ICLR 2025 论文列表

The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with rigid structures, limiting their practical application in drug development. While molecular dynamics simulation can theoretically capture all the biologically relevant conformations, the transition rate is dictated by the intrinsic energy barrier between them, making the sampling process computationally expensive. To overcome the aforementioned challenges, we propose to use generative modeling for SBDD considering conformational changes of protein pockets. We curate a dataset of apo and multiple holo states of protein-ligand complexes, simulated by molecular dynamics, and propose a full-atom flow model (and a stochastic version), named DynamicFlow, that learns to transform apo pockets and noisy ligands into holo pockets and corresponding 3D ligand molecules. Our method uncovers promising ligand molecules and corresponding holo conformations of pockets. Additionally, the resultant holo-like states provide superior inputs for traditional SBDD approaches, playing a significant role in practical drug discovery.

Generative Flow Networks (GFlowNets) are an emerging class of sampling methods for distributions over discrete and compositional objects, e.g., graphs. In spite of their remarkable success in problems such as drug discovery and phylogenetic inference, the question of when and whether GFlowNets learn to sample from the target distribution remains underexplored. To tackle this issue, we first assess the extent to which a violation of the detailed balance of the underlying flow network might hamper the correctness of GFlowNet's sampling distribution. In particular, we demonstrate that the impact of an imbalanced edge on the model's accuracy is influenced by the total amount of flow passing through it and, as a consequence, is unevenly distributed across the network. We also argue that, depending on the parameterization, imbalance may be inevitable. In this regard, we consider the problem of sampling from distributions over graphs with GFlowNets parameterized by graph neural networks (GNNs) and show that the representation limits of GNNs delineate which distributions these GFlowNets can approximate. Lastly, we address these limitations by proposing a theoretically sound and computationally tractable metric for assessing GFlowNets, experimentally showing it is a better proxy for correctness than popular evaluation protocols.

In this paper, we tackle the problem of Generalized Category Discovery (GCD). Given a dataset containing both labelled and unlabelled images, the objective is to categorize all images in the unlabelled subset, irrespective of whether they are from known or unknown classes. In GCD, an inherent label bias exists between known and unknown classes due to the lack of ground-truth labels for the latter. State-of-the-art methods in GCD leverage parametric classifiers trained through self-distillation with soft labels, leaving the bias issue unattended. Besides, they treat all unlabelled samples uniformly, neglecting variations in certainty levels and resulting in suboptimal learning. Moreover, the explicit identification of semantic distribution shifts between known and unknown classes, a vital aspect for effective GCD, has been neglected. To address these challenges, we introduce DebGCD, a Debiased learning with distribution guidance framework for GCD. Initially, DebGCD co-trains an auxiliary debiased classifier in the same feature space as the GCD classifier, progressively enhancing the GCD features. Moreover, we introduce a semantic distribution detector in a separate feature space to implicitly boost the learning efficacy of GCD. Additionally, we employ a curriculum learning strategy based on semantic distribution certainty to steer the debiased learning at an optimized pace. Thorough evaluations on GCD benchmarks demonstrate the consistent state-of-the-art performance of our framework, highlighting its superiority. Project page: [https://visual-ai.github.io/debgcd/](https://visual-ai.github.io/debgcd/)

Automated mechanistic interpretation research has attracted great interest due to its potential to scale explanations of neural network internals to large models. Existing automated circuit discovery work relies on activation patching or its approximations to identify subgraphs in models for specific tasks (circuits). They often suffer from slow runtime, approximation errors, and specific requirements of metrics, such as non-zero gradients. In this work, we introduce contextual decomposition for transformers (CD-T) to build interpretable circuits in large language models. CD-T can produce circuits at any level of abstraction and is the first to efficiently produce circuits as fine-grained as attention heads at specific sequence positions. CD-T is compatible to all transformer types, and requires no training or manually-crafted examples. CD-T consists of a set of mathematical equations to isolate contribution of model features. Through recursively computing contribution of all nodes in a computational graph of a model using CD-T followed by pruning, we are able to reduce circuit discovery runtime from hours to seconds compared to state-of-the-art baselines. On three standard circuit evaluation datasets (indirect object identification, greater-than comparisons, and docstring completion), we demonstrate that CD-T outperforms ACDC and EAP by better recovering the manual circuits with an average of 97% ROC AUC under low runtimes. In addition, we provide evidence that faithfulness of CD-T circuits is not due to random chance by showing our circuits are 80% more faithful than random circuits of up to 60% of the original model size. Finally, we show CD-T circuits are able to perfectly replicate original models' behavior(faithfulness = 1) using fewer nodes than the baselines for all tasks. Our results underscore the great promise of CD-T for efficient automated mechanistic interpretability, paving the way for new insights into the workings of large language models.

Generalized Category Discovery (GCD) is a challenging task in which, given a partially labelled dataset, models must categorize all unlabelled instances, regardless of whether they come from labelled categories or from new ones. In this paper, we challenge a remaining assumption in this task: that all images share the same domain. Specifically, we introduce a new task and method to handle GCD when the unlabelled data also contains images from different domains to the labelled set. Our proposed `HiLo' networks extract High-level semantic and Low-level domain features, before minimizing the mutual information between the representations. Our intuition is that the clusterings based on domain information and semantic information should be independent. We further extend our method with a specialized domain augmentation tailored for the GCD task, as well as a curriculum learning approach. Finally, we construct a benchmark from corrupted fine-grained datasets as well as a large-scale evaluation on DomainNet with real-world domain shifts, reimplementing a number of GCD baselines in this setting. We demonstrate that HiLo outperforms SoTA category discovery models by a large margin on all evaluations.

We present InvMSAFold, an inverse folding method for generating protein sequences optimized for diversity and speed. For a given structure, InvMSAFold generates the parameters of a pairwise probability distribution over the space of sequences, capturing the amino acid covariances observed in Multiple Sequence Alignments (MSA) of homologous proteins. This allows for the efficient generation of highly diverse protein sequences while preserving structural and functional integrity. We demonstrate that this increased diversity in sampled sequences translates into greater variability in biochemical properties, highlighting the exciting potential of our method for applications such as protein design. The orders of magnitude improvement in sampling speed compared to existing methods unlocks new possibilities for high-throughput in virtual screening.

We develop ProtComposer to generate protein structures conditioned on spatial protein layouts that are specified via a set of 3D ellipsoids capturing substructure shapes and semantics. At inference time, we condition on ellipsoids that are hand-constructed, extracted from existing proteins, or from a statistical model, with each option unlocking new capabilities. Hand-specifying ellipsoids enables users to control the location, size, orientation, secondary structure, and approximate shape of protein substructures. Conditioning on ellipsoids of existing proteins enables redesigning their substructure's connectivity or editing substructure properties. By conditioning on novel and diverse ellipsoid layouts from a simple statistical model, we improve protein generation with expanded Pareto frontiers between designability, novelty, and diversity. Further, this enables sampling designable proteins with a helix-fraction that matches PDB proteins, unlike existing generative models that commonly oversample conceptually simple helix bundles. Code is available at https://github.com/NVlabs/protcomposer.