Daily Papers

ARC-AGI-3 evaluates agents in interactive environments whose rules and objectives must be inferred from observation. We present Kepler, an open-source harness that represents hypotheses as executable world models and validates them through retrospective transition checks and conditional prediction checks. Under one frozen Claude Opus 5 configuration, Kepler obtained a server-verified 100.00 RHAE on all 25 public games, with no per-game model selection or score-conditioned reruns. On 181 of 183 completed levels, the final Opus attempt used no more actions than the corresponding median-human baseline. The retained board runs used 8,256 environment actions, of which 7,292 occurred in scored levels. Retained local provider-session records yield 858.0 million tokens, 97.37% cache reads, and a \$777.72 cost at September 1, 2026 API list-equivalent rates. We also report three evaluation failures: source-code leakage that produced an invalid perfect run, agents reconstructing a removed harness in a control condition, and autonomous repair masking a broken planner. A single-game observation case study showed that animation frames contained task-relevant information absent from settled text grids. Across the final Claude Opus 5 and GPT-5.6 Sol boards, 48 of 50 game-model cells reached 100. These results indicate that public-set score alone has limited discriminative value and motivate first-attempt, cost-conditioned, and verification-aware reporting.

The Game of Life (Life), a well known algorithm within the broader class of cellular automata (CA), exhibits complex emergent dynamics, with extreme sensitivity to initial conditions. Modeling and predicting such intricate behavior without explicit knowledge of the system's underlying topology presents a significant challenge, motivating the development of algorithms that can generalize across various grid configurations and boundary conditions. We develop a decoder-only generative pretrained transformer model to solve this problem, showing that our model can simulate Life on a toroidal grid with no prior knowledge on the size of the grid, or its periodic boundary conditions (LifeGPT). LifeGPT is topology-agnostic with respect to its training data and our results show that a GPT model is capable of capturing the deterministic rules of a Turing-complete system with near-perfect accuracy, given sufficiently diverse training data. We also introduce the idea of an `autoregressive autoregressor' to recursively implement Life using LifeGPT. Our results pave the path towards true universal computation within a large language model (LLM) framework, synthesizing of mathematical analysis with natural language processing, and probing AI systems for situational awareness about the evolution of such algorithms without ever having to compute them. Similar GPTs could potentially solve inverse problems in multicellular self-assembly by extracting CA-compatible rulesets from real-world biological systems to create new predictive models, which would have significant consequences for the fields of bioinspired materials, tissue engineering, and architected materials design.

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

Large language models (LLMs) are transforming cellular biology by enabling the development of "virtual cells"--computational systems that represent, predict, and reason about cellular states and behaviors. This work provides a comprehensive review of LLMs for virtual cell modeling. We propose a unified taxonomy that organizes existing methods into two paradigms: LLMs as Oracles, for direct cellular modeling, and LLMs as Agents, for orchestrating complex scientific tasks. We identify three core tasks--cellular representation, perturbation prediction, and gene regulation inference--and review their associated models, datasets, evaluation benchmarks, as well as the critical challenges in scalability, generalizability, and interpretability.

Virtual cell modeling aims to predict cellular responses to perturbations. Existing virtual cell models rely heavily on large-scale single-cell datasets, learning explicit mappings between gene expression and perturbations. Although recent models attempt to incorporate multi-source biological information, their generalization remains constrained by data quality, coverage, and batch effects. More critically, these models often function as black boxes, offering predictions without interpretability or consistency with biological principles, which undermines their credibility in scientific research. To address these challenges, we present VCWorld, a cell-level white-box simulator that integrates structured biological knowledge with the iterative reasoning capabilities of large language models to instantiate a biological world model. VCWorld operates in a data-efficient manner to reproduce perturbation-induced signaling cascades and generates interpretable, stepwise predictions alongside explicit mechanistic hypotheses. In drug perturbation benchmarks, VCWorld achieves state-of-the-art predictive performance, and the inferred mechanistic pathways are consistent with publicly available biological evidence.

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.

Playing games has a long history of describing intricate interactions in simplified forms. In this paper we explore if large language models (LLMs) can play games, investigating their capabilities for randomisation and strategic adaptation through both simultaneous and sequential game interactions. We focus on GPT-4o-Mini-2024-08-17 and test two games between LLMs: Rock Paper Scissors (RPS) and games of strategy (Prisoners Dilemma PD). LLMs are often described as stochastic parrots, and while they may indeed be parrots, our results suggest that they are not very stochastic in the sense that their outputs - when prompted to be random - are often very biased. Our research reveals that LLMs appear to develop loss aversion strategies in repeated games, with RPS converging to stalemate conditions while PD shows systematic shifts between cooperative and competitive outcomes based on prompt design. We detail programmatic tools for independent agent interactions and the Agentic AI challenges faced in implementation. We show that LLMs can indeed play games, just not very well. These results have implications for the use of LLMs in multi-agent LLM systems and showcase limitations in current approaches to model output for strategic decision-making.

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells in quantitative, predictive, and mechanistic ways. We discuss the role of mathematical models in the context of cell-fate decision making systems across the tree of life. Complex multi-cellular organisms have been a particular focus, but single celled organisms also have to sense and respond to their environment. We center our discussion around the idea of design principles which we can learn from observations and modeling, and exploit in order to (re)-design or guide cellular behavior.

The deployment of ever-larger machine learning models reflects a growing consensus that the more expressive the modelx2013and the more data one has access tox2013the more one can improve performance. As models get deployed in a variety of real world scenarios, they inevitably face strategic environments. In this work, we consider the natural question of how the interplay of models and strategic interactions affects scaling laws. We find that strategic interactions can break the conventional view of scaling lawsx2013meaning that performance does not necessarily monotonically improve as models get larger and/ or more expressive (even with infinite data). We show the implications of this phenomenon in several contexts including strategic regression, strategic classification, and multi-agent reinforcement learning through examples of strategic environments in whichx2013by simply restricting the expressivity of one's model or policy classx2013one can achieve strictly better equilibrium outcomes. Motivated by these examples, we then propose a new paradigm for model-selection in games wherein an agent seeks to choose amongst different model classes to use as their action set in a game.

The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells. Here we propose a vision of leveraging advances in AI to construct virtual cells, high-fidelity simulations of cells and cellular systems under different conditions that are directly learned from biological data across measurements and scales. We discuss desired capabilities of such AI Virtual Cells, including generating universal representations of biological entities across scales, and facilitating interpretable in silico experiments to predict and understand their behavior using virtual instruments. We further address the challenges, opportunities and requirements to realize this vision including data needs, evaluation strategies, and community standards and engagement to ensure biological accuracy and broad utility. We envision a future where AI Virtual Cells help identify new drug targets, predict cellular responses to perturbations, as well as scale hypothesis exploration. With open science collaborations across the biomedical ecosystem that includes academia, philanthropy, and the biopharma and AI industries, a comprehensive predictive understanding of cell mechanisms and interactions has come into reach.

Game theory is a foundational framework for analyzing strategic interactions, and its intersection with large language models (LLMs) is a rapidly growing field. However, existing surveys mainly focus narrowly on using game theory to evaluate LLM behavior. This paper provides the first comprehensive survey of the bidirectional relationship between Game Theory and LLMs. We propose a novel taxonomy that categorizes the research in this intersection into four distinct perspectives: (1) evaluating LLMs in game-based scenarios; (2) improving LLMs using game-theoretic concepts for better interpretability and alignment; (3) modeling the competitive landscape of LLM development and its societal impact; and (4) leveraging LLMs to advance game models and to solve corresponding game theory problems. Furthermore, we identify key challenges and outline future research directions. By systematically investigating this interdisciplinary landscape, our survey highlights the mutual influence of game theory and LLMs, fostering progress at the intersection of these fields.

Language-model agents are vulnerable to indirect prompt injection (IPI) during tool use: adversarial instructions hidden in untrusted tool outputs can covertly redirect legitimate task execution. Existing work often trains and evaluates defenses against fixed attacks that do not adapt to the defender's behavior, so the resulting defenses may struggle against adaptive attacks. We combine adaptive attacker-defender co-training with subsequent refinement: continued interaction improves both roles, while learned attackers provide training challenges for further gains in defender safety and task utility. We therefore model adaptive IPI as a general-sum Markov game: the defender advances the task through successive tool calls, while the attacker can inject multiple times within the same task and adapt subsequent attacks to the defender's responses. Building on this formulation, we propose CoER, a verifier-grounded co-evolution and refinement framework. After initializing the attacker from successful trajectories, Co-PPO retains historical policies from both roles as opponent populations and mixes current and historical opponents for bilateral reinforcement learning, extending training beyond the latest matchup. Attackers from these populations are then reused to challenge teacher agents, and only demonstrations verified for both safety and task completion are used to fine-tune the co-evolved defender. In our main seven-domain evaluation, CoER reduces observed overall attack success from 38.5% to 0.2% and raises task utility from 63.2% to 76.3%, with improved attack resistance on external benchmarks.

Drug discovery is fundamentally a process of inferring the effects of treatments on patients, and would therefore benefit immensely from computational models that can reliably simulate patient responses, enabling researchers to generate and test large numbers of therapeutic hypotheses safely and economically before initiating costly clinical trials. Even a more specific model that predicts the functional response of cells to a wide range of perturbations would be tremendously valuable for discovering safe and effective treatments that successfully translate to the clinic. Creating such virtual cells has long been a goal of the computational research community that unfortunately remains unachieved given the daunting complexity and scale of cellular biology. Nevertheless, recent advances in AI, computing power, lab automation, and high-throughput cellular profiling provide new opportunities for reaching this goal. In this perspective, we present a vision for developing and evaluating virtual cells that builds on our experience at Recursion. We argue that in order to be a useful tool to discover novel biology, virtual cells must accurately predict the functional response of a cell to perturbations and explain how the predicted response is a consequence of modifications to key biomolecular interactions. We then introduce key principles for designing therapeutically-relevant virtual cells, describe a lab-in-the-loop approach for generating novel insights with them, and advocate for biologically-grounded benchmarks to guide virtual cell development. Finally, we make the case that our approach to virtual cells provides a useful framework for building other models at higher levels of organization, including virtual patients. We hope that these directions prove useful to the research community in developing virtual models optimized for positive impact on drug discovery outcomes.

Modeling cellular states and predicting their responses to perturbations are central challenges in computational biology and the development of virtual cells. Existing foundation models for single-cell transcriptomics provide powerful static representations, but they do not explicitly model the distribution of cellular states for generative simulation. Here, we introduce Lingshu-Cell, a masked discrete diffusion model that learns transcriptomic state distributions and supports conditional simulation under perturbation. By operating directly in a discrete token space that is compatible with the sparse, non-sequential nature of single-cell transcriptomic data, Lingshu-Cell captures complex transcriptome-wide expression dependencies across approximately 18,000 genes without relying on prior gene selection, such as filtering by high variability or ranking by expression level. Across diverse tissues and species, Lingshu-Cell accurately reproduces transcriptomic distributions, marker-gene expression patterns and cell-subtype proportions, demonstrating its ability to capture complex cellular heterogeneity. Moreover, by jointly embedding cell type or donor identity with perturbation, Lingshu-Cell can predict whole-transcriptome expression changes for novel combinations of identity and perturbation. It achieves leading performance on the Virtual Cell Challenge H1 genetic perturbation benchmark and in predicting cytokine-induced responses in human PBMCs. Together, these results establish Lingshu-Cell as a flexible cellular world model for in silico simulation of cell states and perturbation responses, laying the foundation for a new paradigm in biological discovery and perturbation screening.

Predicting cellular responses to perturbations supports the study of gene function, disease mechanisms, and therapeutic strategies. Despite advances in single-cell perturbation modeling, existing models typically optimize surrogate losses that do not directly reflect the biological criteria used for evaluation, so better data fitting need not yield better biological predictions. To address this mismatch, we introduce CellRFT, a reinforcement fine-tuning framework that uses biological evaluation as direct training feedback. CellRFT uses policy-gradient optimization to learn from non-differentiable evaluations of generated cell populations and integrates multiple biological rewards through hierarchical reward aggregation. Comprehensive experiments demonstrate CellRFT's applicability across different pretrained models and effectiveness in improving perturbation prediction, reveal that optimizing one biological criterion can help or hinder others, and show that complementary rewards can improve criteria beyond those directly optimized, offering a way to probe how biological metrics shape model behavior, with the potential to inform evaluation design. Code will be made available.

Predicting cellular responses to genetic perturbations is a central capability for virtual cells and a key step toward computational modeling of biological interventions. Most existing models directly map an unperturbed molecular profile and perturba- tion to the resulting observation without explicitly representing the latent cellular transition induced by the intervention. We introduce a mechanism-centric virtual cell world model that represents cellular state as a set of Latent Mechanism Units (LMUs) and treats genetic perturbations as actions on these latent states. Each LMU combines a reusable identity grounded in multimodal biological evidence with an observation-specific state, allowing a perturbation to induce mechanism- specific stochastic transitions before decoding the resulting transcriptional response. We train VCLMU through two-stage pretraining, first on around 200K pseudo-bulk perturbation profiles and then on gene-aligned single-cell perturbation data. Across six perturbation-disjoint benchmarks, VCLMU consistently improves perturbation- specific response recovery over strong baselines while maintaining competitive global response accuracy. We further analyze learned LMUs through enrichment between perturbation responses and LMU gene sets and show that they capture structured biological response programs. These results support mechanism-level latent state transition as a useful formulation for virtual cell models that aim to predict and interpret cellular responses to biological interventions.

Recent advances in machine learning and large-scale biological data collections have revived the prospect of building a virtual cell, a computational model of cellular behavior that could accelerate biological discovery. One of the most compelling promises of this vision is the ability to perform in silico phenotypic screens, in which a model predicts the effects of cellular perturbations in unseen biological contexts. This task combines heterogeneous textual inputs with diverse phenotypic outputs, making it particularly well-suited to LLMs and agentic systems. Yet, no standard benchmark currently exists for this task, as existing efforts focus on narrower molecular readouts that are only indirectly aligned with the phenotypic endpoints driving many real-world drug discovery workflows. In this work, we present AssayBench, a benchmark for phenotypic screen prediction, built from 1,920 publicly available CRISPR screens spanning five broad classes of cellular phenotypes. We formulate the screen prediction task as a gene rank prediction for each screen and introduce the adjusted nDCG, a continuous metric for comparing performance across heterogeneous assays. Our extensive evaluation shows that existing methods remain far from empirically estimated performance ceilings and zero-shot generalist LLMs outperform biology-specific LLMs and trainable baselines. Optimization techniques such as fine-tuning, ensembling, and prompt optimization can further improve LLM performance on this task. Overall, AssayBench offers a practical testbed for measuring progress toward in silico phenotypic screening and, more broadly, virtual cell models.

This paper introduces Alympics (Olympics for Agents), a systematic simulation framework utilizing Large Language Model (LLM) agents for game theory research. Alympics creates a versatile platform for studying complex game theory problems, bridging the gap between theoretical game theory and empirical investigations by providing a controlled environment for simulating human-like strategic interactions with LLM agents. In our pilot case study, the "Water Allocation Challenge," we explore Alympics through a challenging strategic game focused on the multi-round auction on scarce survival resources. This study demonstrates the framework's ability to qualitatively and quantitatively analyze game determinants, strategies, and outcomes. Additionally, we conduct a comprehensive human assessment and an in-depth evaluation of LLM agents in strategic decision-making scenarios. Our findings not only expand the understanding of LLM agents' proficiency in emulating human strategic behavior but also highlight their potential in advancing game theory knowledge, thereby enriching our understanding of both game theory and empowering further research into strategic decision-making domains with LLM agents. Codes, prompts, and all related resources are available at https://github.com/microsoft/Alympics.

Large language models (LLMs) and emerging agentic frameworks are beginning to transform single-cell biology by enabling natural-language reasoning, generative annotation, and multimodal data integration. However, progress remains fragmented across data modalities, architectures, and evaluation standards. LLM4Cell presents the first unified survey of 58 foundation and agentic models developed for single-cell research, spanning RNA, ATAC, multi-omic, and spatial modalities. We categorize these methods into five families-foundation, text-bridge, spatial, multimodal, epigenomic, and agentic-and map them to eight key analytical tasks including annotation, trajectory and perturbation modeling, and drug-response prediction. Drawing on over 40 public datasets, we analyze benchmark suitability, data diversity, and ethical or scalability constraints, and evaluate models across 10 domain dimensions covering biological grounding, multi-omics alignment, fairness, privacy, and explainability. By linking datasets, models, and evaluation domains, LLM4Cell provides the first integrated view of language-driven single-cell intelligence and outlines open challenges in interpretability, standardization, and trustworthy model development.

The advent of single-cell technology has significantly improved our understanding of cellular states and subpopulations in various tissues under normal and diseased conditions by employing data-driven approaches such as clustering and trajectory inference. However, these methods consider cells as independent data points of population distributions. With spatial transcriptomics, we can represent cellular organization, along with dynamic cell-cell interactions that lead to changes in cell state. Still, key computational advances are necessary to enable the data-driven learning of such complex interactive cellular dynamics. While agent-based modeling (ABM) provides a powerful framework, traditional approaches rely on handcrafted rules derived from domain knowledge rather than data-driven approaches. To address this, we introduce Spatio Temporal Agent-Based Graph Evolution Dynamics(STAGED) integrating ABM with deep learning to model intercellular communication, and its effect on the intracellular gene regulatory network. Using graph ODE networks (GDEs) with shared weights per cell type, our approach represents genes as vertices and interactions as directed edges, dynamically learning their strengths through a designed attention mechanism. Trained to match continuous trajectories of simulated as well as inferred trajectories from spatial transcriptomics data, the model captures both intercellular and intracellular interactions, enabling a more adaptive and accurate representation of cellular dynamics.

Virtual cell (VC) models aim to predict cellular responses to any perturbations in silico and have emerged as a promising approach for drug discovery and precision medicine. Yet, a clear gap still remains: while models routinely reported impressive results on standard benchmarks, it is unclear whether their predictions are truly meaningful in practice. This is mainly due to limitations in current evaluation setups, which are often overly simplified or inconsistent, and do not reflect the complexity and variability of real biological systems. Here, we introduce a standardized and modular benchmarking framework for virtual cell prediction. Our framework evaluates diverse models under in-the-wild challenging scenarios, including unseen cell contexts, unseen perturbations, and cross-dataset generalization, which better reflect practical applications. Our analysis shows that model performance is highly context-dependent and shaped by task design and evaluation criteria. In commonly used setups, performance is often overestimated, and naive dataset aggregation can even reduce performance. When evaluated under more strict conditions, model performance drops markedly, indicating limited robustness to shifts across cellular contexts. In unseen perturbation settings, models including simple linear approaches capture global transcriptional trends but fail to recover fine-grained perturbation-specific effects. In addition, different evaluation metrics focus on different biological properties, leading to substantially different model rankings. Together, our framework provides a more reliable and biologically grounded evaluation, offering clearer guidance for applying virtual cell models in real scenarios.

Recent game world models support realistic visual simulation and interactive gameplay based on player inputs. However, they typically learn environment dynamics from pixel-level supervision, jointly modeling perception, memory, state transitions, and rendering within a single end-to-end framework. While this design enables open-ended, action-controllable generation, it still falls short of delivering a complete gameplay experience. Games are governed by explicit mechanics, such as health deduction, skill activation, combat rules, and termination conditions. These mechanics depend on precise and consistent state transitions that generative models alone cannot reliably enforce. In contrast, game engines can guarantee such mechanics through hard-coded rules, but provide limited flexibility for player-driven creation. To bridge these paradigms, we introduce GameDirector, the first agentic framework that decouples rule-based gameplay logic from visual rendering. Given player-defined configurations, the framework acts as an intelligent director that interprets visual observations, updates game states, tactically controls NPCs, and enforces gameplay rules. It then translates these decisions into text prompts that guide the video world model to render the resulting gameplay. This separation allows players to configure characters, states, and rules much like a game developer while preserving coherent game mechanics. Experiments on three games, using data collected by our automated gameplay agent, show that GameDirector achieves accurate state tracking, reliable rule following, and improves boss action quality by more than 39.9% over various end-to-end game world model settings. Overall, by externalizing player-controllable game logic, GameDirector establishes a middle ground between hard-coded simulation and generative modeling, enabling more flexible and closed-loop gameplay experiences.

The challenge of translating vast, multimodal biological data into predictive and mechanistic understanding of cellular function is a central theme in modern biology. Virtual cells, or digital cellular twins, have emerged as a critical paradigm to meet this challenge by creating integrative computational models of cellular processes. This review synthesizes the evolution and current state of the virtual cell, from foundational mechanistic frameworks like the Virtual Cell that employ deterministic and stochastic simulations to the recent transformative impact of artificial intelligence and foundation models. We examine the core technological pillars required to build these models, including the integration of various data types, such as single-cell and spatial omics, the spectrum of modeling approaches, and the bioengineering principles that connect simulation to application. We further discuss key applications, frameworks for model benchmarking and validation, and the significant hurdles that remain, including computational scalability, parameter inference, and ethical considerations, which provides a roadmap for development of predictive virtual cells that promise to revolutionize biomedical research and clinical practice.

Gene perturbation analysis plays a critical role in drug discovery by enabling researchers to investigate how interventions on specific genes influence global gene expression patterns within cells. Recent advances in artificial intelligence-driven virtual cell models have made it possible to predict gene expression outcomes for a wide range of perturbation strategies in silico, substantially reducing reliance on costly and time-consuming biological experiments. However, effectively exploring and interpreting the high-dimensional perturbation spaces produced by these models remains challenging because of the combinatorial nature of perturbations and the complex cell-specific gene expression responses they generate. In this work, we present CellPrism, a visual analytics system designed to support the systematic exploration of gene perturbation strategies for drug discovery. Specifically, CellPrism integrates clustering-based overviews to summarize perturbation outcomes, a glyph-based representation to compactly encode gene expression patterns across cell types, and coordinated views that enable fine-grained comparison and interpretation of perturbation effects. We demonstrate the effectiveness of CellPrism through a real-world case study and expert interviews. This work highlights the value of visual analytics in bridging virtual cell modeling with expert-driven decision making in drug discovery.

This paper introduces SC2LE (StarCraft II Learning Environment), a reinforcement learning environment based on the StarCraft II game. This domain poses a new grand challenge for reinforcement learning, representing a more difficult class of problems than considered in most prior work. It is a multi-agent problem with multiple players interacting; there is imperfect information due to a partially observed map; it has a large action space involving the selection and control of hundreds of units; it has a large state space that must be observed solely from raw input feature planes; and it has delayed credit assignment requiring long-term strategies over thousands of steps. We describe the observation, action, and reward specification for the StarCraft II domain and provide an open source Python-based interface for communicating with the game engine. In addition to the main game maps, we provide a suite of mini-games focusing on different elements of StarCraft II gameplay. For the main game maps, we also provide an accompanying dataset of game replay data from human expert players. We give initial baseline results for neural networks trained from this data to predict game outcomes and player actions. Finally, we present initial baseline results for canonical deep reinforcement learning agents applied to the StarCraft II domain. On the mini-games, these agents learn to achieve a level of play that is comparable to a novice player. However, when trained on the main game, these agents are unable to make significant progress. Thus, SC2LE offers a new and challenging environment for exploring deep reinforcement learning algorithms and architectures.

Large Language Models (LLMs) are transforming society and permeating into diverse applications. As a result, LLMs will frequently interact with us and other agents. It is, therefore, of great societal value to understand how LLMs behave in interactive social settings. Here, we propose to use behavioral game theory to study LLM's cooperation and coordination behavior. To do so, we let different LLMs (GPT-3, GPT-3.5, and GPT-4) play finitely repeated games with each other and with other, human-like strategies. Our results show that LLMs generally perform well in such tasks and also uncover persistent behavioral signatures. In a large set of two players-two strategies games, we find that LLMs are particularly good at games where valuing their own self-interest pays off, like the iterated Prisoner's Dilemma family. However, they behave sub-optimally in games that require coordination. We, therefore, further focus on two games from these distinct families. In the canonical iterated Prisoner's Dilemma, we find that GPT-4 acts particularly unforgivingly, always defecting after another agent has defected only once. In the Battle of the Sexes, we find that GPT-4 cannot match the behavior of the simple convention to alternate between options. We verify that these behavioral signatures are stable across robustness checks. Finally, we show how GPT-4's behavior can be modified by providing further information about the other player as well as by asking it to predict the other player's actions before making a choice. These results enrich our understanding of LLM's social behavior and pave the way for a behavioral game theory for machines.

Communication games, which we refer to as incomplete information games that heavily depend on natural language communication, hold significant research value in fields such as economics, social science, and artificial intelligence. In this work, we explore the problem of how to engage large language models (LLMs) in communication games, and in response, propose a tuning-free framework. Our approach keeps LLMs frozen, and relies on the retrieval and reflection on past communications and experiences for improvement. An empirical study on the representative and widely-studied communication game, ``Werewolf'', demonstrates that our framework can effectively play Werewolf game without tuning the parameters of the LLMs. More importantly, strategic behaviors begin to emerge in our experiments, suggesting that it will be a fruitful journey to engage LLMs in communication games and associated domains.

Game theory, as an analytical tool, is frequently utilized to analyze human behavior in social science research. With the high alignment between the behavior of Large Language Models (LLMs) and humans, a promising research direction is to employ LLMs as substitutes for humans in game experiments, enabling social science research. However, despite numerous empirical researches on the combination of LLMs and game theory, the capability boundaries of LLMs in game theory remain unclear. In this research, we endeavor to systematically analyze LLMs in the context of game theory. Specifically, rationality, as the fundamental principle of game theory, serves as the metric for evaluating players' behavior -- building a clear desire, refining belief about uncertainty, and taking optimal actions. Accordingly, we select three classical games (dictator game, Rock-Paper-Scissors, and ring-network game) to analyze to what extent LLMs can achieve rationality in these three aspects. The experimental results indicate that even the current state-of-the-art LLM (GPT-4) exhibits substantial disparities compared to humans in game theory. For instance, LLMs struggle to build desires based on uncommon preferences, fail to refine belief from many simple patterns, and may overlook or modify refined belief when taking actions. Therefore, we consider that introducing LLMs into game experiments in the field of social science should be approached with greater caution.

Game-playing agents like AlphaGo have achieved superhuman performance through self-play, which is theoretically guaranteed to yield optimal policies in competitive games. However, most language tasks are partially or fully cooperative, so it is an open question whether techniques like self-play can effectively be used to improve language models. We empirically investigate this question in a negotiation game setting known as Deal or No Deal (DoND). Crucially, the objective in DoND can be modified to produce a fully cooperative game, a strictly competitive one, or anything in between. We finetune language models in self-play over multiple rounds of filtered behavior cloning in DoND for each of these objectives. Contrary to expectations, we find that language model self-play leads to significant performance gains in both cooperation and competition with humans, suggesting that self-play and related techniques have promise despite a lack of theoretical guarantees.

During 2023, two interesting results were proven about the limit behavior of game dynamics: First, it was shown that there is a game for which no dynamics converges to the Nash equilibria. Second, it was shown that the sink equilibria of a game adequately capture the limit behavior of natural game dynamics. These two results have created a need and opportunity to articulate a principled computational theory of the meaning of the game that is based on game dynamics. Given any game in normal form, and any prior distribution of play, we study the problem of computing the asymptotic behavior of a class of natural dynamics called the noisy replicator dynamics as a limit distribution over the sink equilibria of the game. When the prior distribution has pure strategy support, we prove this distribution can be computed efficiently, in near-linear time to the size of the best-response graph. When the distribution can be sampled -- for example, if it is the uniform distribution over all mixed strategy profiles -- we show through experiments that the limit distribution of reasonably large games can be estimated quite accurately through sampling and simulation.

We present GameNGen, the first game engine powered entirely by a neural model that enables real-time interaction with a complex environment over long trajectories at high quality. GameNGen can interactively simulate the classic game DOOM at over 20 frames per second on a single TPU. Next frame prediction achieves a PSNR of 29.4, comparable to lossy JPEG compression. Human raters are only slightly better than random chance at distinguishing short clips of the game from clips of the simulation. GameNGen is trained in two phases: (1) an RL-agent learns to play the game and the training sessions are recorded, and (2) a diffusion model is trained to produce the next frame, conditioned on the sequence of past frames and actions. Conditioning augmentations enable stable auto-regressive generation over long trajectories.

Foundation models, alongside advances in learned game-world models, are reshaping AI across the game lifecycle. Beyond playing games, recent systems model players and game dynamics, support design and development, adapt player-facing experiences at runtime, and evaluate resulting artifacts. Yet these directions have evolved largely separately, obscuring which capabilities transfer across settings and which remain tied to particular games, engines, interfaces, or player populations. We organize the literature into six roles according to the immediate use of AI output: playing and acting; modeling players and games; designing games; building and maintaining games; generating and adapting at runtime; and testing and evaluating games. For each role, we examine what structure is supplied by the game or workflow, what AI learns or produces, which capabilities and artifacts transfer across settings and roles, and what evidence supports the claims. We identify cross-role connections: trajectories train world models, learned environments provide experience for agents, design specifications drive executable implementations, and play or testing feedback guides revision. However, control schemes, rules, engine interfaces, state representations, and player contexts often remain setting-specific, so downstream claims require validation in the target setting. Evaluation is most standardized for bounded game playing and selected learned environments, while persistent state in learned worlds, repeated software revision, validated player modeling, sustained runtime adaptation, and representative automated testing remain less established. The central challenge is to reuse or transfer outputs and capabilities across roles while re-establishing evidence for effectiveness in the game-specific contexts where they are used.

People are remarkably capable of generating their own goals, beginning with child's play and continuing into adulthood. Despite considerable empirical and computational work on goals and goal-oriented behavior, models are still far from capturing the richness of everyday human goals. Here, we bridge this gap by collecting a dataset of human-generated playful goals (in the form of scorable, single-player games), modeling them as reward-producing programs, and generating novel human-like goals through program synthesis. Reward-producing programs capture the rich semantics of goals through symbolic operations that compose, add temporal constraints, and allow for program execution on behavioral traces to evaluate progress. To build a generative model of goals, we learn a fitness function over the infinite set of possible goal programs and sample novel goals with a quality-diversity algorithm. Human evaluators found that model-generated goals, when sampled from partitions of program space occupied by human examples, were indistinguishable from human-created games. We also discovered that our model's internal fitness scores predict games that are evaluated as more fun to play and more human-like.

Large language models (LLMs) are increasingly applied in scientific research, offering new capabilities for knowledge discovery and reasoning. In single-cell biology, however, evaluation practices for both general and specialized LLMs remain inadequate: existing benchmarks are fragmented across tasks, adopt formats such as multiple-choice classification that diverge from real-world usage, and rely on metrics lacking interpretability and biological grounding. We present SC-ARENA, a natural language evaluation framework tailored to single-cell foundation models. SC-ARENA formalizes a virtual cell abstraction that unifies evaluation targets by representing both intrinsic attributes and gene-level interactions. Within this paradigm, we define five natural language tasks (cell type annotation, captioning, generation, perturbation prediction, and scientific QA) that probe core reasoning capabilities in cellular biology. To overcome the limitations of brittle string-matching metrics, we introduce knowledge-augmented evaluation, which incorporates external ontologies, marker databases, and scientific literature to support biologically faithful and interpretable judgments. Experiments and analysis across both general-purpose and domain-specialized LLMs demonstrate that (i) under the Virtual Cell unified evaluation paradigm, current models achieve uneven performance on biologically complex tasks, particularly those demanding mechanistic or causal understanding; and (ii) our knowledge-augmented evaluation framework ensures biological correctness, provides interpretable, evidence-grounded rationales, and achieves high discriminative capacity, overcoming the brittleness and opacity of conventional metrics. SC-Arena thus provides a unified and interpretable framework for assessing LLMs in single-cell biology, pointing toward the development of biology-aligned, generalizable foundation models.

We develop a method of adapting the AlphaZero model to General Game Playing (GGP) that focuses on faster model generation and requires less knowledge to be extracted from the game rules. The dataset generation uses MCTS playing instead of self-play; only the value network is used, and attention layers replace the convolutional ones. This allows us to abandon any assumptions about the action space and board topology. We implement the method within the Regular Boardgames GGP system and show that we can build models outperforming the UCT baseline for most games efficiently.

Virtual-cell models aim to predict how cell populations respond to perturbations, but control and treated cells are measured as unpaired populations, complicating the learning of perturbation-specific effects. We present SCALE, a conditional transport model that represents cells as unordered sets and predicts treated populations without cell-level matching. A shared set-aware encoder and conditional DiT backbone learn latent transport, making endpoint supervision directly delta-aligned without an auxiliary delta objective. Across genetic, chemical, developmental and immune perturbations, SCALE recovered gene-expression changes, response directions and population structure. In CRISPR data with dominant cell-line effects, SCALE outperformed competing methods across seven metrics and maintained separation among gene-target representations rather than collapsing them into a shared region. SCALE further prioritized cytokines predicted to produce distinct immune activation and inflammatory responses. Experiments using matched PBMC samples from three donors confirmed these predicted differences. Together, SCALE enables perturbation-specific prediction from unpaired populations and supports experimental prioritization.

In this paper, we present a conceptual model game to examine the dynamics of asymmetric interactions in games with imperfect information. The game involves two agents with starkly contrasting capabilities: one agent can take actions but has no information of the state of the game, whereas the other agent has perfect information of the state but cannot act or observe the other agent's actions. This duality manifests an extreme form of asymmetry, and how differing abilities influence the possibility of attaining common knowledge. Using Kripke structures and epistemic logic we demonstrate that, under these conditions, common knowledge of the current game state becomes unattainable. Our findings advance the discussion on the strategic limitations of knowledge in environments where information and action are unevenly distributed.

Machine learning models of cellular interaction dynamics hold promise for understanding cell behavior. Natural killer (NK) cell cytotoxicity is a prominent example of such interaction dynamics and is commonly studied using time-resolved multi-channel fluorescence microscopy. Although tumor cell death events can be annotated at single frames, NK cytotoxic outcome emerges over time from cellular interactions and cannot be reliably inferred from frame-wise classification alone. We introduce BLINK, a trajectory-based recurrent state-space model that serves as a cell world model for NK-tumor interactions. BLINK learns latent interaction dynamics from partially observed NK-tumor interaction sequences and predicts apoptosis increments that accumulate into cytotoxic outcomes. Experiments on long-term time-lapse NK-tumor recordings show improved cytotoxic outcome detection and enable forecasting of future outcomes, together with an interpretable latent representation that organizes NK trajectories into coherent behavioral modes and temporally structured interaction phases. BLINK provides a unified framework for quantitative evaluation and structured modeling of NK cytotoxic behavior at the single-cell level.

Normal-form games (NFGs) are the fundamental model of strategic interaction. We study their representation using neural networks. We describe the inherent equivariance of NFGs -- any permutation of strategies describes an equivalent game -- as well as the challenges this poses for representation learning. We then propose the NfgTransformer architecture that leverages this equivariance, leading to state-of-the-art performance in a range of game-theoretic tasks including equilibrium-solving, deviation gain estimation and ranking, with a common approach to NFG representation. We show that the resulting model is interpretable and versatile, paving the way towards deep learning systems capable of game-theoretic reasoning when interacting with humans and with each other.

As Large Language Models (LLMs) integrate into our social and economic interactions, we need to deepen our understanding of how humans respond to LLMs opponents in strategic settings. We present the results of the first controlled monetarily-incentivised laboratory experiment looking at differences in human behaviour in a multi-player p-beauty contest against other humans and LLMs. We use a within-subject design in order to compare behaviour at the individual level. We show that, in this environment, human subjects choose significantly lower numbers when playing against LLMs than humans, which is mainly driven by the increased prevalence of `zero' Nash-equilibrium choices. This shift is mainly driven by subjects with high strategic reasoning ability. Subjects who play the zero Nash-equilibrium choice motivate their strategy by appealing to perceived LLM's reasoning ability and, unexpectedly, propensity towards cooperation. Our findings provide foundational insights into the multi-player human-LLM interaction in simultaneous choice games, uncover heterogeneities in both subjects' behaviour and beliefs about LLM's play when playing against them, and suggest important implications for mechanism design in mixed human-LLM systems.

Large language models (LLMs) have demonstrated strong reasoning, planning, and communication abilities, enabling them to operate as autonomous agents in open environments. While single-agent systems remain limited in adaptability and coordination, recent progress has shifted attention toward multi-agent systems (MAS) composed of interacting LLMs that pursue cooperative, competitive, or mixed objectives. This emerging paradigm provides a powerful testbed for studying social dynamics and strategic behaviors among intelligent agents. However, current research remains fragmented and lacks a unifying theoretical foundation. To address this gap, we present a comprehensive survey of LLM-based multi-agent systems through a game-theoretic lens. By organizing existing studies around the four key elements of game theory: players, strategies, payoffs, and information, we establish a systematic framework for understanding, comparing, and guiding future research on the design and analysis of LLM-based MAS.

Recent game world models can generate visually realistic and interactive environments conditioned on player actions. However, games are not defined by pixels alone; they are governed by explicit mechanics, namely state-dependent rules that control health reduction, skill activation, and game termination. These mechanics depend on precise internal states, such as health points, skill meters, and timers, which are tightly coupled with visual observations and determine how gameplay evolves. Without modeling these state dynamics, existing game world models may generate visually plausible rollouts but violate the underlying game rules. In this paper, we propose StatePlay, a novel state-aware game world model that jointly predicts visual content and game states to promote mechanics-consistent generation. StatePlay adopts a mixture-of-transformers (MoT)-style architecture that preserves specialized visual and state representations while enabling cross-modal interaction, allowing predicted states to guide frame generation. Each branch is further optimized with a distinct objective suited to its modality. Experiments show that StatePlay achieves an average normalized L1 distance below 0.06 for state prediction. Furthermore, compared with models without explicit state modeling, our method improves mechanics fidelity in generated game rollouts by 18.6%. Overall, our work highlights the importance of state-aware game world modeling and advances beyond pixel-level realism toward complete and mechanically faithful game generation.

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlux models distribution-wise transformations from unperturbed to perturbed cell states, effectively distinguishing actual perturbation effects from experimental artifacts such as batch effects -- a major challenge in biological data. Evaluated on chemical (BBBC021), genetic (RxRx1), and combined perturbation (JUMP) datasets, CellFlux generates biologically meaningful cell images that faithfully capture perturbation-specific morphological changes, achieving a 35% improvement in FID scores and a 12% increase in mode-of-action prediction accuracy over existing methods. Additionally, CellFlux enables continuous interpolation between cellular states, providing a potential tool for studying perturbation dynamics. These capabilities mark a significant step toward realizing virtual cell modeling for biomedical research. Project page: https://yuhui-zh15.github.io/CellFlux/.

Useful social science theories predict behavior across settings. However, applying a theory to make predictions in new settings is challenging: rarely can it be done without ad hoc modifications to account for setting-specific factors. We argue that AI agents put in simulations of those novel settings offer an alternative for applying theory, requiring minimal or no modifications. We present an approach for building such "general" agents that use theory-grounded natural language instructions, existing empirical data, and knowledge acquired by the underlying AI during training. To demonstrate the approach in settings where no data from that data-generating process exists--as is often the case in applied prediction problems--we design a heterogeneous population of 883,320 novel games. AI agents are constructed using human data from a small set of conceptually related but structurally distinct "seed" games. In preregistered experiments, on average, agents predict initial human play in a random sample of 1,500 games from the population better than (i) a cognitive hierarchy model, (ii) game-theoretic equilibria, and (iii) out-of-the-box agents. For a small set of separate novel games, these simulations predict responses from a new sample of human subjects better even than the most plausibly relevant published human data.

Constructing agents with planning capabilities has long been one of the main challenges in the pursuit of artificial intelligence. Tree-based planning methods have enjoyed huge success in challenging domains, such as chess and Go, where a perfect simulator is available. However, in real-world problems the dynamics governing the environment are often complex and unknown. In this work we present the MuZero algorithm which, by combining a tree-based search with a learned model, achieves superhuman performance in a range of challenging and visually complex domains, without any knowledge of their underlying dynamics. MuZero learns a model that, when applied iteratively, predicts the quantities most directly relevant to planning: the reward, the action-selection policy, and the value function. When evaluated on 57 different Atari games - the canonical video game environment for testing AI techniques, in which model-based planning approaches have historically struggled - our new algorithm achieved a new state of the art. When evaluated on Go, chess and shogi, without any knowledge of the game rules, MuZero matched the superhuman performance of the AlphaZero algorithm that was supplied with the game rules.

Large Language Models (LLMs) show significant potential in economic and strategic interactions, where communication via natural language is often prevalent. This raises key questions: Do LLMs behave rationally? Can they mimic human behavior? Do they tend to reach an efficient and fair outcome? What is the role of natural language in the strategic interaction? How do characteristics of the economic environment influence these dynamics? These questions become crucial concerning the economic and societal implications of integrating LLM-based agents into real-world data-driven systems, such as online retail platforms and recommender systems. While the ML community has been exploring the potential of LLMs in such multi-agent setups, varying assumptions, design choices and evaluation criteria across studies make it difficult to draw robust and meaningful conclusions. To address this, we introduce a benchmark for standardizing research on two-player, sequential, language-based games. Inspired by the economic literature, we define three base families of games with consistent parameterization, degrees of freedom and economic measures to evaluate agents' performance (self-gain), as well as the game outcome (efficiency and fairness). We develop an open-source framework for interaction simulation and analysis, and utilize it to collect a dataset of LLM vs. LLM interactions across numerous game configurations and an additional dataset of human vs. LLM interactions. Through extensive experimentation, we demonstrate how our framework and dataset can be used to: (i) compare the behavior of LLM-based agents to human players in various economic contexts; (ii) evaluate agents in both individual and collective performance measures; and (iii) quantify the effect of the economic characteristics of the environments on the behavior of agents.

Language models have shown unprecedented capabilities, sparking debate over the source of their performance. Is it merely the outcome of learning syntactic patterns and surface level statistics, or do they extract semantics and a world model from the text? Prior work by Li et al. investigated this by training a GPT model on synthetic, randomly generated Othello games and found that the model learned an internal representation of the board state. We extend this work into the more complex domain of chess, training on real games and investigating our model's internal representations using linear probes and contrastive activations. The model is given no a priori knowledge of the game and is solely trained on next character prediction, yet we find evidence of internal representations of board state. We validate these internal representations by using them to make interventions on the model's activations and edit its internal board state. Unlike Li et al's prior synthetic dataset approach, our analysis finds that the model also learns to estimate latent variables like player skill to better predict the next character. We derive a player skill vector and add it to the model, improving the model's win rate by up to 2.6 times.

As Large Language Models (LLMs) rapidly evolve, their influence in science is becoming increasingly prominent. The emerging capabilities of LLMs in task generalization and free-form dialogue can significantly advance fields like chemistry and biology. However, the field of single-cell biology, which forms the foundational building blocks of living organisms, still faces several challenges. High knowledge barriers and limited scalability in current methods restrict the full exploitation of LLMs in mastering single-cell data, impeding direct accessibility and rapid iteration. To this end, we introduce ChatCell, which signifies a paradigm shift by facilitating single-cell analysis with natural language. Leveraging vocabulary adaptation and unified sequence generation, ChatCell has acquired profound expertise in single-cell biology and the capability to accommodate a diverse range of analysis tasks. Extensive experiments further demonstrate ChatCell's robust performance and potential to deepen single-cell insights, paving the way for more accessible and intuitive exploration in this pivotal field. Our project homepage is available at https://zjunlp.github.io/project/ChatCell.

The primary focus of multi-agent reinforcement learning (MARL) has been to study interactions among a fixed number of agents embedded in an environment. However, in the real world, the number of agents is neither fixed nor known a priori. Moreover, an agent can decide to create other agents (for example, a cell may divide, or a company may spin off a division). In this paper, we propose a framework that allows agents to create other agents; we call this a fluid-agent environment. We present game-theoretic solution concepts for fluid-agent games and empirically evaluate the performance of several MARL algorithms within this framework. Our experiments include fluid variants of established benchmarks such as Predator-Prey and Level-Based Foraging, where agents can dynamically spawn, as well as a new environment we introduce that highlights how fluidity can unlock novel solution strategies beyond those observed in fixed-population settings. We demonstrate that this framework yields agent teams that adjust their size dynamically to match environmental demands.

Virtual cells are evolving from single-task predictive models toward programmable biological simulation systems, yet heterogeneous data, models, and validation evidence still lack a unified organizational framework. Here, we present PRAXIS-VirtualCell, a modular framework that organizes biological data, predictive models, perturbations, adapters, execution environments, and validation evidence to enable reproducible and auditable virtual experiments. The system supports cross-species tasks spanning Escherichia coli, Saccharomyces cerevisiae, and human K562 cells, while using biological contracts and evidence-aware execution to distinguish supported predictions from extrapolation and abstention. By further integrating agentic orchestration, PRAXIS-VirtualCell automatically translates natural-language questions into traceable virtual experiments, providing a unified runtime foundation for trustworthy and scalable Virtual Cell systems.

Recent advances in generative models have significantly impacted game generation. However, despite producing high-quality graphics and adequately receiving player input, existing models often fail to maintain fundamental game properties such as numerical and spatial consistency. Numerical consistency ensures gameplay mechanics correctly reflect score changes and other quantitative elements, while spatial consistency prevents jarring scene transitions, providing seamless player experiences. In this paper, we revisit the paradigm of generative games to explore what truly constitutes a Model as a Game (MaaG) with a well-developed mechanism. We begin with an empirical study on ``Traveler'', a 2D game created by an LLM featuring minimalist rules yet challenging generative models in maintaining consistency. Based on the DiT architecture, we design two specialized modules: (1) a numerical module that integrates a LogicNet to determine event triggers, with calculations processed externally as conditions for image generation; and (2) a spatial module that maintains a map of explored areas, retrieving location-specific information during generation and linking new observations to ensure continuity. Experiments across three games demonstrate that our integrated modules significantly enhance performance on consistency metrics compared to baselines, while incurring minimal time overhead during inference.

Post-training large language models (LLMs) on two-player zero-sum games provides a verifiable reward, and the gains have been shown to transfer to general reasoning. Existing pipelines, however, rely on a handful of hand-written games and on advantage estimators tied to them, so both the supply of games and the advantage estimate on a large corpus limit scaling. We present GameSmith, which scales both. An LLM synthesises games inside templates whose reward, observation, and hidden-information code is fixed. Each game is verified by seed-paired replay and by an independent re-implementation of its specification, then expanded into encoding, rule, and size variants, giving 26 new games in 29 families and 336 verified variants from the three SPIRAL templates. The model is distilled from the self-play of a larger teacher (Qwen3-32B) on these games and then trained by self-play reinforcement learning with CRAB, an advantage estimator that credits each decision against a shrinkage estimate of the expected return of its position and is defined on every variant. On Qwen3-4B-Base, distillation raises the 13-benchmark mean pass@1 from 45.5 to 62.5, above the three SPIRAL games at the same budget, and self-play with CRAB reaches 64.9. The ordering holds across models, and transfer grows with the number of game families.

Cellular automata (CAs) are fully-discrete dynamical models that have received much attention due to the fact that their relatively simple setup can nonetheless express highly complex phenomena. Despite the model's theoretical maturity and abundant computational power, the current lack of a complete survey on the 'taxonomy' of various families of CAs impedes efficient and interdisciplinary progress. This review paper mitigates that deficiency; it provides a methodical overview of five important CA 'families': asynchronous, stochastic, multi-state, extended-neighbourhood, and non-uniform CAs. These five CA families are subsequently presented from four angles. First, a rigorous mathematical definition is given. Second, we map prominent variations within each CA family, as such highlighting mathematical equivalences with types from other families. Third, we discuss the genotype and phenotype of these CA types by means of mathematical tools, indicating when established tools break down. Fourth, we conclude each section with a brief overview of applications related to information theory and mathematical modelling.

Automatically generating novel and interesting games is a complex task. Challenges include representing game rules in a computationally workable form, searching through the large space of potential games under most such representations, and accurately evaluating the originality and quality of previously unseen games. Prior work in automated game generation has largely focused on relatively restricted rule representations and relied on domain-specific heuristics. In this work, we explore the generation of novel games in the comparatively expansive Ludii game description language, which encodes the rules of over 1000 board games in a variety of styles and modes of play. We draw inspiration from recent advances in large language models and evolutionary computation in order to train a model that intelligently mutates and recombines games and mechanics expressed as code. We demonstrate both quantitatively and qualitatively that our approach is capable of generating new and interesting games, including in regions of the potential rules space not covered by existing games in the Ludii dataset. A sample of the generated games are available to play online through the Ludii portal.

Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, perturbation prediction requires mapping unpaired control and perturbed populations. Existing models address this by learning maps between distributions, but typically assume a single fixed response distribution when conditioned on observed cellular context (e.g., cell type) and the perturbation type. In reality, responses vary systematically due to unobservable latent factors such as microenvironmental fluctuations and complex batch effects, forming a manifold of possible distributions for the same observed conditions. To account for this variability, we introduce PerturbDiff, which shifts modeling from individual cells to entire distributions. By embedding distributions as points in a Hilbert space, we define a diffusion-based generative process operating directly over probability distributions. This allows PerturbDiff to capture population-level response shifts across hidden factors. Benchmarks on established datasets show that PerturbDiff achieves state-of-the-art performance in single-cell response prediction and generalizes substantially better to unseen perturbations. See our project page (https://katarinayuan.github.io/PerturbDiff-ProjectPage/), where code and data will be made publicly available (https://github.com/DeepGraphLearning/PerturbDiff).

A central task in virtual cell modeling is predicting single-cell transcriptional responses to unseen genetic perturbations and drug combinations, and biological networks provide valuable priors on gene relationships. Existing graph-based models commonly use the same network to structure gene representations and mediate intergene interactions, thereby implicitly treating stable associations as perturbation-response pathways. Gene Ontology and control-derived coexpression networks encode relatively stable relationships rather than intervention-specific response directions or magnitudes. We therefore propose GeneGeoFlow, which conditions a control-anchored residual flow on gene-wise geometry derived from biological networks to learn intervention-specific transcriptional responses. GeneGeoFlow derives multi-scale spectral coordinates from Gene Ontology and control-derived coexpression networks. A perturbation-conditioned, gene-wise gating module selects relevant structural scales and network sources, yielding intervention-specific gene geometry. The resulting geometry conditions a control-anchored residual flow without explicitly propagating target-derived signals along the graph. Condition-wise optimal transport couples unpaired control and perturbed populations for training, while a Delta-correlation objective aligns the predicted and observed condition-level expression-shift directions. GeneGeoFlow achieves Pearson Delta scores of 0.8979 on the Norman additive benchmark and 0.9088 on five held-out drug combinations in the fixed ComboSciPlex test split. These results support perturbation-conditioned gene geometry as an effective structural prior for intervention-specific response prediction, without conflating stable gene relationships with response propagation.

The game industry is challenged to cope with increasing growth in demand and game complexity while maintaining acceptable quality standards for released games. Classic approaches solely depending on human efforts for quality assurance and game testing do not scale effectively in terms of time and cost. Game-testing AI agents that learn by interaction with the environment have the potential to mitigate these challenges with good scalability properties on time and costs. However, most recent work in this direction depends on game state information for the agent's state representation, which limits generalization across different game scenarios. Moreover, game test engineers usually prefer exploring a game in a specific style, such as exploring the golden path. However, current game testing AI agents do not provide an explicit way to satisfy such a preference. This paper addresses these limitations by proposing an agent design that mainly depends on pixel-based state observations while exploring the environment conditioned on a user's preference specified by demonstration trajectories. In addition, we propose an imitation learning method that couples self-supervised and supervised learning objectives to enhance the quality of imitation behaviors. Our agent significantly outperforms state-of-the-art pixel-based game testing agents over exploration coverage and test execution quality when evaluated on a complex open-world environment resembling many aspects of real AAA games.

The rapid advancement of large language models (LLMs) has accelerated their application in reasoning, with strategic reasoning drawing increasing attention. To evaluate LLMs' strategic reasoning capabilities, game theory, with its concise structure, has become a preferred approach. However, current research focuses on a limited selection of games, resulting in low coverage. Classic game scenarios risk data leakage, and existing benchmarks often lack extensibility, making them inadequate for evaluating state-of-the-art models. To address these challenges, we propose TMGBench, a benchmark with comprehensive game type coverage, novel scenarios, and flexible organization. Specifically, we incorporate all 144 game types summarized by the Robinson-Goforth topology of 2x2 games, constructed as classic games. We also employ synthetic data generation to create diverse, higher-quality scenarios through topic guidance and human inspection, referred to as story-based games. Lastly, we provide a sustainable framework for increasingly powerful LLMs by treating these games as atomic units and organizing them into more complex forms via sequential, parallel, and nested structures. Our comprehensive evaluation of mainstream LLMs covers tests on rational reasoning, robustness, Theory-of-Mind (ToM), and reasoning in complex forms. Results reveal flaws in accuracy, consistency, and varying mastery of ToM. Additionally, o1-mini, OpenAI's latest reasoning model, achieved accuracy rates of 66.6%, 60.0%, and 70.0% on sequential, parallel, and nested games, highlighting TMGBench's challenges.

We introduce a comprehensive framework for modeling single cell transcriptomic responses to perturbations, aimed at standardizing benchmarking in this rapidly evolving field. Our approach includes a modular and user-friendly model development and evaluation platform, a collection of diverse perturbational datasets, and a set of metrics designed to fairly compare models and dissect their performance. Through extensive evaluation of both published and baseline models across diverse datasets, we highlight the limitations of widely used models, such as mode collapse. We also demonstrate the importance of rank metrics which complement traditional model fit measures, such as RMSE, for validating model effectiveness. Notably, our results show that while no single model architecture clearly outperforms others, simpler architectures are generally competitive and scale well with larger datasets. Overall, this benchmarking exercise sets new standards for model evaluation, supports robust model development, and furthers the use of these models to simulate genetic and chemical screens for therapeutic discovery.

Rigorously evaluating machine intelligence against the broad spectrum of human general intelligence has become increasingly important and challenging in this era of rapid technological advance. Conventional AI benchmarks typically assess only narrow capabilities in a limited range of human activity. Most are also static, quickly saturating as developers explicitly or implicitly optimize for them. We propose that a more promising way to evaluate human-like general intelligence in AI systems is through a particularly strong form of general game playing: studying how and how well they play and learn to play all conceivable human games, in comparison to human players with the same level of experience, time, or other resources. We define a "human game" to be a game designed by humans for humans, and argue for the evaluative suitability of this space of all such games people can imagine and enjoy -- the "Multiverse of Human Games". Taking a first step towards this vision, we introduce the AI GameStore, a scalable and open-ended platform that uses LLMs with humans-in-the-loop to synthesize new representative human games, by automatically sourcing and adapting standardized and containerized variants of game environments from popular human digital gaming platforms. As a proof of concept, we generated 100 such games based on the top charts of Apple App Store and Steam, and evaluated seven frontier vision-language models (VLMs) on short episodes of play. The best models achieved less than 10\% of the human average score on the majority of the games, and especially struggled with games that challenge world-model learning, memory and planning. We conclude with a set of next steps for building out the AI GameStore as a practical way to measure and drive progress toward human-like general intelligence in machines.

We introduce Kaggle Game Arena, an open and ever-expanding platform to evaluate large language models (LLMs) through competitive games. Different from static benchmarks, game arena enables models to play head-to-head matchups in structured environments where the gameplay strength naturally increases as models evolve, preventing performance saturation. This technical report details the infrastructure behind Game Arena and describes the three pilot game environments: Chess, Poker, and Werewolf. These environments span perfect information, imperfect information, and multiplayer game settings, enabling a systematic study of models' strategic planning, adaptation, and robustness under uncertainty. For each game, we provide a detailed description of the environment, evaluation metrics, and results from running full competitions across models. Through robust infrastructure and large-scale ground-truth based evaluation, Game Arena ensures reproducibility, transparency and generalizability to new games and variants over time.

Computer games, as fully controlled simulated environments, have been utilized in significant scientific studies demonstrating the application of Reinforcement Learning (RL). Gaming and esports are key areas influenced by the application of Artificial Intelligence (AI) and Machine Learning (ML) solutions at scale. Tooling simplifies scientific workloads and is essential for developing the gaming and esports research area. In this work, we present ``SC2Tools'', a toolset containing multiple submodules responsible for working with, and producing larger datasets. We provide a modular structure of the implemented tooling, leaving room for future extensions where needed. Additionally, some of the tools are not StarCraft~2 exclusive and can be used with other types of data for dataset creation. The tools we present were leveraged in creating one of the largest StarCraft~2 tournament datasets to date with a separate PyTorch and PyTorch Lightning application programming interface (API) for easy access to the data. We conclude that alleviating the burden of data collection, preprocessing, and custom code development is essential for less technically proficient researchers to engage in the growing gaming and esports research area. Finally, our solution provides some foundational work toward normalizing experiment workflow in StarCraft~2

Artificial intelligence (AI) has enabled agents to master complex video games, from first-person shooters like Counter-Strike to real-time strategy games such as StarCraft II and racing games like Gran Turismo. While these achievements are notable, applying these AI methods in commercial video game production remains challenging due to computational constraints. In commercial scenarios, the majority of computational resources are allocated to 3D rendering, leaving limited capacity for AI methods, which often demand high computational power, particularly those relying on pixel-based sensors. Moreover, the gaming industry prioritizes creating human-like behavior in AI agents to enhance player experience, unlike academic models that focus on maximizing game performance. This paper introduces a novel methodology for training neural networks via imitation learning to play a complex, commercial-standard, VALORANT-like 2v2 tactical shooter game, requiring only modest CPU hardware during inference. Our approach leverages an innovative, pixel-free perception architecture using a small set of ray-cast sensors, which capture essential spatial information efficiently. These sensors allow AI to perform competently without the computational overhead of traditional methods. Models are trained to mimic human behavior using supervised learning on human trajectory data, resulting in realistic and engaging AI agents. Human evaluation tests confirm that our AI agents provide human-like gameplay experiences while operating efficiently under computational constraints. This offers a significant advancement in AI model development for tactical shooter games and possibly other genres.

In this paper, we evaluate whether LLMs learn to make human-like preference judgements in strategic scenarios as compared with known empirical results. Solar and Mistral are shown to exhibit stable value-based preference consistent with humans and exhibit human-like preference for cooperation in the prisoner's dilemma (including stake-size effect) and traveler's dilemma (including penalty-size effect). We establish a relationship between model size, value-based preference, and superficiality. Finally, results here show that models tending to be less brittle have relied on sliding window attention suggesting a potential link. Additionally, we contribute a novel method for constructing preference relations from arbitrary LLMs and support for a hypothesis regarding human behavior in the traveler's dilemma.

Game-theoretic benchmarks claim that large language model (LLM) strategic decision-making varies across game types, interaction structures, and capability dimensions. However, they only evaluate strategic performance across individual fixed models. In parallel, contemporary LLM routers pick models under quality-cost trade-offs, but with no notion of a strategic structure. They do not account for an opponent that might be unknown, and that can adapt over time and shift the feedback signal. To address this, we extend the game-theoretic evaluations and define strategic selection as the meta game layered on top of the base game. In each round, a strategic selector fields an LLM from a portfolio of models to navigate a game payoff matrix that is latent and learned online. We find that the evaluation signal is game-specific, and that extracting a reliable signal requires a much higher number of seed runs N compared to traditional benchmarking setups. Evaluating across 5 games and 10 LLMs, we show a model's strategic competence varies significantly depending on the game setup and the opponent faced. Building on this, we implement a suite of selector methods and find that approaches that rely on query embeddings or LLM self-reflection do not consistently capture the underlying strategic signal. A lightweight multi-armed bandit algorithm performs more reliably across games, though it still falls short of the best fixed model. Finally, we show that simple non-stationary and adversarial bandit variants fail to outperform a stationary bandit baseline, pointing to a gap in how current methods handle a shifting opponent in strategic settings.

Immune therapies act across cell-intrinsic programs, tissue ecosystems, and patient-specific immune states, yet most predictors address these scales separately. We used a governed evolutionary AI Scientist to construct the Immune World Model, an action-conditioned model that learns how interventions move immune states across cellular, tissue, and individual levels. The Immune World Model--building Scientist searched candidate architectures and workflows, and the resulting world model was frozen before independent confirmation. The frozen model generalized to unseen interventions and biological contexts, recovered intervention-specific cellular programs, integrated cell and tissue information to improve ecosystem and patient-response prediction, and forecast unseen perturbation combinations. Immune World Model--guided analysis then combined measured perturbations with cross-axis inference to nominate IL-36γ plus SIRPα inhibition as a complementary-axis therapeutic hypothesis, whereas a governed self-correction audit rejected every screened cytokine pair. The Immune World Model provides a framework for multiscale immune simulation that connects AI Scientist-driven model construction, intervention forecasting, and the generation of prospectively testable therapeutic hypotheses.

The prototyping of computer games, particularly card games, requires extensive human effort in creative ideation and gameplay evaluation. Recent advances in Large Language Models (LLMs) offer opportunities to automate and streamline these processes. However, it remains challenging for LLMs to design novel game mechanics beyond existing databases, generate consistent gameplay environments, and develop scalable gameplay AI for large-scale evaluations. This paper addresses these challenges by introducing a comprehensive automated card game prototyping framework. The approach highlights a graph-based indexing method for generating novel game designs, an LLM-driven system for consistent game code generation validated by gameplay records, and a gameplay AI constructing method that uses an ensemble of LLM-generated action-value functions optimized through self-play. These contributions aim to accelerate card game prototyping, reduce human labor, and lower barriers to entry for game developers.

Artificial Intelligence Virtual Cells (AIVCs) aim to learn executable, decision-relevant models of cell state from multimodal, multiscale measurements. Recent studies have introduced single-cell and spatial foundation models, improved cross-modality alignment, scaled perturbation atlases, and explored pathway-level readouts. Nevertheless, although held-out validation is standard practice, evaluations remain predominantly within single datasets and settings; evidence indicates that transport across laboratories and platforms is often limited, that some data splits are vulnerable to leakage and coverage bias, and that dose, time and combination effects are not yet systematically handled. Cross-scale coupling also remains constrained, as anchors linking molecular, cellular and tissue levels are sparse, and alignment to scientific or clinical readouts varies across studies. We propose a model-agnostic Cell-State Latent (CSL) perspective that organizes learning via an operator grammar: measurement, lift/project for cross-scale coupling, and intervention for dosing and scheduling. This view motivates a decision-aligned evaluation blueprint across modality, scale, context and intervention, and emphasizes function-space readouts such as pathway activity, spatial neighborhoods and clinically relevant endpoints. We recommend operator-aware data design, leakage-resistant partitions, and transparent calibration and reporting to enable reproducible, like-for-like comparisons.

LLMs can appear cautious in risk decision-making tasks, yet cautious-looking outputs do not necessarily indicate alignment with human decision-making mechanisms. We investigate this distinction using the St. Petersburg game as a controlled testbed, a classical paradox in which the expected payoff is infinite, yet humans typically report low, finite willingness to pay. We evaluate 28 LLMs with a structured prompt suite that includes the original game; controlled decision variants that perturb truncation, repeated play, numeric endowment, and occupational identity; a human-perspective prompt that asks models to reason as human decision makers; and paired comparisons between base models and their instruction-tuned counterparts. In the original game, most models generate finite bids, creating the appearance of human-like risk behavior. However, this outcome-level resemblance masks substantial mechanism-level differences. The controlled variants reveal that rather than maintaining human-like behavior seen in the original game, models often shift to conditionally and computationally rational behavior. Human-cue prompting and instruction tuning often lower bids and reduce some visible pathologies, but most mechanism-level response patterns remain largely unchanged. These findings show that behavioral alignment in risk decision-making can be surface-level: LLMs may produce human-like risk decisions without exhibiting human-consistent mechanisms. High-stakes evaluations of LLM decision-making should therefore move beyond outcome similarity and examine whether the alignment is supported by mechanism-level consistency.

We introduce the first multiplayer world model for highly dynamic environments governed by complex physical interactions. Whereas single-player world models treat the other agents as part of the environment, ours conditions on the action streams of multiple agents, learning to attribute changes in the scene to the correct player and to stay coherent under arbitrary combinations of their actions. We study this problem in the game of Rocket League, where players compete and cooperate under fast, tightly coupled dynamics. Trained on 10,000 hours of gameplay collected with publicly available bots, our 5-billion-parameter latent diffusion model generates four-player matches in real time, producing 20 frames per second on a single Nvidia B200 GPU. Although trained only on short clips, its rollouts stay stable far beyond the training horizon: distributional quality holds steady out to five minutes, the longest horizon we measure, and in practice we observe rollouts continuing for hours with no sign of collapse. We systematically investigate the central design choices: the video codec, the generative objective, and the multiplayer conditioning scheme. In addition, we characterize how behavior changes with model and data scale, including the capabilities that emerge and the failure modes that persist. We further develop targeted evaluations that probe the model's physical understanding rather than visual appearance alone. To support continued research on multiplayer world models, we release our dataset, our full training and inference codebase, and a live demo.

Bayesian optimization (BO) is a powerful framework to optimize black-box expensive-to-evaluate functions via sequential interactions. In several important problems (e.g. drug discovery, circuit design, neural architecture search, etc.), though, such functions are defined over large combinatorial and unstructured spaces. This makes existing BO algorithms not feasible due to the intractable maximization of the acquisition function over these domains. To address this issue, we propose GameOpt, a novel game-theoretical approach to combinatorial BO. GameOpt establishes a cooperative game between the different optimization variables, and selects points that are game equilibria of an upper confidence bound acquisition function. These are stable configurations from which no variable has an incentive to deviate- analog to local optima in continuous domains. Crucially, this allows us to efficiently break down the complexity of the combinatorial domain into individual decision sets, making GameOpt scalable to large combinatorial spaces. We demonstrate the application of GameOpt to the challenging protein design problem and validate its performance on four real-world protein datasets. Each protein can take up to 20^{X} possible configurations, where X is the length of a protein, making standard BO methods infeasible. Instead, our approach iteratively selects informative protein configurations and very quickly discovers highly active protein variants compared to other baselines.

Post-training alignment optimizes language models to match human preference signals, but this objective is not equivalent to modeling observed human behavior. We compare 120 base-aligned model pairs on more than 10,000 real human decisions in multi-round strategic games - bargaining, persuasion, negotiation, and repeated matrix games. In these settings, base models outperform their aligned counterparts in predicting human choices by nearly 10:1, robustly across model families, prompt formulations, and game configurations. This pattern reverses, however, in settings where human behavior is more likely to follow normative predictions: aligned models dominate on one-shot textbook games across all 12 types tested and on non-strategic lottery choices - and even within the multi-round games themselves, at round one, before interaction history develops. This boundary-condition pattern suggests that alignment induces a normative bias: it improves prediction when human behavior is relatively well captured by normative solutions, but hurts prediction in multi-round strategic settings, where behavior is shaped by descriptive dynamics such as reciprocity, retaliation, and history-dependent adaptation. These results reveal a fundamental trade-off between optimizing models for human use and using them as proxies for human behavior.

Complex games have long been an important benchmark for testing the progress of artificial intelligence algorithms. AlphaGo, AlphaZero, and MuZero have defeated top human players in Go and Chess, garnering widespread societal attention towards artificial intelligence. Concurrently, large language models (LLMs) have exhibited remarkable capabilities across various tasks, raising the question of whether LLMs can achieve similar success in complex games. In this paper, we explore the potential of LLMs in mastering complex card games. We systematically assess the learning capabilities of LLMs across eight diverse card games, evaluating the impact of fine-tuning on high-quality gameplay data, and examining the models' ability to retain general capabilities while mastering these games. Our findings indicate that: (1) LLMs can approach the performance of strong game AIs through supervised fine-tuning on high-quality data, (2) LLMs can achieve a certain level of proficiency in multiple complex card games simultaneously, with performance augmentation for games with similar rules and conflicts for dissimilar ones, and (3) LLMs experience a decline in general capabilities when mastering complex games, but this decline can be mitigated by integrating a certain amount of general instruction data. The evaluation results demonstrate strong learning ability and versatility of LLMs. The code is available at https://github.com/THUDM/LLM4CardGame

This paper generalises the treatment of compositional game theory as introduced by the second and third authors with Ghani and Winschel, where games are modelled as morphisms of a symmetric monoidal category. From an economic modelling perspective, the existing notion of an open game is not expressive enough for many applications. This includes stochastic environments, stochastic choices by players, as well as incomplete information regarding the game being played. The current paper addresses these three issue all at once. To achieve this we make significant use of category theory, especially the 'coend optics' of Riley.

Language carries thought and coordination among humans but rarely reaches further along the spectrum of diverse intelligence. Yet non-neural systems -- from gene regulatory networks and microbial consortia to fungi -- are increasingly recognized as substrates of computation, decision-making and memory, making dialogue with non-human intelligence newly conceivable. Today such dialogue is attempted only by proxy: a large language model speaks on the system's behalf, so any intelligence on display originates from the model while the system itself remains silent. Here we ask whether the system can speak in its own voice. Following Wittgenstein, who located meaning in use, we treat communication as a game played with the system. Its internal dynamics are frozen as the nonlinear core of a reinforcement-learning policy, with only linear input and output interfaces trained. Through use and reward, the system's states and responses acquire meaning within the game, so playing becomes speaking. Because different architectures playing the same game optimize the same reward, their behaviors can all be read as pursuit of that reward; the game serves as a lingua franca across otherwise irreconcilable representations. Given a human prompt, a language model routes it to the game whose semantics best match it and designs an environmental state for which the desired action is the rational response, letting the system reply through its own behavior. Applied across diverse gene regulatory networks and reinforcement-learning tasks, the framework yields fluent dialogue without altering any system parameter, shows that well-trained agents of disparate origin converge on similar behavior, and reveals that specific GRN properties make a system easier or harder to talk with -- an inductive bias of the reservoir itself. Our framework opens a new route to conversing with any dynamical system on its own terms.

Existing game AI research mainly focuses on enhancing agents' abilities to win games, but this does not inherently make humans have a better experience when collaborating with these agents. For example, agents may dominate the collaboration and exhibit unintended or detrimental behaviors, leading to poor experiences for their human partners. In other words, most game AI agents are modeled in a "self-centered" manner. In this paper, we propose a "human-centered" modeling scheme for collaborative agents that aims to enhance the experience of humans. Specifically, we model the experience of humans as the goals they expect to achieve during the task. We expect that agents should learn to enhance the extent to which humans achieve these goals while maintaining agents' original abilities (e.g., winning games). To achieve this, we propose the Reinforcement Learning from Human Gain (RLHG) approach. The RLHG approach introduces a "baseline", which corresponds to the extent to which humans primitively achieve their goals, and encourages agents to learn behaviors that can effectively enhance humans in achieving their goals better. We evaluate the RLHG agent in the popular Multi-player Online Battle Arena (MOBA) game, Honor of Kings, by conducting real-world human-agent tests. Both objective performance and subjective preference results show that the RLHG agent provides participants better gaming experience.

Progress in multiagent intelligence research is fundamentally limited by the number and quality of environments available for study. In recent years, simulated games have become a dominant research platform within reinforcement learning, in part due to their accessibility and interpretability. Previous works have targeted and demonstrated success on arcade, first person shooter (FPS), real-time strategy (RTS), and massive online battle arena (MOBA) games. Our work considers massively multiplayer online role-playing games (MMORPGs or MMOs), which capture several complexities of real-world learning that are not well modeled by any other game genre. We present Neural MMO, a massively multiagent game environment inspired by MMOs and discuss our progress on two more general challenges in multiagent systems engineering for AI research: distributed infrastructure and game IO. We further demonstrate that standard policy gradient methods and simple baseline models can learn interesting emergent exploration and specialization behaviors in this setting.

Cell type annotation is a key task in analyzing the heterogeneity of single-cell RNA sequencing data. Although recent foundation models automate this process, they typically annotate cells independently, without considering batch-level cellular context or providing explanatory reasoning. In contrast, human experts often annotate distinct cell types for different cell clusters based on their domain knowledge. To mimic this workflow, we introduce the CellPuzzles task, where the objective is to assign unique cell types to a batch of cells. This benchmark spans diverse tissues, diseases, and donor conditions, and requires reasoning across the batch-level cellular context to ensure label uniqueness. We find that off-the-shelf large language models (LLMs) struggle on CellPuzzles, with the best baseline (OpenAI's o1) achieving only 19.0% batch-level accuracy. To fill this gap, we propose Cell-o1, a 7B LLM trained via supervised fine-tuning on distilled reasoning traces, followed by reinforcement learning with batch-level rewards. Cell-o1 achieves state-of-the-art performance, outperforming o1 by over 73% and generalizing well across contexts. Further analysis of training dynamics and reasoning behaviors provides insights into batch-level annotation performance and emergent expert-like reasoning. Code and data are available at https://github.com/ncbi-nlp/cell-o1.

We improve the framework of open games with agency by showing how the players' counterfactual analysis giving rise to Nash equilibria can be described in the dynamics of the game itself (hence diegetically), getting rid of devices such as equilibrium predicates. This new approach overlaps almost completely with the way gradient-based learners are specified and trained. Indeed, we show feedback propagation in games can be seen as a form of backpropagation, with a crucial difference explaining the distinctive character of the phenomenology of non-cooperative games. We outline a functorial construction of arena of games, show players form a subsystem over it, and prove that their 'fixpoint behaviours' are Nash equilibria.

When one agent interacts with a multi-agent environment, it is challenging to deal with various opponents unseen before. Modeling the behaviors, goals, or beliefs of opponents could help the agent adjust its policy to adapt to different opponents. In addition, it is also important to consider opponents who are learning simultaneously or capable of reasoning. However, existing work usually tackles only one of the aforementioned types of opponents. In this paper, we propose model-based opponent modeling (MBOM), which employs the environment model to adapt to all kinds of opponents. MBOM simulates the recursive reasoning process in the environment model and imagines a set of improving opponent policies. To effectively and accurately represent the opponent policy, MBOM further mixes the imagined opponent policies according to the similarity with the real behaviors of opponents. Empirically, we show that MBOM achieves more effective adaptation than existing methods in a variety of tasks, respectively with different types of opponents, i.e., fixed policy, na\"ive learner, and reasoning learner.

We introduce a framework for translating game descriptions in natural language into extensive-form representations in game theory, leveraging Large Language Models (LLMs) and in-context learning. Given the varying levels of strategic complexity in games, such as perfect versus imperfect information, directly applying in-context learning would be insufficient. To address this, we introduce a two-stage framework with specialized modules to enhance in-context learning, enabling it to divide and conquer the problem effectively. In the first stage, we tackle the challenge of imperfect information by developing a module that identifies information sets along and the corresponding partial tree structure. With this information, the second stage leverages in-context learning alongside a self-debugging module to produce a complete extensive-form game tree represented using pygambit, the Python API of a recognized game-theoretic analysis tool called Gambit. Using this python representation enables the automation of tasks such as computing Nash equilibria directly from natural language descriptions. We evaluate the performance of the full framework, as well as its individual components, using various LLMs on games with different levels of strategic complexity. Our experimental results show that the framework significantly outperforms baseline models in generating accurate extensive-form games, with each module playing a critical role in its success.

With the sheer constant advancements raining down in the field of Artificial Intelligence, one particular possibility that may cross our mind is whether it is possible to model agents after humans and, in turn, use these agents to carry out synthetic interactions that predict their real counterparts, or even interactions at a larger scale such as groups or societies. In this paper, we test a more controlled version of this question through chess. We use 8 elite chess players, seal their direct pairwise games, learn each player independently using different methods, and then compose the resulting models on the withheld dyads. To evaluate the generated interactions, we use two measurements: opening-family total variation distance and win-draw-loss (WDL) total variation distance. M1 reduces WDL-TV while leaving opening-family TV largely unchanged, whereas M2 substantially reduces opening-family TV while having little effect on WDL-TV. An additional post-hoc method combining components of the other two retains improvements across both measurements. These results suggest that independently learned models can recover aspects of previously unseen interactions, and that recovery across different behavioural aspects need not be mutually exclusive.

We introduce an Implicit Game-Theoretic MPC (IGT-MPC), a decentralized algorithm for two-agent motion planning that uses a learned value function that predicts the game-theoretic interaction outcomes as the terminal cost-to-go function in a model predictive control (MPC) framework, guiding agents to implicitly account for interactions with other agents and maximize their reward. This approach applies to competitive and cooperative multi-agent motion planning problems which we formulate as constrained dynamic games. Given a constrained dynamic game, we randomly sample initial conditions and solve for the generalized Nash equilibrium (GNE) to generate a dataset of GNE solutions, computing the reward outcome of each game-theoretic interaction from the GNE. The data is used to train a simple neural network to predict the reward outcome, which we use as the terminal cost-to-go function in an MPC scheme. We showcase emerging competitive and coordinated behaviors using IGT-MPC in scenarios such as two-vehicle head-to-head racing and un-signalized intersection navigation. IGT-MPC offers a novel method integrating machine learning and game-theoretic reasoning into model-based decentralized multi-agent motion planning.

Single-cell perturbation models can reduce costly wet-lab screening by predicting how cells respond transcriptionally to interventions. While recent generative models improve population-level prediction, individual generated cells are not explicitly checked for biological consistency. We introduce PerturbCellRL, a reinforcement learning (RL) framework that post-trains a pretrained single-cell transcriptomic generator using a suite of cell-level verifiers as rewards. These verifiers define four rewards: Pearson top-k similarity, RMSE top-k proximity, DE Spearman, and Pathway activity. The Pathway activity verifier rewards cells whose pathway responses match known perturbation biology. We evaluate PerturbCellRL on multiple genetic and chemical perturbation benchmarks. Across these benchmarks, PerturbCellRL improves over the pretrained flow-matching generator on reward-aligned evaluation metrics and a held-out evaluation metric. Moreover, PerturbCellRL remains competitive with state-of-the-art methods on population-level metrics. Together, these results frame trustworthy single-cell prediction as verifier-guided generative alignment, moving beyond matching expression distributions toward predictions whose single-cell perturbation effects are explicitly checked for biological consistency.

Cell Painting is a high-content morphological profiling assay widely used for phenotype-based biological inference, with mechanism of action (MOA) prediction as a central application. Existing approaches largely formulate Cell Painting-based inference as representation matching, assigning predictions from nearby reference perturbations in morphological feature space. However, retrieved neighbors are often noisy and partially misleading evidence due to batch effects, non-specific cytotoxicity, phenotypic convergence, and source-dependent variability. We reformulate Cell Painting-based MOA prediction as a calibrated evidence reasoning problem, where retrieved neighbors are treated as uncertain observations that must be evaluated, compared, and sometimes rejected before supporting a mechanistic conclusion. We propose PhenoAIR, a reliability-aware multi-agent framework that maintains a candidate-centric evidence memory and performs controller-guided refinement over phenotype- and mechanism-side evidence. PhenoAIR uses offline reference-set calibration to weight evidence by source reliability, phenotype stability, and mechanism-level confusion. We evaluate PhenoAIR on a benchmark constructed from JUMP Cell Painting profiles and annotations, covering controlled, realistic, and discovery-oriented open-world MOA prediction settings. PhenoAIR outperforms representation-matching and LLM-based baselines across all settings.

Generative AI foundation models offer transformative potential for processing structured biological data, particularly in single-cell RNA sequencing, where datasets are rapidly scaling toward billions of cells. We propose the use of agentic foundation models with real-time web search to automate the labeling of experimental data, achieving up to 82.5% accuracy. This addresses a key bottleneck in supervised learning for structured omics data by increasing annotation throughput without manual curation and human error. Our approach enables the development of virtual cell foundation models capable of downstream tasks such as cell-typing and perturbation prediction. As data volume grows, these models may surpass human performance in labeling, paving the way for reliable inference in large-scale perturbation screens. This application demonstrates domain-specific innovation in health monitoring and diagnostics, aligned with efforts like the Human Cell Atlas and Human Tumor Atlas Network.

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce LangCell, the first Language-Cell pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

Vision-Language Models (VLMs) excel in many direct multimodal tasks but struggle to translate this prowess into effective decision-making within interactive, visually rich environments like games. This ``knowing-doing'' gap significantly limits their potential as autonomous agents, as leading VLMs often performing badly in simple games. To address this, we introduce VLM-Gym, a curated reinforcement learning (RL) environment featuring diverse visual games with unified interfaces and adjustable, compositional difficulty, specifically designed for scalable multi-game parallel training. Leveraging VLM-Gym, we train G0 models using pure RL-driven self-evolution, which demonstrate emergent perception and reasoning patterns. To further mitigate challenges arising from game diversity, we develop G1 models. G1 incorporates a perception-enhanced cold start prior to RL fine-tuning. Our resulting G1 models consistently surpass their teacher across all games and outperform leading proprietary models like Claude-3.7-Sonnet-Thinking. Systematic analysis reveals an intriguing finding: perception and reasoning abilities mutually bootstrap each other throughout the RL training process. Source code including VLM-Gym and RL training are released at https://github.com/chenllliang/G1 to foster future research in advancing VLMs as capable interactive agents.

We show that GPT-4's reasoning and planning capabilities extend to the 1993 first-person shooter Doom. This large language model (LLM) is able to run and play the game with only a few instructions, plus a textual description--generated by the model itself from screenshots--about the state of the game being observed. We find that GPT-4 can play the game to a passable degree: it is able to manipulate doors, combat enemies, and perform pathing. More complex prompting strategies involving multiple model calls provide better results. While further work is required to enable the LLM to play the game as well as its classical, reinforcement learning-based counterparts, we note that GPT-4 required no training, leaning instead on its own reasoning and observational capabilities. We hope our work pushes the boundaries on intelligent, LLM-based agents in video games. We conclude by discussing the ethical implications of our work.

The rapid advancements in large language models (LLMs) have presented challenges in evaluating those models. Existing evaluation methods are either reference-based or preference based, which inevitably need human intervention or introduce test bias caused by evaluator models. In this paper, we propose GameEval, a novel approach to evaluating LLMs through goal-driven conversational games, overcoming the limitations of previous methods. GameEval treats LLMs as game players and assigns them distinct roles with specific goals achieved by launching conversations of various forms, including discussion, question answering, and voting. We design three unique games with cooperative or adversarial objectives, accompanied by corresponding evaluation metrics, to show how this new paradigm comprehensively evaluates model performance.Through extensive experiments, we show that GameEval can effectively differentiate the capabilities of various LLMs, providing a comprehensive assessment of their integrated abilities to solve complex problems. Our public anonymous code is available at https://github.com/GameEval/GameEval.

Single-cell and spatial foundation models promise transferable biological representations, yet their generality remains largely untested across modalities, biological domains and analytical tasks. We benchmarked six representative models, Nicheformer, CellPLM, scGPT-spatial, GenePT, scELMo and Novae, using a harmonised framework spanning scRNA-seq, spatial transcriptomics and Perturb-seq. We evaluated zero-shot and continually pretrained clustering, supervised annotation, marker-gene concordance and perturbation prediction. Model performance was strongly conditional: expression-trained cell-level transformers best resolved many cell-identity tasks, spatial and graph-aware models better preserved tissue architecture, and language-derived gene embeddings were competitive for selected perturbation-response metrics. No model dominated across tasks, and rankings shifted with modality, preprocessing, tokenisation, biological prior, domain shift and metric choice. This benchmark provides practical guidance for model selection and argues that future models should be judged by biological generalisation, interpretability and perturbation-grounded validity, not by scale or leaderboard performance alone.

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

Cell painting is a popular technique for creating human-interpretable, high-contrast images of cell morphology. There are two major issues with cell paint: (1) it is labor-intensive and (2) it requires chemical fixation, making the study of cell dynamics impossible. We train a diffusion model (Morphological Observation Neural Enhancement Tool, or MONET) on a large dataset to predict cell paint channels from brightfield images. We show that model quality improves with scale. The model uses a consistency architecture to generate time-lapse videos, despite the impossibility of obtaining cell paint video training data. In addition, we show that this architecture enables a form of in-context learning, allowing the model to partially transfer to out-of-distribution cell lines and imaging protocols. Virtual cell painting is not intended to replace physical cell painting completely, but to act as a complementary tool enabling novel workflows in biological research.

Single-cell perturbation studies face dual heterogeneity bottlenecks: (i) semantic heterogeneity--identical biological concepts encoded under incompatible metadata schemas across datasets; and (ii) statistical heterogeneity--distribution shifts from biological variation demanding dataset-specific inductive biases. We propose HarmonyCell, an end-to-end agent framework resolving each challenge through a dedicated mechanism: an LLM-driven Semantic Unifier autonomously maps disparate metadata into a canonical interface without manual intervention; and an adaptive Monte Carlo Tree Search engine operates over a hierarchical action space to synthesize architectures with optimal statistical inductive biases for distribution shifts. Evaluated across diverse perturbation tasks under both semantic and distribution shifts, HarmonyCell achieves a 95% valid execution rate on heterogeneous input datasets (versus 0% for general agents) while matching or even exceeding expert-designed baselines in rigorous out-of-distribution evaluations. This dual-track orchestration enables scalable automatic virtual cell modeling without dataset-specific engineering.

Recent advancements in single-cell multi-omics, particularly RNA-seq, have provided profound insights into cellular heterogeneity and gene regulation. While pre-trained language model (PLM) paradigm based single-cell foundation models have shown promise, they remain constrained by insufficient integration of in-depth individual profiles and neglecting the influence of noise within multi-modal data. To address both issues, we propose an Open-world Language Knowledge-Aided Robust Single-Cell Foundation Model (OKR-CELL). It is built based on a cross-modal Cell-Language pre-training framework, which comprises two key innovations: (1) leveraging Large Language Models (LLMs) based workflow with retrieval-augmented generation (RAG) enriches cell textual descriptions using open-world knowledge; (2) devising a Cross-modal Robust Alignment (CRA) objective that incorporates sample reliability assessment, curriculum learning, and coupled momentum contrastive learning to strengthen the model's resistance to noisy data. After pretraining on 32M cell-text pairs, OKR-CELL obtains cutting-edge results across 6 evaluation tasks. Beyond standard benchmarks such as cell clustering, cell-type annotation, batch-effect correction, and few-shot annotation, the model also demonstrates superior performance in broader multi-modal applications, including zero-shot cell-type annotation and bidirectional cell-text retrieval.

We introduce an approach to evaluate language model (LM) agency using negotiation games. This approach better reflects real-world use cases and addresses some of the shortcomings of alternative LM benchmarks. Negotiation games enable us to study multi-turn, and cross-model interactions, modulate complexity, and side-step accidental evaluation data leakage. We use our approach to test six widely used and publicly accessible LMs, evaluating performance and alignment in both self-play and cross-play settings. Noteworthy findings include: (i) only closed-source models tested here were able to complete these tasks; (ii) cooperative bargaining games proved to be most challenging to the models; and (iii) even the most powerful models sometimes "lose" to weaker opponents

Strategic decision-making in multi-agent settings is a key challenge for large language models (LLMs), particularly when coordination and negotiation must unfold over extended conversations. While recent work has explored the use of LLMs in isolated decision tasks, little attention has been given to optimizing long-term objectives through dialogue. We introduce GameTalk, a framework for training LLMs to make strategic decisions via multi-turn interactions. Unlike prior work that focuses on single-turn objectives or static action prediction, we train LLMs to optimize a global objective across full conversations. We achieve this by adapting fine-tuning methods like GRPO, DPO, and STaR to incorporate reward signals that depend on the entire interaction. We evaluate this approach on a suite of increasingly complex games, designed to stress different aspects of reasoning, coordination, and opponent modeling. Our results show that GameTalk significantly outperforms untrained models, especially under reward shaping, with DPO consistently yielding the strongest gains. These findings position conversational fine-tuning as a promising path for LLMs to reason, negotiate, and act in interactive environments.

Decision-making, a complicated task requiring various types of abilities, presents an excellent framework for assessing Large Language Models (LLMs). Our research investigates LLMs' decision-making capabilities through the lens of a well-established field, Game Theory. We focus specifically on games that support the participation of more than two agents simultaneously. Subsequently, we introduce our framework, GAMA-Bench, including eight classical multi-agent games. We design a scoring scheme to assess a model's performance in these games quantitatively. Through GAMA-Bench, we investigate LLMs' robustness, generalizability, and enhancement strategies. Results reveal that while GPT-3.5 shows satisfying robustness, its generalizability is relatively limited. However, its performance can be improved through approaches such as Chain-of-Thought. Additionally, we conduct evaluations across various LLMs and find that GPT-4 outperforms other models on GAMA-Bench, achieving a score of 60.5. Moreover, Gemini-1.0-Pro and GPT-3.5 (0613, 1106, 0125) demonstrate similar intelligence on GAMA-Bench. The code and experimental results are made publicly available via https://github.com/CUHK-ARISE/GAMABench.

As Large Language Models (LLMs) are integrated into critical real-world applications, their strategic and logical reasoning abilities are increasingly crucial. This paper evaluates LLMs' reasoning abilities in competitive environments through game-theoretic tasks, e.g., board and card games that require pure logic and strategic reasoning to compete with opponents. We first propose GTBench, a language-driven environment composing 10 widely-recognized tasks, across a comprehensive game taxonomy: complete versus incomplete information, dynamic versus static, and probabilistic versus deterministic scenarios. Then, we investigate two key problems: (1) Characterizing game-theoretic reasoning of LLMs; (2) LLM-vs-LLM competitions as reasoning evaluation. We observe that (1) LLMs have distinct behaviors regarding various gaming scenarios; for example, LLMs fail in complete and deterministic games yet they are competitive in probabilistic gaming scenarios; (2) Open-source LLMs, e.g., CodeLlama-34b-Instruct, are less competitive than commercial LLMs, e.g., GPT-4, in complex games. In addition, code-pretraining greatly benefits strategic reasoning, while advanced reasoning methods such as Chain-of-Thought (CoT) and Tree-of-Thought (ToT) do not always help. Detailed error profiles are also provided for a better understanding of LLMs' behavior.

In hematology, computational models offer significant potential to improve diagnostic accuracy, streamline workflows, and reduce the tedious work of analyzing single cells in peripheral blood or bone marrow smears. However, clinical adoption of computational models has been hampered by the lack of generalization due to large batch effects, small dataset sizes, and poor performance in transfer learning from natural images. To address these challenges, we introduce DinoBloom, the first foundation model for single cell images in hematology, utilizing a tailored DINOv2 pipeline. Our model is built upon an extensive collection of 13 diverse, publicly available datasets of peripheral blood and bone marrow smears, the most substantial open-source cohort in hematology so far, comprising over 380,000 white blood cell images. To assess its generalization capability, we evaluate it on an external dataset with a challenging domain shift. We show that our model outperforms existing medical and non-medical vision models in (i) linear probing and k-nearest neighbor evaluations for cell-type classification on blood and bone marrow smears and (ii) weakly supervised multiple instance learning for acute myeloid leukemia subtyping by a large margin. A family of four DinoBloom models (small, base, large, and giant) can be adapted for a wide range of downstream applications, be a strong baseline for classification problems, and facilitate the assessment of batch effects in new datasets. All models are available at github.com/marrlab/DinoBloom.

Game environments provide rich, controllable settings that stimulate many aspects of real-world complexity. As such, game agents offer a valuable testbed for exploring capabilities relevant to Artificial General Intelligence. Recently, the emergence of Large Language Models (LLMs) provides new opportunities to endow these agents with generalizable reasoning, memory, and adaptability in complex game environments. This survey offers an up-to-date review of LLM-based game agents (LLMGAs) through a unified reference architecture. At the single-agent level, we synthesize existing studies around three core components: memory, reasoning, and perception-action interfaces, which jointly characterize how language enables agents to perceive, think, and act. At the multi-agent level, we outline how communication protocols and organizational models support coordination, role differentiation, and large-scale social behaviors. To contextualize these designs, we introduce a challenge-centered taxonomy linking six major game genres to their dominant agent requirements, from low-latency control in action games to open-ended goal formation in sandbox worlds. A curated list of related papers is available at https://github.com/git-disl/awesome-LLM-game-agent-papers

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.

Multi-agent football poses an unsolved challenge in AI research. Existing work has focused on tackling simplified scenarios of the game, or else leveraging expert demonstrations. In this paper, we develop a multi-agent system to play the full 11 vs. 11 game mode, without demonstrations. This game mode contains aspects that present major challenges to modern reinforcement learning algorithms; multi-agent coordination, long-term planning, and non-transitivity. To address these challenges, we present TiZero; a self-evolving, multi-agent system that learns from scratch. TiZero introduces several innovations, including adaptive curriculum learning, a novel self-play strategy, and an objective that optimizes the policies of multiple agents jointly. Experimentally, it outperforms previous systems by a large margin on the Google Research Football environment, increasing win rates by over 30%. To demonstrate the generality of TiZero's innovations, they are assessed on several environments beyond football; Overcooked, Multi-agent Particle-Environment, Tic-Tac-Toe and Connect-Four.

Agent-based modeling has been around for decades, and applied widely across the social and natural sciences. The scope of this research method is now poised to grow dramatically as it absorbs the new affordances provided by Large Language Models (LLM)s. Generative Agent-Based Models (GABM) are not just classic Agent-Based Models (ABM)s where the agents talk to one another. Rather, GABMs are constructed using an LLM to apply common sense to situations, act "reasonably", recall common semantic knowledge, produce API calls to control digital technologies like apps, and communicate both within the simulation and to researchers viewing it from the outside. Here we present Concordia, a library to facilitate constructing and working with GABMs. Concordia makes it easy to construct language-mediated simulations of physically- or digitally-grounded environments. Concordia agents produce their behavior using a flexible component system which mediates between two fundamental operations: LLM calls and associative memory retrieval. A special agent called the Game Master (GM), which was inspired by tabletop role-playing games, is responsible for simulating the environment where the agents interact. Agents take actions by describing what they want to do in natural language. The GM then translates their actions into appropriate implementations. In a simulated physical world, the GM checks the physical plausibility of agent actions and describes their effects. In digital environments simulating technologies such as apps and services, the GM may handle API calls to integrate with external tools such as general AI assistants (e.g., Bard, ChatGPT), and digital apps (e.g., Calendar, Email, Search, etc.). Concordia was designed to support a wide array of applications both in scientific research and for evaluating performance of real digital services by simulating users and/or generating synthetic data.

We present a general computational theory of cancer and its developmental dynamics. The theory is based on a theory of the architecture and function of developmental control networks which guide the formation of multicellular organisms. Cancer networks are special cases of developmental control networks. Cancer results from transformations of normal developmental networks. Our theory generates a natural classification of all possible cancers based on their network architecture. Each cancer network has a unique topology and semantics and developmental dynamics that result in distinct clinical tumor phenotypes. We apply this new theory with a series of proof of concept cases for all the basic cancer types. These cases have been computationally modeled, their behavior simulated and mathematically described using a multicellular systems biology approach. There are fascinating correspondences between the dynamic developmental phenotype of computationally modeled {\em in silico} cancers and natural {\em in vivo} cancers. The theory lays the foundation for a new research paradigm for understanding and investigating cancer. The theory of cancer networks implies that new diagnostic methods and new treatments to cure cancer will become possible.

Previous work has found a gap between the scale of neural networks that reliably learn Conway's Game of Life, and minimal networks capable of representing the classic cellular automaton with hard-coded parameter values. Viewing neural network learning as a search process suggests a dependence on networks large enough to contain sub-networks with lucky initializations (sometimes known as 'winning tickets') that actually learn the task. In this work, we reorient our perspective from discovering Life rules as a search problem back to a learning problem, and reason that with fitting inductive biases, the problem should be much more amenable to minimal networks. We find that network variants with several alternative activation functions meaningfully outperform the default choice of Rectified Linear Units, and in particular, that a 2nd degree polynomial activation function consistently learns Life dynamics with or without the benefit of learning neural weights. Our results provide an informative demonstration of the benefits of matching learning to the task at hand and challenge the easy default choice of scale for all problems. In particular, we advocate for the use of cellular automata as simple test domains for developing strategies that can benefit machine learning for science, physics-based deep learning, and interpretable machine learning.

AIVC (AI Virtual Cell) is a learned simulator of cellular behavior across conditions. Predicting how a cell population responds transcriptionally to a genetic perturbation is a core task. Perturb-seq records that response by destructive sequencing, so a control cell and a perturbed cell are never observed as a pair, and cells under one condition remain heterogeneous and noisy. Regression on individual cells absorbs sampling variation into the estimated effect, whereas interpretation requires the reproducible population effect. P2P (Perturbation-to-Perturbation) takes a stochastic cell-set view as its supervision unit. Two views drawn from the same condition share a reproducible population effect and differ by view-specific variation. A permutation-invariant set encoder summarizes the control population, a structured encoder represents perturbation tokens, cellular context, dose, and combination interactions, and a gate blends empirical condition-effect memory with a neural residual. A heteroscedastic head predicts the population mean and gene-wise response variance. Under one protocol and five seeds, P2P attains the lowest expression RMSE and the highest Effect Pearson, DEG F1, and DEG average precision on each of Adamson, Norman, Replogle K562, and Replogle RPE1 relative to GenePert, LinearPert, SLIM, Scouter, and scPILOT. On Replogle K562, Effect Pearson rises from 0.643 to 0.702 and DEG F1 rises from 0.067 to 0.178 relative to Scouter, the strongest baseline on both metrics.

We present a new dataset containing 10K human-annotated games of Go and show how these natural language annotations can be used as a tool for model interpretability. Given a board state and its associated comment, our approach uses linear probing to predict mentions of domain-specific terms (e.g., ko, atari) from the intermediate state representations of game-playing agents like AlphaGo Zero. We find these game concepts are nontrivially encoded in two distinct policy networks, one trained via imitation learning and another trained via reinforcement learning. Furthermore, mentions of domain-specific terms are most easily predicted from the later layers of both models, suggesting that these policy networks encode high-level abstractions similar to those used in the natural language annotations.

Single-cell RNA sequencing (scRNA-seq) data analysis is crucial for biological research, as it enables the precise characterization of cellular heterogeneity. However, manual manipulation of various tools to achieve desired outcomes can be labor-intensive for researchers. To address this, we introduce CellAgent (http://cell.agent4science.cn/), an LLM-driven multi-agent framework, specifically designed for the automatic processing and execution of scRNA-seq data analysis tasks, providing high-quality results with no human intervention. Firstly, to adapt general LLMs to the biological field, CellAgent constructs LLM-driven biological expert roles - planner, executor, and evaluator - each with specific responsibilities. Then, CellAgent introduces a hierarchical decision-making mechanism to coordinate these biological experts, effectively driving the planning and step-by-step execution of complex data analysis tasks. Furthermore, we propose a self-iterative optimization mechanism, enabling CellAgent to autonomously evaluate and optimize solutions, thereby guaranteeing output quality. We evaluate CellAgent on a comprehensive benchmark dataset encompassing dozens of tissues and hundreds of distinct cell types. Evaluation results consistently show that CellAgent effectively identifies the most suitable tools and hyperparameters for single-cell analysis tasks, achieving optimal performance. This automated framework dramatically reduces the workload for science data analyses, bringing us into the "Agent for Science" era.

In many multi-agent systems, agents interact repeatedly and are expected to settle into stable, rational behavior over time. Yet in practice, behavior often drifts, and detecting such deviations in real time remains an open challenge. We introduce a sequential testing framework that monitors whether observed play is consistent with a benchmark of strategic behavior, without assuming a fixed sample size. Our approach builds on the e-value framework for safe anytime-valid inference: by "betting" against the benchmark, we construct a test supermartingale that accumulates evidence whenever observed payoffs systematically violate the expected conditions. For repeated normal-form games, we take equilibrium as the benchmark, yielding a statistically sound, interpretable measure of departure from equilibrium that can be monitored online; our framework unifies the treatment of Nash, correlated, and coarse correlated equilibria, offering finite-time guarantees and a detailed analysis of detection times. We also leverage Benjamini-Hochberg-type procedures to increase detection power in large games while rigorously controlling the false discovery rate. Finally, we extend our method to stochastic games, verifying online whether observed trajectories adhere to a specified target policy, such as a computed equilibrium, broadening the framework's applicability to dynamic, state-dependent settings.

A successful tactic that is followed by the scientific community for advancing AI is to treat games as problems, which has been proven to lead to various breakthroughs. We adapt this strategy in order to study Rocket League, a widely popular but rather under-explored 3D multiplayer video game with a distinct physics engine and complex dynamics that pose a significant challenge in developing efficient and high-performance game-playing agents. In this paper, we present Lucy-SKG, a Reinforcement Learning-based model that learned how to play Rocket League in a sample-efficient manner, outperforming by a notable margin the two highest-ranking bots in this game, namely Necto (2022 bot champion) and its successor Nexto, thus becoming a state-of-the-art agent. Our contributions include: a) the development of a reward analysis and visualization library, b) novel parameterizable reward shape functions that capture the utility of complex reward types via our proposed Kinesthetic Reward Combination (KRC) technique, and c) design of auxiliary neural architectures for training on reward prediction and state representation tasks in an on-policy fashion for enhanced efficiency in learning speed and performance. By performing thorough ablation studies for each component of Lucy-SKG, we showed their independent effectiveness in overall performance. In doing so, we demonstrate the prospects and challenges of using sample-efficient Reinforcement Learning techniques for controlling complex dynamical systems under competitive team-based multiplayer conditions.

This paper introduces LLM-MARL, a unified framework that incorporates large language models (LLMs) into multi-agent reinforcement learning (MARL) to enhance coordination, communication, and generalization in simulated game environments. The framework features three modular components of Coordinator, Communicator, and Memory, which dynamically generate subgoals, facilitate symbolic inter-agent messaging, and support episodic recall. Training combines PPO with a language-conditioned loss and LLM query gating. LLM-MARL is evaluated in Google Research Football, MAgent Battle, and StarCraft II. Results show consistent improvements over MAPPO and QMIX in win rate, coordination score, and zero-shot generalization. Ablation studies demonstrate that subgoal generation and language-based messaging each contribute significantly to performance gains. Qualitative analysis reveals emergent behaviors such as role specialization and communication-driven tactics. By bridging language modeling and policy learning, this work contributes to the design of intelligent, cooperative agents in interactive simulations. It offers a path forward for leveraging LLMs in multi-agent systems used for training, games, and human-AI collaboration.

Given a strategically complex board game, human players can quickly learn to devise strategies after playing a few rounds. Autonomous agents require similar capabilities in realistic interactive environments, yet existing agent benchmarks often fail to fully capture such strategic and evolving decision-making scenarios. We present PTCG-Bench, a benchmark built on the Pok'{e}mon Trading Card Game (PTCG) that evaluates LLM agents at two complementary levels: (1) their decision-making performance within a single complex environment, and (2) their ability to self-evolving through accumulated experience. We further include a modular harness ablation to better interpret agent performance without conflating it with model capability. Our experiments show that, although LLM agents can achieve non-trivial gameplay performance, sustained and stable self-evolution remains challenging, and performance is sensitive to harness design. We hope that PTCG-Bench will facilitate future research on harness-aware and self-evolving agents in realistic interactive environments.

Large Language Models (LLMs) reasoning abilities are increasingly being applied to classical board and card games, but the dominant approach -- involving prompting for direct move generation -- has significant drawbacks. It relies on the model's implicit fragile pattern-matching capabilities, leading to frequent illegal moves and strategically shallow play. Here we introduce an alternative approach: We use the LLM to translate natural language rules and game trajectories into a formal, executable world model represented as Python code. This generated model -- comprising functions for state transition, legal move enumeration, and termination checks -- serves as a verifiable simulation engine for high-performance planning algorithms like Monte Carlo tree search (MCTS). In addition, we prompt the LLM to generate heuristic value functions (to make MCTS more efficient), and inference functions (to estimate hidden states in imperfect information games). Our method offers three distinct advantages compared to directly using the LLM as a policy: (1) Verifiability: The generated CWM serves as a formal specification of the game's rules, allowing planners to algorithmically enumerate valid actions and avoid illegal moves, contingent on the correctness of the synthesized model; (2) Strategic Depth: We combine LLM semantic understanding with the deep search power of classical planners; and (3) Generalization: We direct the LLM to focus on the meta-task of data-to-code translation, enabling it to adapt to new games more easily. We evaluate our agent on 10 different games, of which 4 are novel and created for this paper. 5 of the games are fully observed (perfect information), and 5 are partially observed (imperfect information). We find that our method outperforms or matches Gemini 2.5 Pro in 9 out of the 10 considered games.

Open-world survival games pose significant challenges for AI algorithms due to their multi-tasking, deep exploration, and goal prioritization requirements. Despite reinforcement learning (RL) being popular for solving games, its high sample complexity limits its effectiveness in complex open-world games like Crafter or Minecraft. We propose a novel approach, SPRING, to read the game's original academic paper and use the knowledge learned to reason and play the game through a large language model (LLM). Prompted with the LaTeX source as game context and a description of the agent's current observation, our SPRING framework employs a directed acyclic graph (DAG) with game-related questions as nodes and dependencies as edges. We identify the optimal action to take in the environment by traversing the DAG and calculating LLM responses for each node in topological order, with the LLM's answer to final node directly translating to environment actions. In our experiments, we study the quality of in-context "reasoning" induced by different forms of prompts under the setting of the Crafter open-world environment. Our experiments suggest that LLMs, when prompted with consistent chain-of-thought, have great potential in completing sophisticated high-level trajectories. Quantitatively, SPRING with GPT-4 outperforms all state-of-the-art RL baselines, trained for 1M steps, without any training. Finally, we show the potential of games as a test bed for LLMs.

Understanding the biological mechanism of disease is critical for medicine, and in particular drug discovery. AI-powered analysis of genome-scale biological data hold great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models either do not improve or only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving the state-of-the-art. First, we scaled the pre-training dataset to 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the TEDDY family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on two downstream evaluation tasks -- identifying the underlying disease state of held-out donors not seen during training and distinguishing healthy cells from diseased ones for disease conditions and donors not seen during training. Scaling experiments showed that performance improved predictably with both data volume and parameter count. Our models showed substantial improvement over existing work on the first task and more muted improvements on the second.

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.

Chess has long been a testbed for AI's quest to match human intelligence, and in recent years, chess AI systems have surpassed the strongest humans at the game. However, these systems are not human-aligned; they are unable to match the skill levels of all human partners or model human-like behaviors beyond piece movement. In this paper, we introduce Allie, a chess-playing AI designed to bridge the gap between artificial and human intelligence in this classic game. Allie is trained on log sequences of real chess games to model the behaviors of human chess players across the skill spectrum, including non-move behaviors such as pondering times and resignations In offline evaluations, we find that Allie exhibits humanlike behavior: it outperforms the existing state-of-the-art in human chess move prediction and "ponders" at critical positions. The model learns to reliably assign reward at each game state, which can be used at inference as a reward function in a novel time-adaptive Monte-Carlo tree search (MCTS) procedure, where the amount of search depends on how long humans would think in the same positions. Adaptive search enables remarkable skill calibration; in a large-scale online evaluation against players with ratings from 1000 to 2600 Elo, our adaptive search method leads to a skill gap of only 49 Elo on average, substantially outperforming search-free and standard MCTS baselines. Against grandmaster-level (2500 Elo) opponents, Allie with adaptive search exhibits the strength of a fellow grandmaster, all while learning exclusively from humans.

Recently, remarkable progress has been made by approximating Nash equilibrium (NE), correlated equilibrium (CE), and coarse correlated equilibrium (CCE) through function approximation that trains a neural network to predict equilibria from game representations. Furthermore, equivariant architectures are widely adopted in designing such equilibrium approximators in normal-form games. In this paper, we theoretically characterize benefits and limitations of equivariant equilibrium approximators. For the benefits, we show that they enjoy better generalizability than general ones and can achieve better approximations when the payoff distribution is permutation-invariant. For the limitations, we discuss their drawbacks in terms of equilibrium selection and social welfare. Together, our results help to understand the role of equivariance in equilibrium approximators.

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.