ICLR 2026 Papers

International Conference on Learning Representations

Decision breakdown

5,358papers

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

  • Oral
    2244.2%
  • Poster
    5,13495.8%

Browse all papers

Understanding Transformers for Time Series: Rank Structure, Flow-of-ranks, and Compressibility

Annan Yu, Danielle C. Maddix, Boran Han, Xiyuan Zhang, Abdul Fatir Ansari, Oleksandr Shchur, Christos Faloutsos, Andrew Gordon Wilson, Michael W. Mahoney, Bernie Wang

Expand abstract

Transformers are widely used across data modalities, and yet the principles distilled from text models often transfer imperfectly. In this paper, we analyze Transformers through the lens of rank structure. Our focus is on the time series setting, where the structural properties of the data remarkably differ from those of text or vision. Time-series embeddings, unlike text or vision, exhibit sharply decaying singular spectra: small patch sizes and smooth continuous mappings concentrate the data into low-rank subspaces. From this, we prove that the associated $Q/K/V$ projections admit accurate low-rank approximations, and that attention layers become compressible in proportion to the decay of the embedding spectrum. We introduce the concept of *flow-of-ranks*, a mechanism by which nonlinear mixing across depth inflates the rank, explaining why early layers are most amenable to compression and why rank schedules should grow with depth. Guided by these results, we compress Chronos, a large time series foundation model, achieving a reduction of $65\\%$ in inference time and $81\\%$ in memory without loss of accuracy. These findings provide principled guidance for allocating width, depth, and heads in time series foundation models, and for exploiting their inherent compressibility.

Poster
Navigating the Accuracy-Size Trade-Off with Flexible Model Merging

Akash Dhasade, Divyansh Jhunjhunwala, Milos Vujasinovic, Gauri Joshi, Anne-Marie Kermarrec

Expand abstract

Model merging has emerged as an efficient method to combine multiple single-task fine-tuned models. The merged model can enjoy multi-task capabilities without expensive training. While promising, merging into a single model often suffers from an accuracy gap with respect to individual fine-tuned models. On the other hand, deploying all individual fine-tuned models incurs high storage costs. We propose FlexMerge, a novel data-free model merging framework that: (a) flexibly generates merged models of varying sizes, spanning the full spectrum from a single merged model to retaining all individual fine-tuned models; and (b) supports multiple merging algorithms in a unified framework. Using FlexMerge, we systematically characterize the accuracy–size trade-off of different algorithms. Our study reveals two key findings: first, even modestly larger merged models can yield steep accuracy gains (up to 13.5% when just doubling the size); second, algorithm rankings are not consistent as size increases, with some methods overtaking others beyond the one-model regime. These results uncover a new design dimension for model merging: developing and comparing algorithms across the full spectrum of sizes rather than only at the single-model limit. Extensive experiments on vision and NLP benchmarks, with up to 30 tasks, confirm the generality and practicality of FlexMerge.

Poster
Reliable Probabilistic Forecasting of Irregular Time Series through Marginalization-Consistent Flows

Vijaya Krishna Yalavarthi, Randolf Scholz, Christian Klötergens, Kiran Madhusudhanan, Stefan Born, Lars Schmidt-Thieme

Expand abstract

Probabilistic forecasting of joint distributions for irregular time series with missing values is an underexplored area in machine learning. Existing models, such as Gaussian Process Regression and ProFITi, are limited: while ProFITi is highly expressive due to its use of normalizing flows, it often produces unrealistic predictions because it lacks marginalization consistency—marginal distributions of subsets of variables may not match those predicted directly, leading to inaccurate marginal forecasts when trained on joints. We propose MOSES (Mixtures of Separable Flows), a novel model that parametrizes a stochastic process via a mixture of normalizing flows, where each component combines a latent multivariate Gaussian with separable univariate transformations. This design allows MOSES to be analytically marginalized, enabling accurate and reliable predictions for various probabilistic queries. Experiments on four datasets show that MOSES achieves highly accurate joint and marginal predictions. Thanks to its inherent marginalization consistency, MOSES significantly outperforms all baselines—including ProFITi—on marginal predictions. For joint predictions, it beats all other consistent models and performs close to or slightly worse than ProFITi.

Poster
PairFlow: Closed-Form Source-Target Coupling for Few-Step Generation in Discrete Flow Models

Mingue Park, Jisung Hwang, Seungwoo Yoo, Kyeongmin Yeo, Minhyuk Sung

Expand abstract

We introduce $\texttt{PairFlow}$, a lightweight preprocessing step for training Discrete Flow Models (DFMs) to achieve few-step sampling without requiring a pretrained teacher. DFMs have recently emerged as a new class of generative models for discrete data, offering strong performance. However, they suffer from slow sampling due to their iterative nature. Existing acceleration methods largely depend on finetuning, which introduces substantial additional training overhead. $\texttt{PairFlow}$ addresses this issue with a lightweight preprocessing step. Inspired by ReFlow and its extension to DFMs, we train DFMs from coupled samples of source and target distributions, without requiring any pretrained teacher. At the core of our approach is a closed-form inversion for DFMs, which allows efficient construction of paired source–target samples. Despite its extremely low cost, taking only up to 1.7\% of the compute needed for full model training, $\texttt{PairFlow}$ matches or even surpasses the performance of two-stage training involving finetuning. Furthermore, models trained with our framework provide stronger base models for subsequent distillation, yielding further acceleration after finetuning. Experiments on molecular data as well as binary and RGB images demonstrate the broad applicability and effectiveness of our approach.

Poster
ASSESS: A Semantic and Structural Evaluation Framework for Statement Similarity

Xiaoyang Liu, Tao Zhu, Zineng Dong, Yuntian Liu, Guo qingfeng, Liu ZhaoXuan, Yu Chen, Tao Luo

Expand abstract

Despite significant strides in statement autoformalization, a critical gap remains in the development of automated evaluation metrics capable of assessing formal translation quality. Existing metrics often fail to balance semantic and structural information: string-based methods neglect semantics, whereas proof-based approaches offer no graded similarity when proofs fail. To address these issues, we introduce ASSESS (A Semantic and Structural Evaluation Framework for Statement Similarity), which captures syntactic structure by transforming formal statements into operator trees and computes a real-valued similarity score using our novel TransTED (Transformation Tree Edit Distance) Similarity metric by incorporating semantic transformations. For rigorous validation, we present EPLA (Evaluating Provability and Likeness for Autoformalization), a benchmark comprising 1,247 expert-annotated formal statement pairs derived from miniF2F and ProofNet, distinctively labeled for both semantic provability and structural likeness. Experiments on the EPLA benchmark demonstrate that TransTED Similarity surpasses existing methods, achieving state-of-the-art accuracy and Kappa score. The benchmark dataset, code, and detailed experimental results are available at https://github.com/XiaoyangLiu-sjtu/ASSESS.

Poster
New Hybrid Fine-Tuning Paradigm for LLMs: Algorithm Design and Convergence Analysis Framework

Shaocong Ma, Peiran Yu, Heng Huang

Expand abstract

Fine-tuning Large Language Models (LLMs) typically involves either full fine-tuning, which updates all model parameters, or Parameter-Efficient Fine-Tuning (PEFT), which adjusts a small subset of parameters. However, both approaches have inherent limitations: full fine-tuning is computationally expensive, while PEFT often struggles to learn new knowledge and exhibits suboptimal performance. To overcome these issues, we propose a novel *hybrid fine-tuning* approach that jointly updates both LLMs and PEFT modules using a combination of zeroth-order and first-order optimization methods. To analyze our new algorithm, we develop a theoretical framework centered on the concept of *hybrid smoothness condition*, which accounts for the heterogeneous nature of the optimization landscape in joint LLM and PEFT training. We derive a rigorous convergence analysis for the convergence of reshuffling-type SGD algorithm under multiple learning rates and demonstrate its effectiveness through extensive empirical studies across various downstream tasks and model architectures. On the practical side, our results demonstrate consistent performance improvement, making the approach a viable solution for large-scale language model fine-tuning.

Poster
Interp3D: Correspondence-aware Interpolation for Generative Textured 3D Morphing

Xiaolu Liu, Yicong Li, Qiyuan He, Jiayin Zhu, Wei Ji, Angela Yao, Jianke Zhu

Expand abstract

Textured 3D morphing seeks to generate smooth and plausible transitions between two 3D assets, preserving both structural coherence and fine-grained appearance. This ability is crucial not only for advancing 3D generation research but also for practical applications in animation, editing, and digital content creation. Existing approaches either operate directly on geometry, limiting them to shape-only morphing while neglecting textures, or extend 2D interpolation strategies into 3D, which often causes semantic ambiguity, structural misalignment, and texture blurring. These challenges underscore the necessity to jointly preserve geometric consistency, texture alignment, and robustness throughout the transition process. To address this, we propose \textbf{Interp3D}, a novel training-free framework for textured 3D morphing. It harnesses generative priors and adopts a progressive alignment principle to ensure both geometric fidelity and texture coherence. Starting from semantically aligned interpolation in condition space, Interp3D enforces structural consistency via SLAT (Structure Latent)-guided structure interpolation, and finally transfers appearance details through fine-grained texture fusion. For comprehensive evaluations, we construct a dedicated dataset, Interp3DData, with graded difficulty levels and assess generation results from fidelity, transition smoothness, and plausibility. Both quantitative metrics and human studies demonstrate the significant advantages of our proposed approach over previous methods. Our code will be made publicly available.

Poster
FastVGGT: Fast Visual Geometry Transformer

You Shen, Zhipeng Zhang, Yansong Qu, Xiawu Zheng, Jiayi Ji, Shengchuan Zhang, Liujuan Cao

Expand abstract

Scaling visual geometry transformers for long image sequences poses a significant computational and memory challenge. In this work, we diagnose this issue in the state-of-the-art model VGGT, and trace the primary bottleneck to its Global Attention layer. Our analysis reveals a ``token collapse'' phenomenon, where many tokens attend to nearly identical regions, resulting in redundant computation and inefficiency. Motivated by this finding, we propose FastVGGT, a training-free framework that strategically prunes these redundant tokens. Instead of uniform merging, FastVGGT employs a tailored, three-part token partitioning strategy. It preserves initial-frame tokens as a stable global reference, retains salient tokens to maintain fine details, and utilizes region-based random sampling to ensure spatially balanced coverage. Extensive experiments on multiple 3D geometry benchmarks validate our approach's effectiveness. Notably, on sequences of 1000 images, FastVGGT achieves a 4$\times$ speedup over the original VGGT while simultaneously mitigating error accumulation, demonstrating its efficiency and robustness for long-sequence scenarios. For further details, please visit our project page: https://fastvggt.github.io/.

Poster
Contextual Similarity Distillation: Ensemble Uncertainties with a Single Model

Moritz Akiya Zanger, Pascal R. Van der Vaart, Wendelin Boehmer, Matthijs T. J. Spaan

Expand abstract

Uncertainty quantification is a critical aspect of reinforcement learning and deep learning, with numerous applications ranging from efficient exploration and stable offline reinforcement learning to outlier detection in medical diagnostics. The scale of modern neural networks, however, complicates the use of many theoretically well-motivated approaches such as full Bayesian inference. Approximate methods like deep ensembles can provide reliable uncertainty estimates but still remain computationally expensive. In this work, we propose contextual similarity distillation, a novel approach that explicitly estimates the variance of an ensemble of deep neural networks with a single model, without ever learning or evaluating such an ensemble in the first place. Our method builds on the predictable learning dynamics of wide neural networks, governed by the neural tangent kernel, to derive an efficient approximation of the predictive variance of an infinite ensemble. Specifically, we reinterpret the computation of ensemble variance as a supervised regression problem with kernel similarities as regression targets. The resulting model can estimate predictive variance at inference time with a single forward pass, and can make use of unlabeled target-domain data or data augmentations to refine its uncertainty estimates. We empirically validate our method across a variety of out-of-distribution detection benchmarks and sparse-reward reinforcement learning environments. We find that our single-model method performs competitively and sometimes superior to ensemble-based baselines and serves as a reliable signal for efficient exploration. These results, we believe, position contextual similarity distillation as a principled and scalable alternative for uncertainty quantification in reinforcement learning and general deep learning.

Poster
RayI2P: Learning Rays for Image-to-Point Cloud Registration

Xinjun Li, Wenfei Yang, Zhixin Cheng, Jiacheng Deng, Fei Wang, Chen Qian, Tianzhu Zhang

Expand abstract

Image-to-point cloud registration aims to estimate the 6-DoF camera pose of a query image relative to a 3D point cloud map. Existing methods fall into two categories: matching-free methods regress pose directly using geometric priors, but lack fine-grained supervision and struggle with precise alignment; matching-based methods construct dense 2D-3D correspondences for PnP-based pose estimation, but are fundamentally limited by projection ambiguity (where multiple geometrically distinct 3D points project to the same image patch, leading to ambiguous feature representations) and scale inconsistency (where fixed-size image patches correspond to 3D regions of varying physical size, causing misaligned receptive fields across modalities). To address these issues, we propose a novel ray-based registration framework that first predicts patch-wise 3D ray bundles connecting image patches to the 3D scene and then estimates camera pose via a differentiable ray-guided regression module, bypassing the need for explicit 2D-3D correspondences. This formulation naturally resolves projection ambiguity, provides scale-consistent geometry encoding, and enables fine-grained supervision for accurate pose estimation. Experiments on KITTI and nuScenes show that our approach achieves state-of-the-art registration accuracy, outperforming existing methods.

Poster
Decoupled Q-Chunking

Qiyang Li, Seohong Park, Sergey Levine

Expand abstract

Bootstrapping bias problem is a long-standing challenge in temporal-difference (TD) methods in off-policy reinforcement learning (RL). Multi-step return backups can alleviate this issue but require delicate importance sampling to correct their off-policy bias. Recent work has proposed to use chunked critics, which estimate the value of short action sequences ("chunks") rather than individual actions, enabling unbiased multi-step backup. However, extracting policies from chunked critics is challenging: policies must output the entire action chunk open-loop, which can be sub-optimal in environments that require policy reactivity and also challenging to model especially when the chunk length grows. Our key insight is to decouple the chunk length of the critic from that of the policy, allowing the policy to operate over shorter action chunks. We propose a novel algorithm that achieves this by optimizing the policy against a distilled critic for partial action chunks, constructed by optimistically backing up from the original chunked critic to approximate the maximum value achievable when a partial action chunk is extended to a complete one. This design retains the benefits of multi-step value propagation while sidestepping both the open-loop sub-optimality and the difficulty of learning policies over long action chunks. We evaluate our method on challenging, long-horizon offline goal-conditioned benchmarks and show that it reliably outperforms prior methods.

Poster
CE-Nav: Flow-Guided Reinforcement Refinement for Cross-Embodiment Local Navigation

Kai Yang, Tianlin Zhang, Zhengbo Wang, Zedong Chu, Xiaolong Wu, Yang Cai, Mu Xu

Expand abstract

Generalizing local navigation policies across diverse robot morphologies is a critical challenge. Progress is often hindered by the need for costly and embodiment-specific data, the tight coupling of planning and control, and the "disastrous averaging" problem where deterministic models fail to capture multi-modal decisions (e.g., turning left or right). We introduce CE-Nav, a novel two-stage (IL-then-RL) framework that systematically decouples universal geometric reasoning from embodiment-specific dynamic adaptation. First, we train an embodiment-agnostic General Expert offline using imitation learning. This expert, a conditional normalizing flow model named VelFlow, learns the full distribution of kinematically-sound actions from a large-scale dataset generated by a classical planner, completely avoiding real robot data and resolving the multi-modality issue. Second, for a new robot, we freeze the expert and use it as a guiding prior to train a lightweight, Dynamics-Aware Refiner via online reinforcement learning. This refiner rapidly learns to compensate for the target robot's specific dynamics and controller imperfections with minimal environmental interaction. Extensive experiments on quadrupeds, bipeds, and quadrotors show that CE-Nav achieves state-of-the-art performance while drastically reducing adaptation cost. Successful real-world deployments further validate our approach as an efficient and scalable solution for building generalizable navigation systems.

Poster
VER: Vision Expert Transformer for Robot Learning via Foundation Distillation and Dynamic Routing

Yixiao Wang, Mingxiao Huo, Zhixuan Liang, Yushi Du, Lingfeng Sun, Haotian Lin, Jinghuan Shang, Chensheng Peng, Mohit Bansal, Mingyu Ding, Masayoshi Tomizuka

Expand abstract

Pretrained vision foundation models (VFMs) advance robotic learning via rich visual representations, yet individual VFMs typically excel only in specific domains, limiting generality across tasks. Distilling multiple VFMs into a unified representation can mitigate this limitation but often yields inflexible task-specific feature selection and requires costly full retraining to incorporate robot-domain knowledge. We propose VER, a Vision Expert transformer for Robot learning. During pretraining, VER distills multiple VFMs into a vision expert library. We then fine-tune only a lightweight routing network (fewer than 0.4% of parameters) to dynamically select task-relevant experts from the pretrained library for downstream robot tasks. We further introduce Patchwise Expert Routing with Curriculum Top-K Annealing to improve both flexibility and precision of dynamic expert selection. Moreover, VER supports parameter-efficient finetuning for scalable expert utilization and robot-domain knowledge integration. Across 17 diverse robotic tasks and multiple policy heads, VER achieves state-of-the-art performance. We find that VER reduces large-norm outliers in task-irrelevant regions (e.g., background) and concentrates on task-critical regions. Code and checkpoints are available in the supplementary materials.

Poster
SPEED: Scalable, Precise, and Efficient Concept Erasure for Diffusion Models

Ouxiang Li, Yuan Wang, Xinting Hu, Houcheng Jiang, Tao Liang, Yanbin Hao, Guojun Ma, Fuli Feng

Expand abstract

Erasing concepts from large-scale text-to-image (T2I) diffusion models has become increasingly crucial due to the growing concerns over copyright infringement, offensive content, and privacy violations. In scalable applications, fine-tuning-based methods are time-consuming to precisely erase multiple target concepts, while real-time editing-based methods often degrade the generation quality of non-target concepts due to conflicting optimization objectives. To address this dilemma, we introduce SPEED, an efficient concept erasure approach that directly edits model parameters. SPEED searches for a null space, a model editing space where parameter updates do not affect non-target concepts, to achieve scalable and precise erasure. To facilitate accurate null space optimization, we incorporate three complementary strategies: Influence-based Prior Filtering (IPF) to selectively retain the most affected non-target concepts, Directed Prior Augmentation (DPA) to enrich the filtered retain set with semantically consistent variations, and Invariant Equality Constraints (IEC) to preserve key invariants during the T2I generation process. Extensive evaluations across multiple concept erasure tasks demonstrate that SPEED consistently outperforms existing methods in non-target preservation while achieving efficient and high-fidelity concept erasure, successfully erasing 100 concepts within only 5 seconds.

Poster
Poly-attention: a general scheme for higher-order self-attention

Sayak Chakrabarti, Toniann Pitassi, Josh Alman

Expand abstract

The self-attention mechanism, at the heart of the transformer model, is able to effectively model pairwise interactions between tokens. However, numerous recent works have shown that it is unable to perform basic tasks involving detecting triples of correlated tokens, or compositional tasks where multiple input tokens need to be referenced to generate a result. Some higher-dimensional alternatives to self-attention have been proposed to address this, including higher-order attention (Sanford et al., 2023) and Strassen attention (Kozachinskiy et al., 2025), which can perform some of these polyadic tasks in exchange for slower, superquadratic running times. In this work, we define a vast class of generalizations of self-attention, which we call poly-attention mechanisms. Our mechanisms can incorporate arbitrary higher-order (tensor) computations as well as arbitrary relationship structures between the input tokens, and they include the aforementioned alternatives as special cases. We then systematically study their computational complexity and representational strength, including giving new algorithms and matching complexity-theoretic lower bounds on the time complexity of computing the attention matrix exactly as well as approximately, and tightly determining which polyadic tasks they can each perform. Our results give interesting tradeoffs between different desiderata for these mechanisms, including a tight relationship between how expressive a mechanism is, and how large the coefficients in the model may be so that the mechanism can be approximated in almost-linear time. Notably, we give a new attention mechanism which can be computed exactly in quadratic time, and which can perform function composition for any fixed number of functions. Prior mechanisms, even for just composing two functions, could only be computed in superquadratic time, and our new lower bounds show that faster algorithms for them are not possible.

Poster
TimeSeg: An Information-Theoretic Segment-Wise Explainer for Time-Series Predictions

Hwijin Kim, Jaeho Kim, Changhee Lee

Expand abstract

Explaining predictions of black-box time-series models remains a challenging problem due to the dynamically evolving patterns within individual sequences and their complex temporal dependencies. Unfortunately, existing explanation methods largely focus on point-wise explanations, which fail to capture broader temporal context, while methods that attempt to highlight interpretable temporal patterns (e.g., achieved by incorporating a regularizer or fixed-length patches) often lack principled definitions of meaningful segments. This limitation frequently leads to fragmented and confusing explanations for end users. As such, the notion of segment-wise explanations has remained underexplored, with little consensus on what constitutes an *interpretable* segment or how such segments should be identified. To bridge this gap, we define segment-wise explanation for black-box time-series models as the task of selecting contiguous subsequences that maximize their joint mutual information with the target prediction. Building on this formulation, we propose TimeSeg, a novel information-theoretic framework that employs reinforcement learning to sequentially identify predictive temporal segments at a per-instance level. By doing so, TimeSeg produces segment-wise explanations that capture holistic temporal patterns rather than fragmented points, providing class-predictive patterns in a human-interpretable manner. Extensive experiments on both synthetic and real‑world datasets demonstrate that TimeSeg produces more coherent and human-understandable explanations, while achieving performance that matches or surpasses existing methods on downstream tasks using the identified segments.

Poster
PCPO: Proportionate Credit Policy Optimization for Preference Alignment of Image Generation Models

Jeongjae Lee, Jong Chul Ye

Expand abstract

While reinforcement learning has advanced the alignment of text-to-image (T2I) models, state-of-the-art policy gradient methods are still hampered by training instability and high variance, hindering convergence speed and compromising image quality. Our analysis identifies a key cause of this instability: disproportionate credit assignment, in which the mathematical structure of the generative sampler produces volatile and non-proportional feedback across timesteps. To address this, we introduce Proportionate Credit Policy Optimization (PCPO), a framework that enforces proportional credit assignment through a stable objective reformulation and a principled reweighting of timesteps. This correction stabilizes the training process, leading to significantly accelerated convergence and superior image quality. The improvement in quality is a direct result of mitigating model collapse, a common failure mode in recursive training. PCPO substantially outperforms existing policy gradient baselines on all fronts, including the state-of-the-art DanceGRPO.

Poster
Compositional Neuro-Symbolic Concepts in Neural Activities

Yanchen Wang, Joy Hsu, Ehsan Adeli, Jiajun Wu

Expand abstract

We propose NEURONA, a modular neuro-symbolic framework for fMRI decoding and concept grounding in neural activity. Leveraging image- and video-based fMRI question-answering datasets, NEURONA learns to decode interacting concepts from visual stimuli from patterns of fMRI signals, integrating symbolic reasoning and compositional execution with fMRI grounding across brain regions. We demonstrate that incorporating structure into the decoding pipeline improves both decoding accuracy and generalization performance. NEURONA shows that modeling the compositional structure of concepts through hierarchical predicate-argument dependencies enables more precise decoding from fMRI, highlighting neuro-symbolic frameworks as promising tools for neural decoding.

Poster
Self-Jailbreaking: Language Models Can Reason Themselves Out of Safety Alignment After Benign Reasoning Training

Zheng-Xin Yong, Stephen Bach

Expand abstract

We discover a novel and surprising phenomenon of unintentional misalignment in reasoning language models (RLMs), which we call \textit{self-jailbreaking}. Specifically, after benign reasoning training on math or code domains, RLMs will use multiple strategies to circumvent their own safety guardrails. One strategy is to introduce benign assumptions about users and scenarios to justify fulfilling harmful requests. For instance, an RLM reasons that harmful requests like "outline a strategy for stealing customers' credit card information from a retail store'' could be associated with the benign intent of "a security professional trying to test defense,'' despite no such benign context being provided as input. We observe that many open-weight RLMs, including DeepSeek-R1-distilled, s1, Phi-4-mini-reasoning, and Nemotron, suffer from self-jailbreaking despite being aware of the harmfulness of the requests. We also provide a mechanistic interpretation of self-jailbreaking: RLMs are more compliant after benign reasoning training, and self-jailbreaking reduces the perceived harmfulness of malicious requests so models can comply with them. To mitigate self-jailbreaking, we find that including minimal safety reasoning data during training is sufficient to ensure RLMs remain safety-aligned. Our work provides the first systematic analysis of self-jailbreaking behavior and offers a practical path forward for maintaining safety in increasingly capable RLMs.

Poster
h-MINT: Modeling Pocket-Ligand Binding with Hierarchical Molecular Interaction Network

Yanru Qu, Yijie Zhang, Wenjuan Tan, Xiangzhe Kong, Xiangxin Zhou, Chaoran Cheng, Mathieu Blanchette, Jiaxuan You, Ge Liu

Expand abstract

Accurate molecular representations are critical for drug discovery, and a central challenge lies in capturing the chemical environment of molecular fragments, as key interactions, such as H-bond and π stacking—occur only under specific local conditions. Most existing approaches represent molecules as atom-level graphs; however, individual atoms cannot express stereochemistry, lone pairs, conjugation, and other complex features. Fragment-based methods (e.g., principal subgraph or functional group libraries) fail to preserve essential information such as chirality, aromatic bond integrity, and ionic states. This work addresses these limitations from two aspects. (i) **OverlapBPE tokenization**. We propose a novel data-driven molecule tokenization method. Unlike existing approaches, our method allows overlapping fragments, reflecting the inherently fuzzy boundaries of small-molecule substructures and, together with enriched chemical information at the token level, thereby preserving a more complete chemical context. (ii) **h- MINT model**. We develop a hierarchical molecular interaction network capable of jointly modeling drug–target interactions at both atom and fragment levels. By supporting fragment overlaps, the model naturally accommodates the many-to- many atom–fragment mappings introduced by the OverlapBPE scheme. Extensive evaluation against state-of-the-art methods shows our method improves binding affinity prediction by 2-4% Pearson/Spearman correlation on PDBBind and LBA, enhances virtual screening by 1-3% in key metrics on DUD-E and LIT-PCBA, and achieves the best overall HTS performance on PubChem assays. Further analysis demonstrates that our method effectively captures interactive information while maintaining good generalization.

Poster