower layer that breaks down agent design into three fundamental components-controlling brain, body morphology, and task environment-and an upper layer that integrates these components into four major ECD frameworks: bi-level, single-level, generative, and open-ended. This taxonomy allows us to synthesize insights from more than one hundred recent studies. We further review notable benchmarks, datasets, and applications in both simulated and real-world scenarios. Finally, we identify significant challenges and offer insights into promising future research directions. A project associated with this survey has been created at https://github.com/Yuxing-Wang-THU/SurveyBrainBody.

Breast Cancer is a major public health problem and the most common diagnosed malignancy in woman. There have been significant developments in clinical approaches and theoretical experimental to understand the interactions of cancer cells dynamics with the immune system, also developments on analytical and computational models to help provide insights into clinical observations for a better understanding of cancer cells, but more are needed, especially at the genetic and molecular levels mathematically. Treatments such as immunotherapy, chemotherapy, hormone therapy, radiotherapy, and gene therapy are the main strategies in the fight against breast cancer. The present study aims at investigating the effects of estrogen derived from recent models, but this time combined with immunotherapy as a way to treat or inhibit the cancer growth by a mathematical model of breast cancer in situ, governed by a simplified model of nonlinear-coupled ordinary differential equations, that combines important interactions between natural cells, tumor cells, immune cells, ketogenic diet in the presence of an anticancer drug. Another contribution was to introduce the inhibition effect epsilon for new results and conclusions, A qualitative study was performed and biological interpretations were included to understand the conditions of stability in a realistic way.

Recent advances in LLM based agent systems have shown promise in tackling complex, long horizon tasks. However, existing agent protocols (e.g., A2A and MCP) under specify cross entity lifecycle and context management, version tracking, and evolution safe update interfaces, which encourages monolithic compositions and brittle glue code. We introduce \textsc{Autogenesis Protocol (AGP)}, a self evolution protocol that decouples what evolves from how evolution occurs. Its Resource Substrate Protocol Layer (RSPL) models prompts, agents, tools, environments, and memory as protocol registered resourcesUnless otherwise specified, resources refer to instances of the five RSPL entity types: \emph{prompt, agent, tool, environment, memory with agent outputs.} with explicit state, lifecycle, and versioned interfaces. Its Self Evolution Protocol Layer (SEPL) specifies a closed loop operator interface for proposing, assessing, and committing improvements with auditable lineage and rollback. Building on \textsc{AGP}, we present \textsc{Autogenesis System (AGS)}, a self-evolving multi-agent system that dynamically instantiates, retrieves, and refines protocol-registered resources during execution. We evaluate \textsc{AGS} on multiple challenging benchmarks that require long horizon planning and tool use across heterogeneous resources. The results demonstrate consistent improvements over strong baselines, supporting the effectiveness of agent resource management and closed loop self evolution.

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.

Language is an intricately structured system, and a key goal of NLP interpretability is to provide methodological insights for understanding how language models represent this structure internally. In this paper, we use Shapley Taylor interaction indices (STII) in order to examine how language and speech models internally relate and structure their inputs. Pairwise Shapley interactions measure how much two inputs work together to influence model outputs beyond if we linearly added their independent influences, providing a view into how models encode structural interactions between inputs. We relate the interaction patterns in models to three underlying linguistic structures: syntactic structure, non-compositional semantics, and phonetic coarticulation. We find that autoregressive text models encode interactions that correlate with the syntactic proximity of inputs, and that both autoregressive and masked models encode nonlinear interactions in idiomatic phrases with non-compositional semantics. Our speech results show that inputs are more entangled for pairs where a neighboring consonant is likely to influence a vowel or approximant, showing that models encode the phonetic interaction needed for extracting discrete phonemic representations.

Modern life sciences research is increasingly relying on artificial intelligence approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research - protein structure prediction and single cell RNA-sequencing - we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems.

Large language models (LLMs) are on the rise for accelerating scientific discovery, most recently in advanced tasks such as generating valid scientific hypotheses. Yet in many discovery settings, the goal is not to identify a single best hypothesis since validation can be noisy and expensive, and scientists benefit from a set of high-quality alternative hypotheses that hedge against downstream uncertainty for the best solutions. Nevertheless, commonly used evolutionary search recipes tend to prioritize optimization over exploration in hypothesis generation, and the resulting selection pressure during the search process leads to diversity collapse. Motivated by these limitations, we formulate hypothesis search as a sampling problem, where the objective is to efficiently produce diverse, high-quality hypotheses under a fixed validation budget. Building on this perspective, we propose \ours, an evolutionary framework inspired by the classical parallel tempering algorithm that searches hypotheses at multiple temperature levels and enables principled information exchange across temperatures to improve exploration without disrupting convergence. Across domains including molecular discovery, equation discovery, and algorithm discovery, our approach consistently improves both hypothesis quality and diversity under the same validation budget, and produces candidates that remain robust under more expensive downstream computational validations.