ICML 2026 Papers

International Conference on Machine Learning

Decision breakdown

6,341papers

Counted from the official paper list; may differ slightly from the number the conference announced.

  • Spotlight
    5368.5%
  • Poster
    5,80591.5%

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Language Bias in LVLMs: From In-Depth Analysis to Simple and Effective Mitigation

Yangneng Chen, Jing Li

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Large Vision-Language Models (LVLMs) extend large language models with visual understanding, but remain vulnerable to hallucination, where outputs are fluent yet inconsistent with images. Recent studies link this issue to language bias—the tendency of LVLMs to over-rely on text while neglecting visual inputs. Yet most analyses remain empirical without uncovering its underlying cause. In this paper, we provide a systematic study of language bias and identify its root in modality misalignment during training. Our analysis shows that both Visual Instruction Tuning (VIT) and Direct Preference Optimization (DPO) often prioritize textual improvements, which may cause LVLMs to overly lean toward language modeling rather than balanced multimodal understanding. To address this, we propose two simple yet effective methods: Language Bias Regularization (LBR), which mitigates language bias through regularization during instruction tuning, and Language Bias Penalty (LBP), which penalizes language bias in the DPO training process. Extensive experiments across diverse models and benchmarks demonstrate the effectiveness of our approach. LBR consistently improves performance on over ten general benchmarks, while LBP significantly reduces hallucination and improves trustworthiness. Together, these methods not only mitigate language bias but also advance the overall alignment of LVLMs, all without introducing any additional data or auxiliary models. Our code is publicly available at [https://github.com/lab-klc/HAVAE](https://github.com/lab-klc/HAVAE).

Poster
HECTOR: Hybrid Editable Compositional Object References for Video Generation

Guofeng Zhang, Angtian Wang, Jacob Zhiyuan Fang, Liming Jiang, Haotian Yang, Alan Yuille, Chongyang Ma

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Real-world videos naturally portray complex interactions among distinct physical objects, effectively forming dynamic compositions of visual elements. However, most current video generation models synthesize scenes holistically and therefore lack mechanisms for explicit compositional manipulation. To address this limitation, we propose HECTOR, a generative pipeline that enables fine-grained compositional control. In contrast to prior methods, HECTOR supports hybrid reference conditioning, allowing generation to be simultaneously guided by static images and/or dynamic videos. Moreover, users can explicitly specify the trajectory of each referenced element, precisely controlling its location, scale, and speed (see Figure1). This design allows the model to synthesize coherent videos that satisfy complex spatiotemporal constraints while preserving high-fidelity adherence to references. Extensive experiments demonstrate that HECTOR achieves superior visual quality, stronger reference preservation, and improved motion controllability compared with existing approaches.

Poster
You Can Learn Tokenization End-to-End with Reinforcement Learning

Sam Dauncey, Roger Wattenhofer

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Tokenization is a hardcoded compression step which remains in the training pipeline of Large Language Models (LLMs), despite a general trend towards architectures becoming increasingly end-to-end. Prior work has shown promising results at scale in bringing this compression step inside the LLMs' architecture with heuristics to draw token boundaries, and also attempts to learn these token boundaries with straight-through estimates, which treat the problem of drawing discrete token boundaries as a continuous one. We show that these token boundaries can instead be learned using score function estimates, which have tighter theoretical guarantees due to directly optimizing the problem of drawing discrete token boundaries to minimize loss. We observe that techniques from reinforcement learning, such as time discounting, are necessary to reduce the variance of this score function sufficiently to make it practicable. We demonstrate that the resultant method outperforms prior proposed straight-through estimates, both qualitatively and quantitatively at the $100$ million parameter scale.

Poster
SWE-fficiency: Can Language Models Optimize Real-World Repositories on Real Workloads?

Jeffrey Jian Ma, Milad Hashemi, Amir Yazdanbakhsh, Kevin Swersky, Ofir Press, Enhui Li, Vijay Janapa Reddi, Parthasarathy Ranganathan

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Optimizing the performance of large-scale software repositories demands expertise in code reasoning and software engineering (SWE) to reduce runtime while preserving program correctness. However, most benchmarks emphasize what to fix rather than how to fix code. We introduce SWE-fficiency, a benchmark for evaluating repository-level performance optimization on real workloads. Our suite contains 498 tasks across nine widely used data-science, machine-learning, and HPC repositories (e.g., numpy, pandas, scipy): given a complete codebase and a slow workload, an agent must investigate code semantics, localize bottlenecks and relevant tests, and produce a patch that matches or exceeds expert speedup while passing the same unit tests. To enable this how-to-fix evaluation, our automated pipeline scrapes GitHub pull requests for performance-improving edits, combining keyword filtering, static analysis, coverage tooling, and execution validation to both confirm expert speedup baselines and identify relevant repository unit tests. Empirical evaluation of state-of-the-art agents reveals significant underperformance. On average, top agents achieve less than 0.23x the expert speedup: agents struggle in localizing optimization opportunities, reasoning about execution across functions, and maintaining correctness in proposed edits. We release the benchmark and accompanying data pipeline to facilitate research on automated performance engineering and long-horizon software reasoning.

Poster
Inverse Entropic Optimal Transport Solves Semi-supervised Learning via Data Likelihood Maximization

Mikhail Persiianov, Arip Asadulaev, Nikita Andreev, Nikita Starodubcev, Dmitry Baranchuk, Anastasis Kratsios, Evgeny Burnaev, Alexander Korotin

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Learning conditional distributions $\pi^\star(\cdot|x)$ is a central problem in machine learning, which is typically approached via supervised methods with paired data $(x,y) \sim \pi^\star$. However, acquiring paired data samples is often challenging, especially in problems such as domain translation. This necessitates the development of *semi-supervised* models that utilize both limited paired data and additional unpaired i.i.d. samples $x \sim \pi^\star_x$ and $y \sim \pi^\star_y$ from the marginal distributions. The usage of such combined data is complex and often relies on heuristic approaches. To tackle this issue, we propose a new learning paradigm that integrates both paired and unpaired data seamlessly using data likelihood maximization techniques. We demonstrate that our approach also connects intriguingly with inverse entropic optimal transport (OT). This finding allows us to apply recent advances in computational OT to establish an *end-to-end* learning algorithm to get $\pi^\star(\cdot|x)$. In addition, we derive the universal approximation property, demonstrating that our approach can theoretically recover true conditional distributions with arbitrarily small error. Finally, we demonstrate through empirical tests that our method effectively learns conditional distributions using paired and unpaired data simultaneously.

Poster
Toward Training Superintelligent Software Agents through Self-Play SWE-RL

Yuxiang Wei, Zhiqing Sun, Emily McMilin, Jonas Gehring, David W. Zhang, Gabriel Synnaeve, Daniel Fried, Lingming Zhang, Sida Wang

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While current software agents powered by large language models (LLMs) and reinforcement learning (RL) can boost programmer productivity, their reliance on human-curated training data and environments creates a fundamental barrier to superintelligence. In this paper, we present Self-play SWE-RL (SSR), a first step toward training superintelligent software agents under minimal data assumptions. SSR requires only access to sandboxed repositories with source code and dependencies, no need for human-labeled issues or test commands. Grounded in real-world codebases, a single LLM agent is trained via RL in a self-play setting to inject and repair increasingly complex bugs. The bugs are formally specified by test suite improvements proposed by the agent rather than natural language issue descriptions. On the SWE-bench Verified and SWE-Bench Pro benchmarks, SSR achieves clear self-improvement (+10.4 and +7.8 points) and consistently outperforms the human-data baseline throughout training, generalizing to natural language bug descriptions not seen in training. Overall, our results point toward a paradigm where agents autonomously gather extensive learning experiences from real software repositories, ultimately enabling superintelligent systems that exceed human capabilities in understanding, modifying, and creating software from scratch.

Poster
Incomplete Multi-View Clustering via Neighborhood-Conditioned Diffusion

Qian Guo, Gaohui Zuo, Bingbing Jiang, Guangrui Fan, Zhihua Cui, Xinyan Liang, Jianjian Ding

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Incomplete multi-view clustering (IMVC) aims to uncover shared clustering structures from heterogeneous views with partial observations. Recently, existing generative IMVC methods have made significant progress in this field; however, they still remain limited in two aspects. On the one hand, they rely on weak cross-view signals, resulting in unstable latent recovery when facing missing data. On the other hand, they overlook stable cross-view neighborhood structures, leading to weak structural constraint. To address these limitations, we propose neighborhood-conditioned diffusion for incomplete multi-view clustering (IMVC-NCD), which achieves robust latent completion. Our method learns compact view-specific latent representations and constructs a unified conditioning vector by aggregating stable local neighborhood structures from available views while encoding missingness states, providing reliable guidance for diffusion-based denoising. With neighborhood-level conditioning, IMVC-NCD produces semantically aligned and view-consistent latent representations that are well suited for clustering, even under high missing-view ratios. Extensive experiments on four benchmark datasets demonstrate the effectiveness and robustness of our method compared with state-of-the-art IMVC approaches. Our code is available at https://github.com/zgh1115/IMVC-NCD.

Poster
Efficiently Solving Discounted MDPs via Predictions with Unknown Prediction Errors

Lixing Lyu, Jiashuo Jiang, Wang Chi Cheung

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We study infinite-horizon discounted Markov decision processes (DMDPs) under a generative model. Motivated by the Algorithms with Advice framework (Mitzenmacher and Vassilvitskii, 2022), we propose a novel framework to investigate how black-box predictions of the transition matrix can enhance sample efficiency in solving DMDPs and improve sample complexity bounds. We focus on DMDPs with $N$ state–action pairs and discount factor $\gamma$. We first provide an impossibility result showing that, in the presence of predictions with unknown accuracy, no sampling policy can compute an $\epsilon$-optimal policy with a sample complexity better than $\tilde{O}((1-\gamma)^{-3} N \epsilon^{-2})$, which matches the state-of-the-art minimax sample complexity bound without prediction. In complement, we design an algorithm based on minimax optimization techniques that leverages predictions of the transition matrix without requiring knowledge of the prediction error. Our algorithm achieves a sample complexity bound that depends on the prediction error and is uniformly better than $\tilde{O}((1-\gamma)^{-4} N \epsilon^{-2})$, the previous best result derived from convex optimization methods. In some cases, our bound even improves upon the state-of-the-art $\tilde{O}((1-\gamma)^{-3} N \epsilon^{-2})$, despite not having access to the prediction quality.

Poster
InfraRL: A Benchmark for Constrained Resource Allocation in Large-Scale Infrastructure Asset Management

Yantian Wang, Wenhao Li, Bo Jin

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Optimizing maintenance strategies for large-scale infrastructure is a critical sequential decision-making problem. While Reinforcement Learning (RL) offers a theoretical framework for such problems, practical deployment necessitates offline constrained RL—learning policies solely from static historical datasets under rigid budgetary limits without dangerous on-policy exploration. However, current research is hindered by benchmarks that fail to capture the confluence of distributional shift and hard constraints typical of real-world assets. We introduce InfraRL, a high-fidelity benchmark that uses bridge maintenance as a rigorous testbed for general infrastructure asset management challenges. Constructed from the U.S. National Bridge Inventory, InfraRL defines a rigorous offline task for optimizing maintenance strategies under hard budgetary constraints. We benchmark a diverse suite of baselines, ranging from industry-standard heuristics to single-agent, multi-agent, planning-based, and constrained offline RL methods. Through a comprehensive evaluation protocol, we analyze performance across structural utility, constraint adherence, and behavioral fidelity, revealing critical trade-offs between safety and long-term efficiency. Our code and data are available at https://github.com/BriSky-2021/InfraRL.

Poster
Learning to Approximate Uniform Facility Location via Graph Neural Networks

Chendi Qian, Christopher Morris, Stefanie Jegelka, Christian Sohler

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Neural networks, particularly message-passing neural networks (MPNNs), are increasingly used as heuristics for hard combinatorial optimization problems. Yet many learning-based methods rely on supervision, reinforcement learning, or gradient estimators, causing high computational cost, unstable training, or limited guarantees. Classical approximation algorithms provide worst-case guarantees but are non-differentiable and cannot adapt to structure in natural input distributions. We study this tradeoff through Uniform Facility Location (UniFL), a problem with applications in clustering, summarization, logistics, and supply chains. We propose a fully differentiable MPNN that incorporates approximation-algorithmic principles without solver supervision or discrete relaxations. The model has provable approximation guarantees and empirically improves on standard approximation algorithms, narrowing the gap to integer linear programming.

Poster
DTKG: Dual-Track Knowledge Graph-Verified Reasoning Framework for Multi-Hop QA

Changhao Wang, Yanfang Liu, Xinxin Fan, Ao Tian, Lanzhi Zhou, Yunfeng Lu

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Multi-hop reasoning for question answering (QA) plays a critical role in retrieval-augmented generation (RAG) for large language models (LLMs). Based on inherent relation-dependency and reasoning patterns, it is categorized into parallel fact-verification (simultaneously verifying independent sub-questions) and chained reasoning (sequential multi-step inference). Existing approaches adopt either LLM-based fact verification or KG path-based chain construction, failing to handle both categories well: the former underperforms on chained reasoning, while the latter suffers from redundant paths in parallel tasks. Inspired by the Dual Process Theory in cognitive science and Stanovich’s Cognitive Misers Theory, we propose an effective multi-hop QA framework DTKG (Dual-Track Knowledge Graph) through building a two-stage pipeline: i) Classification Stage (dynamic question categorization via few-shot prompting, emulating "unconscious processing"); and ii) Branch Processing Stage (tailored reasoning paths, emulating "conscious processing"). Multi-facet experiments on six datasets show DTKG achieves 5.0\%-29.5\% performance improvement. The code is available at https://anonymous.4open.science/r/DTKG-621F

Poster
SceneDirector: Bridging Explicit Geometry and Generative Priors for Unified Driving Scene Editing

Yiyuan Liang, Zhiying Yan, Tao Zhang, Shangke Liu, Kai Lin, Xu Zou, Nong Sang, Changxin Gao

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Validating autonomous driving systems requires diverse scenarios, yet real-world data collection is biased and costly. Editing existing driving logs offers a scalable solution, but simultaneously editing objects and ego-trajectory—termed unified editing—remains challenging. Current methods face an inherent dilemma: generative flexibility for object editing and physical precision for trajectory control. To address this, we introduce SceneDirector, a diffusion-based framework that bridges explicit geometry and generative priors. For explicit geometry, we leverage LiDAR-guided depth completion to construct dense scene geometry and integrate editable 3D assets to form a Unified Geometric Scaffold, providing rigorous structural guidance for unified editing. To leverage generative priors, we encode the source video into a Static Texture Bank to provide rich appearance context. Our proposed Mask-Gated Reference Attention bridges these modalities. Guided by a geometric uncertainty metric, this mechanism dynamically regulates the interaction between the scaffold and the bank—preserving reliable geometry while adaptively injecting textures for semantic refinement. Extensive evaluations demonstrate that SceneDirector outperforms state-of-the-art methods in both controllability and visual quality.

Poster
FOCA: Future-Oriented Conditioning for Data-Efficient Vision-Language-Action Adaptation

Minh Duc Nguyen, Nghiem Tuong Diep, Nguyen Gia Binh, Trong-Bao Ho, Doanh Le Thien, Quang Tan Nguyen, Thien-Loc Ha, Tran Van Nhiem, Bao Thach, Tran Xuan Nhat, Tuan Anh Tran, Artur Habuda, Philip Lund Møller, Tran Nguyen Le, Daniel Sonntag, Mathias Niepert, Khoa D Doan, Vu N. Duong, Hung Ngo, Minh Nhat VU, Duy Minh Ho Nguyen, An Thai Le, Vien Anh Ngo

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Vision–Language–Action (VLA) models enable general-purpose robotic control via large-scale multimodal pretraining, yet their effectiveness under few-shot imitation learning remains limited. We conduct a systematic stress test of state-of-the-art VLA models and show that performance degrades sharply as demonstrations are reduced, revealing a key weakness of existing adaptation strategies. To address this, we introduce FOCA, a future-oriented conditioning framework for data-efficient VLA adaptation. FOCA combines explicit prediction of task-grounded future interaction embeddings with implicit alignment to future goal observations, enabling long-horizon reasoning in latent space without pixel-level prediction. This formulation naturally supports action-free co-training with synthetic videos from video world models and can be interpreted as learning a future-conditioned value-like representation. Extensive experiments demonstrate FOCA achieves 95.7\% success with 20 demonstrations on LIBERO, improves 7–12\% on RoboCasa, and delivers up to 26\% absolute gains on real robots, establishing a new state of the art in few-shot VLA adaptation.

Poster
Numina-Lean-Agent: An Open and General Agentic Reasoning System for Formal Mathematics

Junqi Liu, Zihao Zhou, Zekai Zhu, Marco Dos Santos, Weikun He, Jiawei Liu, Yunzhou Xie, Junqiao Zhao, Qiufeng Wang, Lihong Zhi, Jia Li, Wenda Li

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Agentic systems have recently become the dominant paradigm for formal theorem proving, achieving strong performance by coordinating multiple models and tools. However, existing approaches often rely on task-specific pipelines and trained formal provers, limiting their flexibility and reproducibility. In this paper, we propose the paradigm that directly uses a general coding agent as a formal math reasoner. This paradigm is motivated by (1) A general coding agent provides a natural interface for diverse reasoning tasks beyond proving, (2) Performance can be improved by simply replacing the underlying base model, without training., and (3) MCP enables flexible extension and autonomous calling of specialized tools, avoiding complex design. Based on this paradigm, we introduce \textbf{Numina-Lean-Agent}, which combines Claude Code with Numina-Lean-MCP to enable autonomous interaction with Lean, retrieval of relevant theorems, informal proving and auxiliary reasoning tools. Using Claude Opus 4.5 as the base model, Numina-Lean-Agent solves all problems in Putnam 2025 (12/12), matching the best closed-source system. Beyond benchmark evaluation, we further demonstrate its generality by interacting with mathematicians to successfully formalize the Brascamp–Lieb theorem.

Poster
WinDeskGround: A Benchmark for Robust GUI Grounding in Complex Multi-Window Desktop Environments

Haoren Zhao, Tianyi Chen, Zhen Wang

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Multimodal Large Language Models (MLLMs) have revolutionized GUI automation, yet their efficacy is largely established on idealized, single-layer interfaces. This paper identifies a critical reliability gap: state-of-the-art agents face distinct robustness challenges in real-world desktop environments characterized by multi-window stacking, occlusion, and visual clutter. To address this, we introduce WinDeskGround, a novel benchmark and synthesis framework tailored for evaluating GUI grounding robustness. Unlike static datasets, our framework parametrically generates complex desktop scenarios by controlling window occlusion, layout density, and semantic similarity, thereby simulating the distribution shifts of authentic workflows. We construct a diverse meta-dataset of 1,356 high-fidelity instruction-target pairs and conduct comprehensive evaluations of five leading MLLMs. Our results demonstrate that while top-tier agents excel in simplified settings, their accuracy declines under partial occlusion. WinDeskGround provides a valuable benchmark to facilitate the assessment and advancement of GUI agent robustness in realistic environments.

Poster
DyLLM: Efficient Diffusion LLM Inference via Saliency-based Token Selection and Partial Attention

Younjoo Lee, Seungkyun Dan, Junghoo Lee, Jaiyoung Park, Jung Ho Ahn

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Masked diffusion language models enable parallel token decoding, providing a promising alternative to the sequential nature of autoregressive generation. However, their iterative denoising process remains computationally expensive because it repeatedly processes the entire sequence at every step. We observe that across these diffusion steps, most token representations remain stable; only a small subset, which we term *salient tokens*, contributes meaningfully to the next update. Leveraging this temporal sparsity, we present **DyLLM**, a training-free inference framework that accelerates decoding by selectively computing only these salient tokens. DyLLM identifies saliency by measuring the cosine similarity of attention contexts between adjacent denoising steps. It recomputes feed-forward and attention operations only for salient tokens while reusing cached activations for the remainder. Across diverse reasoning and code-generation benchmarks, DyLLM achieves up to 9.6 $\times$ higher throughput while largely preserving the baseline accuracy of representative open-source diffusion LLMs, LLaDA and Dream.

Poster
PRISM: Training-Free Video Anomaly Detection via Intrinsic Statistical Modeling

YUANTONG CHEN, Zhengyan Ding, YanFeng Shang

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While recent training-free video anomaly detection (VAD) methods offer advantages such as interpretability and ease of deployment, they often suffer from computational inefficiency due to complex memory retrieval mechanisms or high-latency visual-language models (VLMs). To address this issue, we propose PRISM (Parameter-less Recognition Based on Intrinsic Statistical Modeling), a novel framework for efficient open-set anomaly detection with minimal computational cost. Built on a pre-trained multimodal embedding model, PRISM introduces differential amplification and whitening mechanisms to statistically suppress common-mode background noise in the embedding space, thereby improving the signal-to-noise ratio of anomalous events. Extensive experiments on three widely datasets demonstrate that PRISM achieves state-of-the-art performance among training-free methods while maintaining real-time inference capability. Furthermore, our statistical analysis offers a complementary perspective on why training-free methods may suffer from lower Average Precision (AP) on complex datasets such as XD-Violence.Code is released at https://github.com/ytC2026/ICML2026-PRISM.

Poster
ACO-MoE-LoRA: Evolving-while-Training for Adapting Segment Anything Model 2 to Specialized Domains

Kaiyi Luo, Bangjun Wang, Li Zhang, Fanzhang Li, Fei Zhu, Jiaqing Fan

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Static fine-tuning paradigms impose rigid structural constraints on foundation models like the Segment Anything Model 2 (SAM2), limiting their adaptability to the varying complexity of specialized downstream tasks. To overcome this limitation, we propose **ACO-MoE-LoRA**, a dynamic framework that introduces an "Evolving-while-Training" strategy by synergizing Ant Colony Optimization (ACO) with a Latent Space Mixture-of-Experts (MoE) architecture. Central to our method is the ACO-ConvLoRA module, which employs a pheromone-guided routing mechanism to actively govern expert selection and topological evolution. By formulating expert assignment as an evolutionary pathfinding problem, this module effectively mitigates the standard routing collapse issue and enables elastic adjustment of LoRA ranks via weight slicing, bridging discrete structural search with continuous parameter training. Extensive experiments across 16 challenging datasets demonstrate that our framework consistently outperforms leading static adapters, while effectively addressing the local optimality limitations of recent dynamic heuristics. This work presents a self-organizing solution that harmonizes swarm intelligence with gradient optimization for efficiently adapting foundation models to specialized domains.

Poster
Solving Time-Dependent Differential Equations with Physical Dynamical Systems

Chuan Liu, Yijie CHEN, Ruibing Song, Wenhao Huang, Chunshu Wu, Deqian Kong, Ying Nian Wu, Kaiyuan Yang, Ang Li, Tony Geng

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Time-Dependent Differential Equations (TDDEs) model dynamical processes across science and engineering, but time-critical applications require solvers that deliver high-fidelity trajectories under stringent latency constraints. Most existing TDDE solvers are limited by time discretization, forcing a latency-accuracy trade-off where smaller step sizes capture high-fidelity trajectories but incur prohibitive runtime, while larger steps meet real-time budgets at the cost of trajectory distortion. Dynamical System Machines (DSMs) offer a promising alternative by computing through continuous physical evolution, yet existing DSMs struggle to capture the spatiotemporal complexity of TDDEs. This work introduces DS-TS, a novel TDDE solver that is both accurate and efficient by leveraging the unique computational advantages of DSMs. DS-TS integrates three key innovations: (1) Excitatory-Inhibitory Inspired Coupling to better model complex spatial interactions; (2) State-aware Dynamic Nonlinearity to enable rich inter-node interactions and state-dependent spatiotemporal correlations; and (3) Hierarchical Temporal Integration to capture high-order temporal dependencies. Experiments demonstrate that DS-TS achieves high-fidelity solutions while delivering orders-of-magnitude improvements in speed ($\sim 10^3\times$) and energy efficiency ($\sim 10^5\times$) compared to baseline solvers.

Spotlight
Supervised Graph Contrastive Learning for Gene Regulatory Networks

Sho Oshima, Yuji Okamoto, Taisei Tosaki, Ryosuke Kojima

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Graph Contrastive Learning (GCL) is a powerful self-supervised learning framework that performs data augmentation through graph perturbations, with growing applications in the analysis of biological networks such as Gene Regulatory Networks (GRNs). The artificial perturbations commonly used in GCL, such as node dropping, induce structural changes that can diverge from biological reality. This concern has contributed to a broader trend in graph representation learning toward augmentation-free methods, which view such structural changes as problematic and should be avoided. However, this trend overlooks the fundamental insight that structural changes from biologically meaningful perturbations are not a problem to be avoided, but rather a rich source of information, thereby ignoring the valuable opportunity to leverage data from real biological experiments. Motivated by this insight, we propose SupGCL (Supervised Graph Contrastive Learning), a new GCL method for GRNs that directly incorporates biological perturbations from gene knockdown experiments as supervision. SupGCL is a probabilistic formulation that continuously generalizes conventional GCL, linking artificial augmentations with real perturbations measured in knockdown experiments, and using the latter as explicit supervision. On patient-derived GRNs from three cancer types, we train GRN representations with SupGCL and evaluate it in two regimes: (i) embedding space analysis, where it yields clearer disease-subtype structure and improves clustering, and (ii) task-specific fine-tuning, where it consistently outperforms strong graph representation learning baselines on 13 downstream tasks spanning gene-level functional annotation and patient-level prediction.

Poster