ICLR 2025 论文列表

Significant advancements have been achieved in PDE modeling using neural fields. Despite their effectiveness, existing methods rely on global modulation, limiting their ability to reconstruct local details. While spatial modulation with vanilla grid-based representations offers a promising alternative, it struggles with inadequate global information modeling and over-fitting to the training spatial domain. To address these challenges, we propose GridMix, a novel approach that models spatial modulation as a mixture of grid-based representations. GridMix effectively explores global structures while preserving locality for fine-grained modulation. Furthermore, we introduce spatial domain augmentation to enhance the robustness of the modulated neural fields against spatial domain variations. With all these innovations, our comprehensive approach culminates in MARBLE, a framework that significantly advancing the capabilities of neural fields in PDE modeling. The effectiveness of MARBLE is extensively validated on diverse benchmarks encompassing dynamics modeling and geometric prediction.

Spatial Transcriptomics (ST) allows a high-resolution measurement of RNA sequence abundance by systematically connecting cell morphology depicted in Hematoxylin and eosin (H\&E) stained histology images to spatially resolved gene expressions. ST is a time-consuming, expensive yet powerful experimental technique that provides new opportunities to understand cancer mechanisms at a fine-grained molecular level, which is critical for uncovering new approaches for disease diagnosis and treatments. Here, we present $\textbf{Stem}$ ($\underline{\textbf{S}}$pa$\underline{\textbf{T}}$ially resolved gene $\underline{\textbf{E}}$xpression inference with diffusion $\underline{\textbf{M}}$odel), a novel computational tool that leverages a conditional diffusion generative model to enable in silico gene expression inference from H&E stained images. Through better capturing the inherent stochasticity and heterogeneity in ST data, $\textbf{Stem}$ achieves state-of-the-art performance on spatial gene expression prediction and generates biologically meaningful gene profiles for new H&E stained images at test time. We evaluate the proposed algorithm on datasets with various tissue sources and sequencing platforms, where it demonstrates clear improvement over existing approaches. $\textbf{Stem}$ generates high-fidelity gene expression predictions that share similar gene variation levels as ground truth data, suggesting that our method preserves the underlying biological heterogeneity. Our proposed pipeline opens up the possibility of analyzing existing, easily accessible H&E stained histology images from a genomics point of view without physically performing gene expression profiling and empowers potential biological discovery from H&E stained histology images. Code is available at: https://github.com/SichenZhu/Stem.

Despite their successes, deep learning models struggle with tasks requiring complex reasoning and function composition. We present a theoretical and empirical investigation into the limitations of Structured State Space Models (SSMs) and Transformers in such tasks. We prove that one-layer SSMs cannot efficiently perform function composition over large domains without impractically large state sizes, and even with Chain-of-Thought prompting, they require a number of steps that scale unfavorably with the complexity of the function composition. Also, the language of a finite-precision SSM is within the class of regular languages. Our experiments corroborate these theoretical findings. Evaluating models on tasks including various function composition settings, multi-digit multiplication, dynamic programming, and Einstein's puzzle, we find significant performance degradation even with advanced prompting techniques. Models often resort to shortcuts, leading to compounding errors. These findings highlight fundamental barriers within current deep learning architectures rooted in their computational capacities. We underscore the need for innovative solutions to transcend these constraints and achieve reliable multi-step reasoning and compositional task-solving, which is critical for advancing toward general artificial intelligence.

The generative modeling of data on manifolds is an important task, for which diffusion models in flat spaces typically need nontrivial adaptations. This article demonstrates how a technique called `trivialization' can transfer the effectiveness of diffusion models in Euclidean spaces to Lie groups. In particular, an auxiliary momentum variable was algorithmically introduced to help transport the position variable between data distribution and a fixed, easy-to-sample distribution. Normally, this would incur further difficulty for manifold data because momentum lives in a space that changes with the position. However, our trivialization technique creates a new momentum variable that stays in a simple fixed vector space. This design, together with a manifold preserving integrator, simplifies implementation and avoids inaccuracies created by approximations such as projections to tangent space and manifold, which were typically used in prior work, hence facilitating generation with high-fidelity and efficiency. The resulting method achieves state-of-the-art performance on protein and RNA torsion angle generation and sophisticated torus datasets. We also, arguably for the first time, tackle the generation of data on high-dimensional Special Orthogonal and Unitary groups, the latter essential for quantum problems. Code is available at https://github.com/yuchen-zhu-zyc/TDM.

Diffusion probabilistic models have achieved mainstream success in many generative modeling tasks, from image generation to inverse problem solving. A distinct feature of these models is that they correspond to deep hierarchical latent variable models optimizing a variational evidence lower bound (ELBO) on the data likelihood. Drawing on a basic connection between likelihood modeling and compression, we explore the potential of diffusion models for progressive coding, resulting in a sequence of bits that can be incrementally transmitted and decoded with progressively improving reconstruction quality. Unlike prior work based on Gaussian diffusion or conditional diffusion models, we propose a new form of diffusion model with uniform noise in the forward process, whose negative ELBO corresponds to the end-to-end compression cost using universal quantization. We obtain promising first results on image compression, achieving competitive rate-distortion-realism results on a wide range of bit-rates with a single model, bringing neural codecs a step closer to practical deployment. Our code can be found at https://github.com/mandt-lab/uqdm.

Probing learned concepts in large language models (LLMs) is crucial for understanding how semantic knowledge is encoded internally. Training linear classifiers on probing tasks is a principle approach to denote the vector of a certain concept in the representation space. However, the single vector identified for a concept varies with both data and training, making it less robust and weakening its effectiveness in real-world applications. To address this challenge, we propose an approach to approximate the subspace representing a specific concept. Built on linear probing classifiers, we extend the concept vectors into Gaussian Concept Subspace (GCS). We demonstrate GCS's effectiveness through measuring its faithfulness and plausibility across multiple LLMs with different sizes and architectures. Additionally, we use representation intervention tasks to showcase its efficacy in real-world applications such as emotion steering. Experimental results indicate that GCS concept vectors have the potential to balance steering performance and maintaining the fluency in natural language generation tasks.

To accelerate biochemical research, e.g., drug and protein discovery, molecular representation learning (MRL) has attracted much attention. However, most existing methods follow the closed-set assumption that training and testing data share identical distribution, which limits their generalization abilities in out-of-distribution (OOD) cases. In this paper, we explore designing a new disentangled mechanism for learning generalized molecular representation that exhibits robustness against distribution shifts. And an approach of Concept-Enhanced Feedback Disentanglement (CFD) is proposed, whose goal is to exploit the feedback mechanism to learn distribution-agnostic representation. Specifically, we first propose two dedicated variational encoders to separately decompose distribution-agnostic and spurious features. Then, a set of molecule-aware concepts are tapped to focus on invariant substructure characteristics. By fusing these concepts into the disentangled distribution-agnostic features, the generalization ability of the learned molecular representation could be further enhanced. Next, we execute iteratively the disentangled operations based on a feedback received from the previous output. Finally, based on the outputs of multiple feedback iterations, we construct a self-supervised objective to promote the variational encoders to possess the disentangled capability. In the experiments, our method is verified on multiple real-world molecular datasets. The significant performance gains over state-of-the-art baselines demonstrate that our method can effectively disentangle generalized molecular representation in the presence of various distribution shifts. The source code will be released at https://github.com/AmingWu/MoleculeCFD.

Verifiers or reward models are often used to enhance the reasoning performance of large language models (LLMs). A common approach is the Best-of-N method, where N candidate solutions generated by the LLM are ranked by a verifier, and the best one is selected. While LLM-based verifiers are typically trained as discriminative classifiers to score solutions, they do not utilize the text generation capabilities of pretrained LLMs. To overcome this limitation, we instead propose training verifiers using the ubiquitous next-token prediction objective, jointly on verification and solution generation. Compared to standard verifiers, such generative verifiers (GenRM) can benefit from several advantages of LLMs: they integrate seamlessly with instruction tuning, enable chain-of-thought reasoning, and can utilize additional test-time compute via majority voting for better verification. We demonstrate that GenRM outperforms discriminative, DPO verifiers, and LLM-as-a-Judge, resulting in large performance gains with Best-of-N, namely 5% → 45.3% on algorithmic tasks, 73% → 93.4% on GSM8K, and 28% →44.6% on easy-to-hard generalization on MATH. Furthermore, we find that training GenRM with synthetic verification rationales is sufficient to pick out subtle errors on math problems. Finally, we demonstrate that generative verifiers scale favorably with model size and inference-time compute.

Aggregating data from multiple sources can be formalized as an *Optimal Transport* (OT) barycenter problem, which seeks to compute the average of probability distributions with respect to OT discrepancies. However, in real-world scenarios, the presence of outliers and noise in the data measures can significantly hinder the performance of traditional statistical methods for estimating OT barycenters. To address this issue, we propose a novel scalable approach for estimating the *robust* continuous barycenter, leveraging the dual formulation of the *(semi-)unbalanced* OT problem. To the best of our knowledge, this paper is the first attempt to develop an algorithm for robust barycenters under the continuous distribution setup. Our method is framed as a $\min$-$\max$ optimization problem and is adaptable to *general* cost functions. We rigorously establish the theoretical underpinnings of the proposed method and demonstrate its robustness to outliers and class imbalance through a number of illustrative experiments. Our source code is publicly available at https://github.com/milenagazdieva/U-NOTBarycenters.

Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, current molecular representation learning methods do not provide a comprehensive view of cell states under these perturbations and struggle to remove noise, hindering model generalization. We introduce the Information Alignment (InfoAlign) approach to learn molecular representations through the information bottleneck method in cells. We integrate molecules and cellular response data as nodes into a context graph, connecting them with weighted edges based on chemical, biological, and computational criteria. For each molecule in a training batch, InfoAlign optimizes the encoder's latent representation with a minimality objective to discard redundant structural information. A sufficiency objective decodes the representation to align with different feature spaces from the molecule's neighborhood in the context graph. We demonstrate that the proposed sufficiency objective for alignment is tighter than existing encoder-based contrastive methods. Empirically, we validate representations from InfoAlign in two downstream applications: molecular property prediction against up to 27 baseline methods across four datasets, plus zero-shot molecule-morphology matching. The code and model are available at https://github.com/liugangcode/InfoAlign.

Graph neural networks excel at modeling pairwise interactions, but they cannot flexibly accommodate higher-order interactions and features. Topological deep learning (TDL) has emerged recently as a promising tool for addressing this issue. TDL enables the principled modeling of arbitrary multi-way, hierarchical higher-order interactions by operating on combinatorial topological spaces, such as simplicial or cell complexes, instead of graphs. However, little is known about how to leverage geometric features such as positions and velocities for TDL. This paper introduces E(n)-Equivariant Topological Neural Networks (ETNNs), which are E(n)-equivariant message-passing networks operating on combinatorial complexes, formal objects unifying graphs, hypergraphs, simplicial, path, and cell complexes. ETNNs incorporate geometric node features while respecting rotation, reflection, and translation equivariance. Moreover, being TDL models, ETNNs are natively ready for settings with heterogeneous interactions. We provide a theoretical analysis to show the improved expressiveness of ETNNs over architectures for geometric graphs. We also show how E(n)-equivariant variants of TDL models can be directly derived from our framework. The broad applicability of ETNNs is demonstrated through two tasks of vastly different scales: i) molecular property prediction on the QM9 benchmark and ii) land-use regression for hyper-local estimation of air pollution with multi-resolution irregular geospatial data. The results indicate that ETNNs are an effective tool for learning from diverse types of richly structured data, as they match or surpass SotA equivariant TDL models with a significantly smaller computational burden, thus highlighting the benefits of a principled geometric inductive bias. Our implementation of ETNNs can be found at https://github.com/NSAPH-Projects/topological-equivariant-networks.

The annotation (assigning structural chemical identities) of MS/MS spectra remains a significant challenge due to the enormous molecular diversity in biological samples and the limited scope of reference databases. Currently, the vast majority of spectral measurements remain in the "dark chemical space" without structural annotations. To improve annotation, we propose MADGEN (Mass-spec Attends to De Novo Molecular GENeration), a scaffold-based method for de novo molecular structure generation guided by mass spectrometry data. MADGEN operates in two stages: scaffold retrieval and spectra-conditioned molecular generation starting with the scaffold. In the first stage, given an MS/MS spectrum, we formulate scaffold retrieval as a ranking problem and employ contrastive learning to align mass spectra with candidate molecular scaffolds. In the second stage, starting from the retrieved scaffold, we employ the MS/MS spectrum to guide an attention-based generative model to generate the final molecule. Our approach constrains the molecular generation search space, reducing its complexity and improving generation accuracy. We evaluate MADGEN on three datasets (NIST23, CANOPUS, and MassSpecGym) and evaluate MADGEN's performance with a predictive scaffold retriever and with an oracle retriever. We demonstrate the effectiveness of using attention to integrate spectral information throughout the generation process to achieve strong results with the oracle retriever.

Despite their wide application across various fields, current molecular property prediction models struggle with the challenge of activity cliff, which refers to the situation where molecules with similar chemical structures display remarkable different properties. This phenomenon hinders existing models' ability to learn distinctive representations for molecules with similar chemical structures, and results in inaccurate predictions on molecules with activity cliff. To address this limitation, we first present empirical evidence demonstrating the ineffectiveness of standard training pipelines on molecules with activity cliff. We propose a novel approach that reformulates molecular property prediction as a node classification problem, introducing two innovative tasks at both the node and edge levels to improve learning outcomes for these challenging molecules with activity cliff. Our method is versatile, allowing seamless integration with a variety of base models, whether pre-trained or randomly initialized. Extensive evaluation across different molecular property prediction datasets validate the effectiveness of our approach.

Video generation requires modeling a vast spatiotemporal space, which demands significant computational resources and data usage. To reduce the complexity, the prevailing approaches employ a cascaded architecture to avoid direct training with full resolution latent. Despite reducing computational demands, the separate optimization of each sub-stage hinders knowledge sharing and sacrifices flexibility. This work introduces a unified pyramidal flow matching algorithm. It reinterprets the original denoising trajectory as a series of pyramid stages, where only the final stage operates at the full resolution, thereby enabling more efficient video generative modeling. Through our sophisticated design, the flows of different pyramid stages can be interlinked to maintain continuity. Moreover, we craft autoregressive video generation with a temporal pyramid to compress the full-resolution history. The entire framework can be optimized in an end-to-end manner and with a single unified Diffusion Transformer (DiT). Extensive experiments demonstrate that our method supports generating high-quality 5-second (up to 10-second) videos at 768p resolution and 24 FPS within 20.7k A100 GPU training hours. All code and models are open-sourced at https://pyramid-flow.github.io.

Neural populations exhibit complex recurrent structures that drive behavior, while continuously receiving and integrating external inputs from sensory stimuli, upstream regions, and neurostimulation. However, neural populations are often modeled as autonomous dynamical systems, with little consideration given to the influence of external inputs that shape the population activity and behavioral outcomes. Here, we introduce BRAID, a deep learning framework that models nonlinear neural dynamics underlying behavior while explicitly incorporating any measured external inputs. Our method disentangles intrinsic recurrent neural population dynamics from the effects of inputs by including a forecasting objective within input-driven recurrent neural networks. BRAID further prioritizes the learning of intrinsic dynamics that are related to a behavior of interest by using a multi-stage optimization scheme. We validate BRAID with nonlinear simulations, showing that it can accurately learn the intrinsic dynamics shared between neural and behavioral modalities. We then apply BRAID to motor cortical activity recorded during a motor task and demonstrate that our method more accurately fits the neural-behavioral data by incorporating measured sensory stimuli into the model and improves the forecasting of neural-behavioral data compared with various baseline methods, whether input-driven or not.

Molecular relational learning (MRL) seeks to understand the interaction behaviors between molecules, a pivotal task in domains such as drug discovery and materials science. Recently, extracting core substructures and modeling their interactions have emerged as mainstream approaches within machine learning-assisted methods. However, these methods still exhibit some limitations, such as insufficient consideration of molecular interactions or capturing substructures that include excessive noise, which hampers precise core substructure extraction. To address these challenges, we present an integrated dynamic framework called Iterative Substructure Extraction (ISE). ISE employs the Expectation-Maximization (EM) algorithm for MRL tasks, where the core substructures of interacting molecules are treated as latent variables and model parameters, respectively. Through iterative refinement, ISE gradually narrows the interactions from the entire molecular structures to just the core substructures. Moreover, to ensure the extracted substructures are concise and compact, we propose the Interactive Graph Information Bottleneck (IGIB) theory, which focuses on capturing the most influential yet minimal interactive substructures. In summary, our approach, guided by the IGIB theory, achieves precise substructure extraction within the ISE framework and is encapsulated in the IGIB-ISE} Extensive experiments validate the superiority of our model over state-of-the-art baselines across various tasks in terms of accuracy, generalizability, and interpretability.

The increasing size of screening libraries poses a significant challenge for the development of virtual screening methods for drug discovery, necessitating a re-evaluation of traditional approaches in the era of big data. Although 3D pharmacophore screening remains a prevalent technique, its application to very large datasets is limited by the computational cost associated with matching query pharmacophores to database molecules. In this study, we introduce PharmacoMatch, a novel contrastive learning approach based on neural subgraph matching. Our method reinterprets pharmacophore screening as an approximate subgraph matching problem and enables efficient querying of conformational databases by encoding query-target relationships in the embedding space. We conduct comprehensive investigations of the learned representations and evaluate PharmacoMatch as pre-screening tool in a zero-shot setting. We demonstrate significantly shorter runtimes and comparable performance metrics to existing solutions, providing a promising speed-up for screening very large datasets.

Foundation models trained on internet-scale data benefit from extensive alignment to human preferences before deployment. However, existing methods typically assume a homogeneous preference shared by all individuals, overlooking the diversity inherent in human values. In this work, we propose a general reward modeling framework for pluralistic alignment (PAL), which incorporates diverse preferences from the ground up. PAL has a modular design that leverages commonalities across users while catering to individual personalization, enabling efficient few-shot localization of preferences for new users. Extensive empirical evaluation demonstrates that PAL matches or outperforms state-of-the-art methods on both text-to-text and text-to-image tasks: on Reddit TL;DR Summary, PAL is 1.7% more accurate for seen users and 36% more accurate for unseen users compared to the previous best method, with 100× less parameters. On Pick-a-Pic v2, PAL is 2.5% more accurate than the best method with 156× fewer learned parameters. Finally, we provide theoretical analysis for generalization of rewards learned via PAL framework showcasing the reduction in number of samples needed per user.

Generative models lack rigorous statistical guarantees with respect to their predictions. In this work, we propose Sequential Conformal Prediction for Generative Models (SCOPE-Gen), a sequential conformal prediction method producing prediction sets that satisfy a rigorous statistical guarantee called conformal admissibility control. This guarantee means that the prediction sets contain at least one admissible (or valid) example, with high probability. To this end, our method first samples an initial set of i.i.d. examples from a black box generative model. Then, this set is iteratively pruned via so-called greedy filters. As a consequence of the iterative generation procedure, admissibility of the final prediction set factorizes as a Markov chain, where each factor can be controlled separately, using conformal prediction. In comparison to prior work, our method demonstrates a large reduction in the number of admissibility evaluations during calibration. This is crucial e.g. in safety-critical applications, where these evaluations must be conducted manually by domain experts and are therefore costly and time consuming. We highlight the advantages of our method in terms of admissibility evaluations and cardinality of the prediction set through experiments in natural language generation and molecular graph extension tasks.