Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but face limitations in binding data, substrate-specific control, and flexibility for de novo enzyme backbone generation. To address this, we introduce EnzyBind, a dataset with 11,100 experimentally validated enzyme-substrate pairs specifically curated from PDBbind. Building on this, we propose EnzyControl, a method that enables functional and substrate-specific control in enzyme backbone generation. Our approach generates enzyme backbones conditioned on MSAannotated catalytic sites and their corresponding substrates, which are automatically extracted from curated enzyme-substrate data. At the core of EnzyControl is EnzyAdapter, a lightweight, modular component integrated into a pretrained motifscaffolding model, allowing it to become substrate-aware. A two-stage training paradigm further refines the model's ability to generate accurate and functional enzyme structures. Experiments show that our EnzyControl achieves the best performance across structural and functional metrics on EnzyBind and EnzyBench benchmarks, with particularly notable improvements of 13% in designability and 13% in catalytic efficiency compared to the baseline models.

A full understanding of the behavior of a large language model (LLM) requires our grasp of its input token space. If this space differs from our assumptions, our comprehension of and conclusions about the LLM will likely be flawed.

In single-cell perturbation prediction, a central task is to forecast the effects of perturbing a gene unseen in the training data. The efficacy of such predictions depends on two factors: (1) the similarity of the target gene to those covered in the training data, which informs model (epistemic) uncertainty, and (2) the quality of the corresponding training data, which reflects data (aleatoric) uncertainty. Both factors are critical for determining the reliability of a prediction, particularly as gene perturbation is an inherently stochastic biochemical process. In this paper, we propose PRESCRIBE (PREdicting Single-Cell Response wIth Bayesian Estimation), a multivariate deep evidential regression framework designed to measure both sources of uncertainty jointly. Our analysis demonstrates that PRESCRIBE effectively estimates a confidence score for each prediction, which strongly correlates with its empirical accuracy. This capability enables the filtering of untrustworthy results, and in our experiments, it achieves steady accuracy improvements of over 3% compared to comparable baselines.

Existing molecular machine learning force fields (MLFFs) generally focus on the learning of atoms, molecules, and simple quantum chemical properties (such as energy and force), but ignore the importance of electron density (ED) ρ(r) in accurately understanding molecular force fields (MFFs). ED describes the probability of finding electrons at specific locations around atoms or molecules, which uniquely determines all ground state properties (such as energy, molecular structure, etc.) of interactive multi-particle systems according to the HohenbergKohn theorem. However, the calculation of ED relies on the time-consuming first-principles density functional theory (DFT), which leads to the lack of largescale ED data and limits its application in MLFFs. In this paper, we introduce EDBench, a large-scale, high-quality dataset of ED designed to advance learningbased research at the electronic scale. Built upon the PCQM4Mv2, EDBench provides accurate ED data, covering 3.3 million molecules. To comprehensively evaluate the ability of models to understand and utilize electronic information, we design a suite of ED-centric benchmark tasks spanning prediction, retrieval, and generation. Our evaluation of several state-of-the-art methods demonstrates that learning from EDBench is not only feasible but also achieves high accuracy. Moreover, we show that learning-based methods can efficiently calculate ED with comparable precision while significantly reducing the computational cost relative to traditional DFT calculations. All data and benchmarks from EDBench will be freely available, laying a robust foundation for ED-driven drug discovery and materials science.

Understanding cellular responses to chemical interventions is critical to the discovery of effective therapeutics. Because individual biological techniques often measure only one axis of cellular response at a time, high-quality multimodal datasets are needed to unlock a holistic understanding of how cells respond to treatments and to advance computational methods that integrate modalities. However, many techniques destroy cells and thus preclude paired measurements, and attempts to match disparate unimodal datasets are often confounded by data being generated in incompatible experimental settings. Here we introduce scGeneScope, a multimodal single-cell RNA sequencing (scRNA-seq) and Cell Painting microscopy image dataset conditionally paired by chemical treatment, designed to facilitate the development and benchmarking of unimodal, multimodal, and multiple profile machine learning methods for cellular profiling.

The ViT-L/14 encoder processes images into visual tokens, which the LLaMA-2-7B decoder converts into text.

Identifying drug-drug interactions (DDIs) is critical for ensuring drug safety and advancing drug development, a topic that has garnered significant research interest. While existing methods have made considerable progress, approaches relying solely on known DDIs face a key challenge when applied to drugs with limited data (e.g., novel and few-shot drugs): insufficient exploration of the space of unlabeled pairwise drugs. To address these issues, we innovatively introduce S2VM, a Selfsupervised Visual pretraining framework for pair-wise Molecules, to fully fuse structural representations and explore the space of drug pairs for DDI prediction. S2VM incorporates the explicit structure and correlations of visual molecules, such as the positional relationships and connectivity between functional substructures. Specifically, we blend the visual fragments of drug pairs into a unified input for joint encoding and then recover molecule-specific visual information for each drug individually.

The interpretation of genomic sequences is crucial for understanding biological processes. To handle the growing volume of DNA sequence data, Genomic Foundation Models (GFMs) have been developed by adapting architectures and training paradigms from Large Language Models (LLMs). Despite their remarkable performance in DNA sequence classification tasks, there remains a lack of systematic understanding regarding the pre-training and task-adaptation processes of GFMs. Moreover, existing GFMs cannot achieve state-of-the-art performance on both short and long-context tasks and lack multimodal abilities. By revisiting pre-training architectures and post-training techniques, we propose OMNI-DNA, a family of models spanning 20M to 1.1B parameters that supports sequence understanding, long-context genomic reasoning, and natural-language annotation. Omni-DNA establishes new state-of-the-art results on 18 of 26 evaluations drawn from Nucleotide Transformer and Genomic Benchmarks. When jointly finetuning on biologically related tasks, Omni-DNA consistently outperforms existing models and demonstrates multi-tasking abilities. Furthermore, we introduce SEQPACK, an adaptive compression mechanism that enables efficient long-context modeling by summarizing historical tokens through position-aware learnable sampling. This allows transformer-based models to process ultra-long genomic sequences with minimal memory and computational overhead.

We propose SPARTAALIGNMENT, an algorithm to collectively align multiple LLMs through competition and combat. To complement a single model's lack of diversity in generation and biases in evaluation, multiple LLMs form a "sparta tribe" to compete against each other in fulfilling instructions while serving as judges for the competition of others. For each iteration, one instruction and two models are selected for a duel, the other models evaluate the two responses, and their evaluation scores are aggregated through a adapted elo-ranking based reputation system, where winners/losers of combat gain/lose weight in evaluating others.

Virtual screening (VS) is a critical component of modern drug discovery, yet most existing methods--whether physics-based or deep learning-based--are developed around holo protein structures with known ligand-bound pockets. Consequently, their performance degrades significantly on apo or predicted structures such as those from AlphaFold2, which are more representative of real-world early-stage drug discovery, where pocket information is often missing. In this paper, we introduce an alignment-and-aggregation framework to enable accurate virtual screening under structural uncertainty. Our method comprises two core components: (1) a tri-modal contrastive learning module that aligns representations of the ligand, the holo pocket, and cavities detected from structures, thereby enhancing robustness to pocket localization error; and (2) a cross-attention based adapter for dynamically aggregating candidate binding sites, enabling the model to learn from activity data even without precise pocket annotations. We evaluated our method on a newly curated benchmark of apo structures, where it significantly outperforms state-of-the-art methods in blind apo setting, improving the early enrichment factor (EF1%) from 11.75 to 37.19. Notably, it also maintains strong performance on holo structures. These results demonstrate the promise of our approach in advancing firstin-class drug discovery, particularly in scenarios lacking experimentally resolved protein-ligand complexes. Our implementation is publicly available at https: //github.com/Wiley-Z/AANet.