ICML 2026 Papers

Function-guided protein design is a crucial task with significant applications in drug discovery and enzyme engineering. However, the field lacks a unified and comprehensive evaluation framework. Current models are assessed using inconsistent and limited subsets of metrics, which prevents fair comparison and a clear understanding of the relationships between different evaluation criteria. To address this gap, we introduce **PDFBench**, the first comprehensive benchmark for function-guided de novo protein design. Our benchmark systematically evaluates eight state-of-the-art models on 16 metrics across two key settings: description-guided design, for which we repurpose the Mol-Instructions dataset, originally lacking quantitative benchmarking, and keyword-guided design, for which we introduce a new test set, SwissTest, created with a strict datetime cutoff to ensure data integrity. By benchmarking across a wide array of metrics and analyzing their correlations, **PDFBench** enables more reliable model comparisons and provides key insights to guide future research.

Real-world machine learning (ML) pipelines rarely produce a single model; instead, they produce a Rashomon set of many near-optimal ones. We show that this multiplicity reshapes key aspects of trustworthiness. At the individual-model level, sparse interpretable models tend to preserve privacy but are fragile to adversarial attacks. In contrast, the diversity within a large Rashomon set enables reactive robustness: even when an attack compromises one model, a practitioner can switch to a different near-optimal model that remains accurate, without retraining. However, the same diversity increases information leakage, as disclosing more near-optimal models provides an attacker with progressively richer views of the training data. This produces a robustness–privacy trade-off governed by diversity, which we analyze theoretically and empirically. Beyond this trade-off, Rashomon sets are stable under small distribution shifts, so a set computed once remains valid under such shifts without re-computation. Our results highlight the dual role of Rashomon sets as both a resource and a risk for trustworthy ML.

Differentially private optimization suffers from a fundamental geometric mismatch: deep networks have highly anisotropic loss landscapes, yet DP-SGD injects isotropic noise. Second-order preconditioning can resolve this, but estimating curvature typically requires private data (consuming privacy budget) or public data (introducing distribution shift). We show that the Fisher Information Matrix decouples into *architectural sensitivity*, recoverable via synthetic noise, and *input correlations*, approximable from modality-specific frequency statistics. We propose DP-KFC, which constructs KFAC preconditioners by probing networks with structured synthetic noise, requiring neither private nor public data. Empirically, DP-KFC consistently outperforms DP-SGD and adaptive baselines across diverse modalities in strong privacy regimes ($\varepsilon \leq 3$). DP-KFC matches private-data preconditioners while public-data variants degrade by up to $4.8$ %, showing that curvature can be estimated without consuming privacy budget or introducing distribution shift. This enables privacy-preserving learning in specialized domains (e.g., medical applications) where regulatory constraints make data scarce.

Large language models (LLMs) are increasingly deployed in high-stakes domains, where free-text explanations such as chain-of-thought and post-hoc rationales are used to justify model outputs. Yet it remains unclear whether these explanations are _sufficient_, i.e., if they contain enough information to explain the model’s output-generating process. We generalize classical sufficiency from feature attributions to arbitrary explanations and prove that explanation sufficiency can change depending on the input distribution, which must be explicitly defined for LLM explanations. We propose using the LLM itself to generate alternative inputs conditioned on an explanation, capturing its beliefs about possible inputs. We formalize _self-consistent sufficiency_ as a goal for free-text explanations and introduce an information-theoretic metric, SCSuff, that enables evaluation of free-text explanations without relying on predefined biases or shortcuts. Our experiments show that SCSuff agrees with targeted perturbation tests where applicable and demonstrate that explanation sufficiency can vary with the input distribution. We find LLM explanations are generally insufficient and weakly correlated with model size, accuracy, or output entropy. Analysis of final-token hidden states shows that top and bottom SCSuff scores can be predicted from internal representations, suggesting that SCSuff can guide detection and improvement of sufficient LLM explanations. The code for this paper is available at https://github.com/rajesh-lab/self-consistent-sufficiency.

While neural representations are central to modern deep learning, the conditions governing their geometry and their roles in downstream adaptability remain poorly understood. We develop a framework clearly separating the underlying world, the data generation process and the resulting model representations to study these questions in a controlled setup: 5,075 city coordinates define the world and 7 geometric tasks generate the training data for autoregressive Transformer training. We find that different tasks give rise to qualitatively and quantitatively distinct world representation geometries. However, multi-task training drives convergence of world representations: models trained on non-overlapping tasks develop aligned geometric representations, providing controlled evidence for the Multitask Scaling Hypothesis of the Platonic Representation Hypothesis. To study adaptation, we pretrain models on all tasks and all cities, then test whether new entities can be consistently integrated into the representation space via fine-tuning. Surprisingly, we find that despite multi-task pretraining, some tasks, which we call divergent, actively harm the representational integration of new entities. Our results show that training on multiple relational tasks reliably produces convergent world representations, but some lurking divergent tasks can catastrophically harm new entity integration via fine-tuning.

Discrete Flow Matching (DFM) presents a promising approach for graph generation; however, existing adaptations often introduce substantial complexity by incorporating task-specific heuristics, compromising the continuity equation and significantly expanding the hyperparameter space. Moreover, their sampling efficiency remains limited, as the required number of steps is often comparable to diffusion models, diminishing DFM’s practical advantages. To address these limitations, we propose SimGFM, a simplified graph DFM for graph generation. Leveraging characteristic patterns in graph-generation trajectories, SimGFM relies only on the scheduler and rate matrix, eliminating heavy heuristics and hyperparameter tuning, and achieves large step reductions while preserving SOTA results. SimGFM achieves strong empirical results: on QM9, it matches prior models requiring 500–1000 steps with only 10 steps, and on most datasets, its performance at 50 steps matches or surpasses these baselines, demonstrating both efficiency and competitiveness. Our source code is available at https://github.com/LUOyk1999/SimGFM.

Autonomous 3D indoor scene synthesis breaks down in non-convex rooms with tightly coupled spatial constraints. Data-driven generators lack topological priors for long-horizon planning, while iterative agents fragment semantics and become geometrically brittle. We present \textbf{ZoneMaestro}, a unified framework that shifts the paradigm from object-centric synthesis to Zone-Graph Orchestration. By internalizing a novel zone-based logic, ZoneMaestro translates high-level semantic intent into functional zones and topological constraints, enabling robust adaptation to diverse architectural forms. To support this, we construct \textit{Zone-Scene-10K}, a large-scale dataset enriched with explicit Zone-Graph annotations. We further introduce an \textit{Alternating Alignment Strategy} that cycles between reasoning internalization and Zone-Aware Group Relative Policy Optimization (\textit{Z-GRPO}), effectively reconciling the tension between semantic richness and geometric validity without relying on external physics engines. To rigorously evaluate spatial intelligence beyond convex primitives, we formally define the task of \textbf{Intricate Spatial Orchestration} and release SCALE, a stress-test benchmark for irregular indoor scenarios with complex, dense spatial relations. Extensive experiments demonstrate that ZoneMaestro resolves the density-safety dichotomy, significantly outperforming state-of-the-art baselines in both structural coherence and intent adherence.

In crowdsourcing scenarios, to mitigate the impact of noisy labels assigned by non-expert workers, each instance is typically annotated multiple times by different workers. However, repeated annotation can introduce instance- or label-level redundancy, thereby inflating annotation costs. Despite its practical importance, research on repeated annotation strategies remains limited, and no existing strategy simultaneously avoids being offline, instance-unaware, and model-centric. In this paper, we propose a model-agnostic active annotation strategy, MA$^3$S, that addresses these limitations: (1) To reduce label redundancy caused by offline procedure, MA$^3$S estimates instance uncertainties with a margin-Beta distribution and updates them online as new labels arrive. (2) To prevent instance redundancy induced by instance-unaware designs, MA$^3$S constructs a nearest-neighbor graph to propagate instance uncertainties, reducing repeated annotations of similar instances. (3) To avoid being model-centric, MA$^3$S actively selects instances for annotation based solely on the estimated uncertainties, without relying on model feedback. Extensive experiments on synthetic and real-world datasets demonstrate that MA$^3$S consistently outperforms existing annotation strategies.

Large language models (LLMs) often fail in systematic, model-specific ways under meaning-preserving question rewrites (paraphrases, format changes, benign distractors). In this work, we address this instability by identifying where the model's reasoning process diverges across semantically-equivalent inputs. For each target LLM, we sample multiple solution traces under rewrites and aggregate them into a graph of recurring intermediate steps, which pinpoints where incorrect traces diverge from correct ones. We then generate a small set of semantics-preserving examples that mirror the rewrite patterns most responsible for these divergences, and use them to steer the model (\emph{targeted alternation training}), either via fine-tuning or via in-context learning. Across MMLU-Pro, Big-MATH, and DROP, this yields consistent gains and cross-dataset generalization. On Humanity’s Last Exam, using 200 in-context examples, it improves GPT-5.2 (xhigh) from 35.4\% to 38.1\%, demonstrating that targeted alternation training can materially improve a frontier, API-accessible closed model under realistic access constraints.

PageRank (PR) is a fundamental algorithm in graph machine learning tasks. Owing to the increasing importance of algorithmic fairness, we consider the problem of computing PR vectors subject to various group-fairness criteria based on sensitive attributes of the vertices. At present, principled algorithms for this problem are lacking - some cannot guarantee that a target fairness level is achieved, while others do not feature optimality guarantees. In order to overcome these shortcomings, we put forth a unified in-processing convex optimization framework, termed FairRARI, for tackling different group-fairness criteria in a ``plug and play'' fashion. Leveraging a variational formulation of PR, the framework computes fair PR vectors by solving a strongly convex optimization problem with fairness constraints, thereby ensuring that a target fairness level is achieved. We further introduce three different fairness criteria which can be efficiently tackled using FairRARI to compute fair PR vectors with the same asymptotic time-complexity as the original PR algorithm. Extensive experiments on real-world datasets showcase that FairRARI outperforms existing methods in terms of utility, while achieving the desired fairness levels across multiple vertex groups; thereby highlighting its effectiveness.

We propose Bayesian Forest Thompson Sampling (BFTS), which performs Thompson sampling using arm-wise Bayesian Additive Regression Trees (BART) to model each action's mean reward and generate MCMC-based posterior draws for decision-making. We derive an information-theoretic Bayesian regret bound of order $\widetilde{\mathcal O}(K\sqrt{T})$ for ideal posterior sampling under a correctly specified Bayesian design. Empirically, BFTS achieves competitive regret on nonlinear synthetic benchmarks with near-nominal uncertainty calibration, attains the best average rank across nine OpenML contextual bandit benchmarks, and yields higher estimated policy values than linear, neural, and tree-ensemble baselines in a Drink Less micro-randomized trial case study. Across OpenML benchmarks, BFTS is robust to hyperparameter choices.

While speculative decoding improves inference throughput for multi-batch long-context Large Language Models (LLMs), its efficiency is often limited by a verification bottleneck where Key-Value (KV) cache loading dominates latency. Existing compression methods fail in this regime: static eviction incurs accuracy loss due to saliency shift, while dynamic selection introduces prohibitive computational overhead during the verification path. We propose Dustin, a sparse verification framework designed for long-context speculative decoding. Dustin integrates lookahead signals from the draft model with historical attention from the target model to identify critical tokens with high fidelity across multi-step verification windows. To reduce recomputation latency, this approach further employs a sparse estimation scheme that restricts importance scoring to a minimal subset of attention heads. Evaluations on PG-19 and LongBench with Qwen2.5-72B demonstrate that Dustin achieves a 27.85× speedup in self-attention and a 9.17× end-to-end decoding speedup at a 32k sequence length, all with negligible accuracy degradation.

Class-incremental learning (CIL) requires models to continuously acquire new knowledge while avoiding catastrophic forgetting. While exemplar replay is effective, it raises concerns regarding privacy and storage. Thus, generative replay has emerged as a viable alternative, synthesizing old data using frozen pretrained text-to-image (T2I) models without any extra training. However, we observe that directly mixing synthetic old-class data with real new-class data during incremental training leads to significant performance degradation. This issue stems from a ‘’domain shortcut'', where models rely on domain-discriminative features instead of semantic class cues. To address this, we propose DREAM (Domain-Regularized Exemplar-free Alignment Model), which uses a training-free generator to synthesize old-class data and eliminates domain shortcut via subspace rectification and orthogonal projection, while reinforcing semantic alignment through real-anchored prototype regularization. Extensive experiments on 4 datasets demonstrate that DREAM outperforms existing exemplar-free CIL methods and achieves state-of-the-art performance.

This paper studies a constrained linear best arm identification problem with covariate selection in the fixed-confidence setting, where each arm is evaluated across multiple performance metrics. The mean performance of each metric depends linearly on the feature vectors of both arms and covariates. The goal is to identify the arm with the highest expected value of one targeted metric while ensuring that the means of the remaining metrics stay below specified thresholds for each covariate. We first establish an instance-dependent lower bound on the sample complexity, formulated as a multi-level optimization problem that captures both feasibility and optimality. We then prove that this bound is tight by designing an algorithm that asymptotically matches it. Since the original algorithm is computationally intensive, we develop a relaxed version of the bound through a surrogate optimization problem and derive its convex dual. Using this bound, we propose a duality-based decomposition algorithm that is computationally efficient, updating only two coordinates and performing a single gradient step per iteration. We further show that the algorithm achieves the relaxed bound in theory and demonstrates its practical effectiveness through numerical experiments.

How do we encode numeric values in transformer-based sequence processing, particularly in electronic health record (EHR) data? We systematically compare discrete, continuous, and hybrid value encoding strategies using synthetic arithmetic tasks embedded within real-world EHR data, as well as real-world clinical prediction tasks. Our study reveals trade-offs between numeric precision, optimisation stability, and architectural flexibility. We find that approaches that explicitly model value-concept interactions perform best on precision-sensitive arithmetic tasks when architectural constraints permit. Hybrid token-based approaches that retain numeric values but apply binning prior to projection provide a more robust and broadly applicable alternative, with the optimal number of bins following a simple empirically derived power-law in dataset size. Across tasks, models consistently exhibit reliable “good enough” numeric computation rather than exact arithmetic, while clinical gains from incorporating laboratory values are task-dependent. This suggests that robustness and deployability often outweigh maximal numeric precision in practice, motivating hybrid token-based approaches as a practical default.

Online Continual Learning (OCL) aims to learn from endless non\text{-}stationary data streams, yet most existing methods assume a flat label space and overlook the hierarchical organization of real\text{-}world concepts that evolves both horizontally (sibling classes) and vertically (coarse or fine categories). To better reflect this context, we introduce a new problem setting, DHOCL (Online Continual Learning from Dynamic Hierarchies), where taxonomies evolve across granularities and each sample provides supervision at a single hierarchical level. In this setting, we find two fundamental issues: (i) partial supervision under mixed granularities provides only point-wise signals over an evolving path-wise hierarchy, which constrains plasticity and undermines cross-level semantic consistency, and (ii) the dynamically evolving hierarchies induce granularity-dependent interference, destabilizing popular replay and regularization mechanisms and thereby exacerbating catastrophic forgetting. To tackle these issues, we propose HALO (Hierarchical Adaptive Learning with Organized Prototypes), which adaptively combines complementary classification heads, regularized by organized learnable hierarchical prototypes, enabling rapid adaptation, hierarchical consistency, and structured knowledge consolidation as the taxonomy evolves. Extensive experiments on multiple benchmarks demonstrate that HALO consistently outperforms existing methods across hierarchical accuracy, mistake severity, and continual performance.

Traditional instrumental variable (IV) estimators cannot accommodate more treatments than instruments, a limitation that is critical for high-dimensional, unstructured data like clinical treatment pathways. Current practice—applying unsupervised dimension reduction before IV estimation—suffers from substantial omitted treatment bias because the representation learning step ignores the instrument. We propose a novel framework that constructs treatment representations by explicitly incorporating instrumental variables. We prove that this instrument-guided approach ensures the identification of optimal outcome-prediction directions even with limited instruments. Validation on large-scale, semi-synthetic clinical data derived from a major hospital, along with other simulations, shows that our approach significantly outperforms conventional two-stage methods.

Humans often specify tasks incompletely, so assistants must know when and how to ask clarifying questions. However, effective clarification remains challenging in software engineering tasks as not all missing information is equally valuable, and questions must target information users can realistically provide. We study clarification in real software engineering tasks by quantifying which types of information most affect task success and which questions elicit useful responses from simulated users. Using Shapley attribution and distributional comparisons, we identify two key properties of effective clarification: task relevance (which information predicts success) and user answerability (what users can realistically provide). We operationalize these properties as multi-stage reinforcement learning rewards to train CLARITI, an 8B-parameter clarification module, that matches GPT-5’s resolution rate on underspecified issues while generating 41% fewer questions. Our results suggest that grounding reward design in empirical analysis of information impact and user answerability improves clarification efficiency.

Voxel-based 3D object detectors typically discretize the spatial domain using a uniform Cartesian grid, which allocates the same voxel size to both near-range and far-range regions. However, this uniform discretization is suboptimal for small objects such as pedestrians and cyclists, as they occupy only a few voxels and thus struggle to capture fine-grained geometric details. Although increasing the global voxel resolution can alleviate this problem, it inevitably increases substantial memory consumption and computational cost. In this paper, we propose Radial Scaling Voxelization (RSV), a simple yet effective non-uniform discretization strategy that adaptively modulates the effective voxel size based on the radial distance from the LiDAR sensor. Unlike previous cylindrical or polar discretization schemes, RSV preserves the Cartesian grid topology by applying a continuous radial scaling function to the input coordinates before standard voxelization. This operation yields a near-high, far-unchanged resolution pattern, i.e., the effective voxel size becomes finer in near regions, where the geometric structures of small objects are difficult to capture, while remaining nearly unchanged in far regions to avoid unnecessary computational cost. Importantly, RSV is architecture-agnostic and can directly replace the discretization module in any voxel-based detector without modifying the backbone, network design, or training pipeline. Extensive experiments on the KITTI and nuScenes datasets demonstrate that integrating our RSV into several voxel-based baselines consistently enhances small-object detection performance, especially for the Pedestrian and Cyclist categories, while incurring only marginal additional computational overhead. Code is available at https://github.com/Zeoy2020/RadialScalingVoxelization.