Nucleic acid-based drugs like aptamers have recently demonstrated great therapeutic potential. However, experimental platforms for aptamer screening are costly, and the scarcity of labeled data presents a challenge for supervised methods to learn protein-aptamer binding. To this end, we develop an unsupervised learning approach based on the predicted pairwise contact map between a protein and a nucleic acid and demonstrate its effectiveness in protein-aptamer binding prediction. Our model is based on FAFormer, a novel equivariant transformer architecture that seamlessly integrates frame averaging (FA) within each transformer block. This integration allows our model to infuse geometric information into node features while preserving the spatial semantics of coordinates, leading to greater expressive power than standard FA models. Our results show that FAFormer outperforms existing equivariant models in contact map prediction across three protein complex datasets, with over 10% relative improvement. Moreover, we curate five real-world protein-aptamer interaction datasets and show that the contact map predicted by FAFormer serves as a strong binding indicator for aptamer screening.

Neural Information Processing Systems http://nips.cc/

Dexterous grasp generation is a fundamental challenge in robotics, requiring both grasp stability and adaptability across diverse objects and tasks. Analytical methods ensure stable grasps but are inefficient and lack task adaptability, while generative approaches improve efficiency and task integration but generalize poorly to unseen objects and tasks due to data limitations. In this paper, we propose a transfer-based framework for dexterous grasp generation, leveraging a conditional diffusion model to transfer high-quality grasps from shape templates to novel objects within the same category. Specifically, we reformulate the grasp transfer problem as the generation of an object contact map, incorporating object shape similarity and task specifications into the diffusion process. To handle complex shape variations, we introduce a dual mapping mechanism, capturing intricate geometric relationship between shape templates and novel objects. Beyond the contact map, we derive two additional object-centric maps, the part map and direction map, to encode finer contact details for more stable grasps. We then develop a cascaded conditional diffusion model framework to jointly transfer these three maps, ensuring their intra-consistency. Finally, we introduce a robust grasp recovery mechanism, identifying reliable contact points and optimizing grasp configurations efficiently. Extensive experiments demonstrate the superiority of our proposed method. Our approach effectively balances grasp quality, generation efficiency, and generalization performance across various tasks. Project homepage: https://cmtdiffusion.github.io/

Deep learning techniques have driven significant progress in various analytical tasks within 3D genomics in computational biology. However, a holistic understanding of 3D genomics knowledge remains underexplored. Here, we propose MIX-HIC, the first multimodal foundation model of 3D genome that integrates both 3D genome structure and epigenomic tracks, which obtains unified and comprehensive semantics. For accurate heterogeneous semantic fusion, we design the cross-modal interaction and mapping blocks for robust unified representation, yielding the accurate aggregation of 3D genome knowledge. Besides, we introduce the first large-scale dataset comprising over 1 million pairwise samples of Hi-C contact maps and epigenomic tracks for high-quality pre-training, enabling the exploration of functional implications in 3D genomics. Extensive experiments show that MIX-HIC can significantly surpass existing state-of-the-art methods in diverse downstream tasks. This work provides a valuable resource for advancing 3D genomics research.

The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by inconsistent evaluation metrics, insufficient sampling of rare conformational states, and the absence of reproducible benchmarks. To address these challenges, we introduce a modular benchmarking framework that systematically evaluates protein MD methods using enhanced sampling analysis. Our approach uses weighted ensemble (WE) sampling via The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis (WESTPA), based on progress coordinates derived from Time-lagged Independent Component Analysis (TICA), enabling fast and efficient exploration of protein conformational space. The framework includes a flexible, lightweight propagator interface that supports arbitrary simulation engines, allowing both classical force fields and machine learning-based models. Additionally, the framework offers a comprehensive evaluation suite capable of computing more than 19 different metrics and visualizations across a variety of domains. We further contribute a dataset of nine diverse proteins, ranging from 10 to 224 residues, that span a variety of folding complexities and topologies. Each protein has been extensively simulated at 300K for one million MD steps per starting point (4 ns). To demonstrate the utility of our framework, we perform validation tests using classic MD simulations with implicit solvent and compare protein conformational sampling using a fully trained versus under-trained CGSchNet model. By standardizing evaluation protocols and enabling direct, reproducible comparisons across MD approaches, our open-source platform lays the groundwork for consistent, rigorous benchmarking across the molecular simulation community.

During training, we explicitly encourage consistency between the global motion and the local poses via a prior defined using the contact maps and future poses. Our approach outperforms the state-of-the-art human motion forecasting and human synthesis methods on both synthetic and real datasets.

Accurately predicting drug-target interactions (DTIs) is pivotal for advancing drug discovery and target validation techniques. While machine learning approaches including those that are based on Graph Neural Networks (GNN) have achieved notable success in DTI prediction, many of them have difficulties in effectively integrating the diverse features of drugs, targets and their interactions. To address this limitation, we introduce a novel framework to take advantage of the power of both transductive learning and inductive learning so that features at molecular level and drug-target interaction network level can be exploited. Within this framework is a GNN-based model called Graph-in-Graph (GiG) that represents graphs of drug and target molecular structures as meta-nodes in a drug-target interaction graph, enabling a detailed exploration of their intricate relationships. To evaluate the proposed model, we have compiled a special benchmark comprising drug SMILES, protein sequences, and their interaction data, which is interesting in its own right. Our experimental results demonstrate that the GiG model significantly outperforms existing approaches across all evaluation metrics, highlighting the benefits of integrating different learning paradigms and interaction data.

The chromatin folding and the spatial arrangement of chromosomes in the cell play a crucial role in DNA replication and genes expression. An improper chromatin folding could lead to malfunctions and, over time, diseases. For eukaryotes, centromeres are essential for proper chromosome segregation and folding. Despite extensive research using de novo sequencing of genomes and annotation analysis, centromere locations in yeasts remain difficult to infer and are still unknown in most species. Recently, genome-wide chromosome conformation capture coupled with next-generation sequencing (Hi-C) has become one of the leading methods to investigate chromosome structures. Some recent studies have used Hi-C data to give a point estimate of each centromere, but those approaches highly rely on a good pre-localization. Here, we present a novel approach that infers in a stochastic manner the locations of all centromeres in budding yeast based on both the experimental Hi-C map and simulated contact maps.

In this paper, we study task-oriented human grasp synthesis, a new grasp synthesis task that demands both task and context awareness. At the core of our method is the task-aware contact maps. Unlike traditional contact maps that only reason about the manipulated object and its relation with the hand, our enhanced maps take into account scene and task information. This comprehensive map is critical for hand-object interaction, enabling accurate grasping poses that align with the task. We propose a two-stage pipeline that first constructs a task-aware contact map informed by the scene and task. In the subsequent stage, we use this contact map to synthesize task-oriented human grasps. We introduce a new dataset and a metric for the proposed task to evaluate our approach. Our experiments validate the importance of modeling both scene and task, demonstrating significant improvements over existing methods in both grasp quality and task performance. See our project page for more details: https://hcis-lab.github.io/TOHGS/