ICML 2026 论文列表

Bottleneck states, which connect distinct regions of the state space, provide a principled and interpretable basis for constructing temporal abstractions in Hierarchical Reinforcement Learning (HRL). However, existing bottleneck identification methods primarily rely on topological analysis of the state-transition graph, limiting their scalability to high-dimensional or continuous domains. To address this challenge, we introduce Value Power Strength (VPS), a value function-based metric inspired by the analogy between the Bellman equation and Kirchhoff’s current law, to quantify bottleneck property via the diffusion of reward in Markov Decision Processes (MDPs). VPS is estimated efficiently using value functions learned from random reward signals and captures reward diffusion bottlenecks in both discrete and continuous state spaces. Leveraging VPS, we design options that guide agents toward or away from bottleneck regions. Experimental results on classic tabular domains, continuous-control PointMaze, and Atari 2600 games demonstrate that the VPS-based framework discovers semantically meaningful subgoals and substantially improves exploration efficiency.

Data markets promise to unlock data value by matching data suppliers with ML consumers. However, market design involves addressing intricate challenges, including data pricing, fairness, and robustness. We propose a pragmatic data-augmented AutoML market that seamlessly integrates with existing cloud-based AutoML platforms, such as Google’s Vertex AI. Unlike standard AutoML solutions, our design automatically augments buyer-submitted training data with valuable external datasets, pricing the resulting models based on their measurable performance improvements rather than computational costs as the status quo. Our key innovation is a pricing mechanism grounded in the instrumental value—the marginal model quality improvement—of externally sourced data. This approach bypasses direct dataset pricing complexities and accommodates diverse buyer valuations through menu-based options, thus providing an economically sustainable framework for monetizing external data.

Randomized linear algebra (RLA) algorithms are a modern class of numerical linear algebra techniques that play an essential role in scientific computing and machine learning, with broad and growing adoption. However, their discovery remains mostly a manual process that requires deep expert knowledge and inspiration. While Reinforcement Learning (RL) offers a pathway to automation, standard approaches struggle with sparse reward landscapes and vast search spaces inherent to high-performing RLA algorithms. In this paper, we present RL4RLA, a general RL framework that automates the discovery of interpretable, symbolic RLA algorithms. Unlike black-box approaches, our method builds explicit algorithms from basic linear algebra primitives, ensuring verifiable and implementable representations. To enable efficient discovery, we introduce: (1) a numerical curriculum that progressively increments problem difficulty to encode inductive bias specific to the RLA domain; (2) Monte Carlo Graph Search, which optimizes exploration by identifying and merging equivalent partial algorithms. We demonstrate that RL4RLA rediscovers state-of-the-art methods, including sketch-and-precondition solvers, Randomized Kaczmarz, and Newton Sketch, and can be targeted to produce algorithms optimized for specific trade-offs between accuracy, speed, and stability. Code is available at https://github.com/Tim-Xiong/RL4RLA.

Disentangled representation learning is a powerful paradigm for robust attribute prediction. While recent methods address attribute correlations, hidden correlations remain underexplored, where data under the value of a certain attribute exhibit underlying modes correlated with other attributes. To preserve mode information and achieve disentanglement, we jointly discover modes and enforce mode-based conditional independence. Yet, the interdependency between these two modules may lead to error amplification under naive iterations. We propose Coordinated Disentanglement with Iterative mode Discovery (CoDID), an end-to-end framework featuring a dynamic architecture that adapts to evolving number of modes, and a coordination mechanism that mitigates error amplification via meta-optimization. Empirical results demonstrate the state-of-the-art performance on diverse tasks.

Classical sample complexity bounds for causal structure learning are minimax in nature, characterizing worst-case difficulty without distinguishing between easy and hard instances. We study instance-specific complexity for Markov equivalence class (MEC) recovery in linear Gaussian structural equation models. We introduce the Fisher dimension, defined as the inverse squared minimum partial correlation that must be detected to recover the MEC. We prove that the Fisher dimension governs sample complexity: it provides both a lower bound and an upper bound (tight up to logarithmic factors) for MEC recovery. A key theoretical finding is that under spectrally well-conditioned models, with bounded noise variances, bounded covariance eigenvalues, and constant-order edge coefficients, the Fisher dimension is uniformly bounded regardless of graph structure. Thus, significant instance-specific variation arises from parametric rather than structural features. Empirical validation shows strong correlation between our predictor and observed sample complexity for structured graph families.

While large language models (LLMs) show promise in scientific discovery, existing research focuses on inference or feedback-driven training, leaving the direct modeling of the generative reasoning process, $P(\text{hypothesis}|\text{background})$ ($P(h|b)$), unexplored. We demonstrate that directly training $P(h|b)$ is mathematically intractable due to the combinatorial complexity ($O(N^k)$) inherent in retrieving and composing inspirations from a vast knowledge base. To break this barrier, we introduce MOOSE-Star, a unified framework that enables tractable and scalable training of $P(h|b)$, while supporting more scalable inference. In the best case, MOOSE-Star reduces complexity from exponential to logarithmic ($O(\log N)$) by (1) training on decomposed subtasks derived from the probabilistic equation of discovery, (2) employing motivation-guided hierarchical search to enable logarithmic retrieval and prune irrelevant subspaces, and (3) utilizing bounded composition for robustness against retrieval noise. To facilitate this, we release TOMATO-Star, a dataset of 108,717 decomposed papers (38,400 GPU hours) for training. Empirically, MOOSE-Star scales continuously with training data and inference budget, whereas direct brute-force sampling hits a "complexity wall."

Unsupervised skill discovery (USD) aims to learn diverse behaviors without reward functions, but often results in task-irrelevant or hazardous behaviors due to uniform exploration. Guided skill discovery (GSD) addresses this issue by incorporating human intent to focus exploration on meaningful regions. However, existing GSD methods typically require training additional guidance models, and rely on pre-defined rules or expert demonstration, which can be ineffective under sparse, online-collected human feedback. To overcome this, we propose COLLIE, a GSD framework that leverages dense unsupervised data to construct a semantically coherent skill latent space. This latent space is well-structured, enabling reliable guidance with sparse online feedback. Moreover, its semantic coherence property enables training-free construction of guidance signals, eliminating the need for additional model training beyond skill learning. Theoretical analysis justifies the effectiveness of our training-free guidance signal, while experiments across diverse state-based and pixel-based tasks show that COLLIE learns diverse, human-aligned skills, avoids hazardous behaviors, and achieves superior downstream performance with minimal human feedback.

Protein language models (pLMs) have emerged as powerful predictors of protein structure and function. However, the computational circuits underlying their predictions remain poorly understood. Recent mechanistic interpretability methods decompose pLM representations into interpretable features, but they treat each layer independently and thus fail to capture cross-layer computation, limiting their ability to approximate the full model. We introduce ProtoMech, a framework for discovering computational circuits in pLMs using cross-layer transcoders that learn sparse latent representations jointly across layers to capture the model’s full computational circuitry. Applied to the pLM ESM2, ProtoMech recovers 82–89\% of the original performance on protein family classification and function prediction tasks. ProtoMech then identifies compressed circuits that use <1\% of the latent space while retaining up to 79\% of model accuracy, revealing correspondence with structural and functional motifs, including binding, signaling, and stability. Steering along these circuits enables high-fitness protein design, surpassing baseline methods in more than 70\% of cases. These results establish ProtoMech as a principled framework for protein circuit tracing.

AI for scientific discovery is entering an agentic era, where protein-engineering systems are expected to prioritize future wet-lab experiments rather than merely fit static measurements. We introduce TadA-Bench, a million-variant wet-lab replay benchmark from 31 TadA directed-evolution rounds for future-round discovery toward agentic protein engineering. TadA-Bench preserves the campaign chronology and defines a fixed-data replay task: given earlier experimental rounds, models rank variants that appear only in later rounds. It provides aligned DNA, RNA, and protein views, and uses Seq2Graph, a graph-based label-unification pipeline, to reconcile noisy enrichment measurements into consistent cross-round activity labels. Random-split controls show strong interpolation, but future-round ranking and finite-budget candidate selection are much weaker. Controlled analyses suggest that evolutionary coverage is more informative than local data density, positioning TadA-Bench as a reproducible wet-lab replay substrate for future-round discovery toward agentic protein engineering; the data and code are released on Hugging Face and GitHub.

Generalized Category Discovery (GCD) aims to learn semantically structured representations for discovering novel categories in unlabeled data using supervision from known classes. Most existing methods rely on self-supervised contrastive learning (CL) with consistency and uniformity objectives. We identify an inherent optimization conflict between these objectives: while uniformity enforces global feature dispersion, it can hinder the formation of class-discriminative and semantically coherent structures. To address this issue, we propose a two-stage framework that decouples representation learning from self-contrastive regularization. The first stage learns category-anchored representations aligned with known class prototypes, while the second stage extends the representation space to novel categories via a consistency objective enhanced with unified semantic regularization. We further introduce a Semantic Exploration Energy mechanism to capture shared semantics across categories and mitigate information loss caused by prototype orthogonalization. The resulting framework, termed *Consistency-under-Unified Semantic Regularization*(**CURE**), achieves state-of-the-art performance on multiple benchmarks and substantially reduces the performance gap between known and novel categories.

Although causal discovery from multivariate time series is widely used, it remains challenging under noise. Convergent cross mapping (CCM) infers causality by reconstructing shadow manifolds via time-delay embedding (TDE) and evaluating cross-map skill between manifolds. Despite Takens’ theorem guarantees in ideal settings, TDE effectively attempts to recover system state from a single noisy view, often yielding geometrically degraded manifolds and unreliable distance-based neighborhoods, which in turn weakens causal identification. We propose TopoDistill, a topology-informed knowledge distillation framework that improves univariate shadow-manifold reconstruction by aligning local neighborhood structure to a multivariate system representation. A global embedder trained on multivariate observations captures a global attractor representation, while a delay embedder is distilled to produce embeddings whose neighborhood distributions match the global topology. This cross-view alignment yields smoother and more reliable neighborhoods, improving cross mapping under noise while maintaining specificity against spurious correlations. Theoretical analysis and experimental results demonstrate that our method enables effective causal discovery.

Modern cloud systems rely on architectures with many interconnected microservices, which enable scalability and flexibility but make troubleshooting failures difficult. Identifying the root cause requires navigating complex dependencies, often beyond the capacity of domain experts. Causal models offer a principled approach to root cause analysis (RCA), but prior methods are typically sample inefficient, as they assume access to the full causal graph or require large numbers of post-failure interventions. We introduce Bayesian Root Cause Discovery (BRCD), which leverages a partial causal structure (a CPDAG learned during the pre-failure period) and performs Bayesian inference without enumerating all DAGs from each interventional Markov equivalence class ($\mathcal{I}$-MEC) for each root cause candidate. Using a recent uniform DAG sampling framework (Wienöbst et al., 2023), BRCD provides the first statistical consistency guarantees for nonparametric RCA, with both identifiability and finite-sample posterior bounds under $\varepsilon$-vanishing approximation. Empirically, across synthetic benchmarks and three microservice systems (Online Boutique, Sockshop, Petshop), BRCD achieves state-of-the-art top-$l$ accuracy while remaining effective in low-failure-sample regimes and scaling to large graphs.

While state-of-the-art language models (LMs) surpass the vast majority of humans in certain domains, their reasoning remains largely opaque, reducing trust and risking deception and hallucination. In this work, we introduce the Prototype Transformer (ProtoT)—an autoregressive LM architecture that replaces the quadratic-cost self-attention in the transformer with a linear-cost module based on prototypes (parameter vectors). In ProtoT, the prototypes create communication channels aggregating contextual information at different time scales. We show that this leads to the prototypes automatically capturing nameable concepts (e.g. “woman”) during training, and it provides the potential to interpret the model’s reasoning and do targeted edits of its behavior. Compared to baselines, ProtoT scales well with model and data size, shows robustness to input perturbations, and performs well on text generation and downstream tasks (GLUE). These results suggest that ProtoT is a promising step toward autoregressive language models that are more interpretable by design.

Large Language Model (LLM)-based scientific agents have accelerated scientific discovery, yet they often suffer from significant inefficiencies due to adherence to fixed initial priors. Existing approaches predominantly operate within a static hypothesis space, which restricts the discovery of novel phenomena, resulting in computational waste when baseline theories fail. To address this, we propose shifting the focus from searching hypotheses to evolving the underlying scientific principles. We present $\textbf{PiEvo}$, a principle-evolvable framework that treats scientific discovery as Bayesian optimization over an expanding principle space. By integrating Information-Directed Hypothesis Selection via Gaussian Process and an anomaly-driven augmentation mechanism, PiEvo enables agents to autonomously refine their theoretical worldview. Evaluation across four benchmarks demonstrates that PiEvo (1) achieves an average solution quality of up to 90.81\%$\sim$93.15\%, representing a 29.7\%$\sim$31.1\% improvement over the state-of-the-art, (2) attains an 83.3\% speedup in convergence step via significantly reduced sample complexity by optimizing the compact principle space, and (3) maintains robust performance across diverse scientific domains and LLM backbones. Code is publicly available at github.com/amair-lab/PiEvo.

Polypharmacology provides a powerful strategy for treating complex diseases, but identifying molecules that simultaneously satisfy coupled constraints across multiple biological targets remains difficult. Existing methods typically model protein pockets in isolation and struggle to jointly account for multiple heterogeneous binding sites when designing a single shared ligand. To address these limitations, we propose a pocket-structure-centric generative framework for polypharmacology. This framework introduces a novel protein topological representation that selectively masks ligand-irrelevant residues while explicitly modeling backbone folding geometry and inter-residue spatial proximity within binding pockets. In addition, structural representations are jointly fused with amino acid and nucleotide sequences to capture their complementary information across targets. Experiments on COVID-19, schizophrenia, and tumor targets show that this framework generates valid candidates with significantly improved binding affinities compared to state-of-the-art methods.

Constraint-based causal discovery relies on conditional independence (CI) tests whose reliability degrades as conditioning sets grow, particularly in hub-dominated graphs. Existing methods constrain adjacency or global structure, but leave conditioning-set dimensionality uncontrolled. In this paper, we propose Ordering-Constrained Markov Blanket discovery (OCMB), a paradigm that treats conditioning-set dimensionality as a first-class constraint. OCMB decouples discovery into two stages: lightweight global ordering estimation providing directional priors, followed by local Markov blanket validation within small, ordering-constrained candidate sets. By enforcing directional constraints before any CI test, OCMB ensures bounded conditioning sets even with hub nodes. We show that OCMB recovers correct parent sets provided a high-recall ordering assumption holds, without requiring the ordering to be globally correct. Experiments demonstrate that OCMB significantly improves precision and robustness over constraint-based and hybrid methods in high-dimensional regimes where conventional CI-based approaches fail.

Inferring the structure of directed acyclic graphs (DAGs) from data is a central challenge in causal discovery, particularly in modern high-dimensional settings where large-scale interventional data are increasingly available. While interventional data can improve identifiability, existing methods remain limited by soft acyclicity constraints, leading to optimization over invalid cyclic graphs, numerical instability, and reduced scalability. We introduce PACER (Perturbation-driven Acyclic Causal Edge Recovery), a scalable framework for causal discovery that guarantees acyclicity by construction. PACER parameterizes a distribution over DAGs through a joint model of variable permutations and edge probabilities, enabling direct optimization over valid causal structures without surrogate penalties. The framework supports a unified likelihood-based treatment of observational and interventional data, flexible conditional density models, and the incorporation of structural prior knowledge. For linear-Gaussian mechanisms, we derive closed-form expressions for the expected interventional log-likelihood and its gradients, yielding substantial computational gains. Empirically, PACER matches or exceeds state-of-the-art methods on protein signaling and large-scale genetic perturbation benchmarks, while scaling efficiently to networks with thousands of variables and achieving up to two orders of magnitude speedups over penalty-based differentiable approaches. These results demonstrate that exact and scalable causal discovery from high-dimensional perturbation data is achievable through principled search space design.

When reliable target structures are unavailable at scale or phenotypes arise from dysregulated pathways, transcriptomic perturbations provide a system-level functional readout for drug action. In this work, we formalize Transcriptome-based Drug Design (TBDD) as a generative inverse problem: designing drug molecules conditioned on desired transcriptomic state transitions. We analyze the inherently ill-posed nature of this task, which is further complicated by the profound domain gap between biology and chemistry and by the sparsity of transcriptomic signals. To address these challenges, we propose CURE (A CellUlar Response Engine), a multi-resolution transcriptome-guided diffusion framework. CURE features a specialized Transcriptome Perturbation Functional Feature Extractor (TFE) that (1) distills function-oriented perturbation embeddings from pre/post states, (2) aligns these signatures to dual chemical views to bridge the cross-modal gap, and (3) performs heterogeneity-aware aggregation to extract robust state-specific signals from noisy transcriptomic data. Extensive evaluations on both standard benchmarks and rigorous out-of-distribution protocols demonstrate that CURE consistently outperforms strong baselines in structural quality and functional consistency. Furthermore, we validate its practical utility via a zero-shot gene-inhibitor design task, highlighting the potential of phenotype-driven generative discovery.

Make-on-demand combinatorial synthesis libraries (CSLs) like Enamine REAL have significantly enabled drug discovery efforts. However, their large size presents a challenge for virtual screening, where the goal is to identify the top compounds in a library according to a computational objective (e.g., optimizing docking score) subject to computational constraints under a limited computational budget. For current library sizes---numbering in the tens of billions of compounds---and scoring functions of interest, a routine virtual screening campaign may be limited to scoring fewer than 0.1% of the available compounds, leaving potentially many high scoring compounds undiscovered. Furthermore, as constraints (and sometimes objectives) change during the course of a virtual screening campaign, existing virtual screening algorithms typically offer little room for amortization. We propose the approximate-but-exhaustive search protocol for CSLs, or APEX. APEX utilizes a neural network surrogate that exploits the structure of CSLs in the prediction of objectives and constraints to make full enumeration on a consumer GPU possible in under a minute, allowing for exact retrieval of approximate top-k sets. To demonstrate APEX's capabilities, we develop a benchmark CSL comprised of more than 10 million compounds, all of which have been annotated with their docking scores on five medically relevant targets along with physicohemical properties measured with RDKit such that, for any objective and set of constraints, the ground truth top-k compounds can be identified and compared against the retrievals from any virtual screening algorithm. We show APEX's consistently strong performance both in retrieval accuracy and runtime compared to alternative methods.