Hongshuai Wang

Zhifeng Gao, Xiaohong Ji, Guojiang Zhao et al. · microsoft-research

Recently deep learning based quantitative structure-activity relationship (QSAR) models has shown surpassing performance than traditional methods for property prediction tasks in drug discovery. However, most DL based QSAR models are restricted to limited labeled data to achieve better performance, and also are sensitive to model scale and hyper-parameters. In this paper, we propose Uni-QSAR, a powerful Auto-ML tool for molecule property prediction tasks. Uni-QSAR combines molecular representation learning (MRL) of 1D sequential tokens, 2D topology graphs, and 3D conformers with pretraining models to leverage rich representation from large-scale unlabeled data. Without any manual fine-tuning or model selection, Uni-QSAR outperforms SOTA in 21/22 tasks of the Therapeutic Data Commons (TDC) benchmark under designed parallel workflow, with an average performance improvement of 6.09\%. Furthermore, we demonstrate the practical usefulness of Uni-QSAR in drug discovery domains.

Yanyi Su, Hongshuai Wang, Zhifeng Gao et al.

Olfaction lies at the intersection of chemical structure, neural encoding, and linguistic perception, yet existing representation methods fail to fully capture this pathway. Current approaches typically model only isolated segments of the olfactory pathway, overlooking the complete chain from molecule to receptors to linguistic descriptions. Such fragmentation yields learned embeddings that lack both biological grounding and semantic interpretability. We propose NOSE (Neural Olfactory-Semantic Embedding), a representation learning framework that aligns three modalities along the olfactory pathway: molecular structure, receptor sequence, and natural language description. Rather than simply fusing these signals, we decouple their contributions via orthogonal constraints, preserving the unique encoded information of each modality. To address the sparsity of olfactory language, we introduce a weak positive sample strategy to calibrate semantic similarity, preventing erroneous repulsion of similar odors in the feature space. Extensive experiments demonstrate that NOSE achieves state-of-the-art (SOTA) performance and excellent zero-shot generalization, confirming the strong alignment between its representation space and human olfactory intuition.Code and data are available at https://github.com/Xianyusyy/NOSE

Hengxing Cai, Xiaochen Cai, Junhan Chang et al.

Recent breakthroughs in Large Language Models (LLMs) have revolutionized scientific literature analysis. However, existing benchmarks fail to adequately evaluate the proficiency of LLMs in this domain, particularly in scenarios requiring higher-level abilities beyond mere memorization and the handling of multimodal data. In response to this gap, we introduce SciAssess, a benchmark specifically designed for the comprehensive evaluation of LLMs in scientific literature analysis. It aims to thoroughly assess the efficacy of LLMs by evaluating their capabilities in Memorization (L1), Comprehension (L2), and Analysis \& Reasoning (L3). It encompasses a variety of tasks drawn from diverse scientific fields, including biology, chemistry, material, and medicine. To ensure the reliability of SciAssess, rigorous quality control measures have been implemented, ensuring accuracy, anonymization, and compliance with copyright standards. SciAssess evaluates 11 LLMs, highlighting their strengths and areas for improvement. We hope this evaluation supports the ongoing development of LLM applications in scientific literature analysis. SciAssess and its resources are available at \url{https://github.com/sci-assess/SciAssess}.

Haoming Yan, Xinyu Chen, Yanran Wang et al.

The discovery of effective molecular modulators is essential for advancing perovskite solar cells (PSCs), but the research process is hindered by the vastness of chemical space and the time-consuming and expensive trial-and-error experimental screening. Concurrently, machine learning (ML) offers significant potential for accelerating materials discovery. However, applying ML to PSCs remains a major challenge due to data scarcity and limitations of traditional quantitative structure-property relationship (QSPR) models. Here, we apply a chemical informed transfer learning framework based on pre-trained deep neural networks, which achieves high accuracy in predicting the molecular modulator's effect on the power conversion efficiency (PCE) of PSCs. This framework is established through systematical benchmarking of diverse molecular representations, enabling lowcost and high-throughput virtual screening over 79,043 commercially available molecules. Furthermore, we leverage interpretability techniques to visualize the learned chemical representation and experimentally characterize the resulting modulator-perovskite interactions. The top molecular modulators identified by the framework are subsequently validated experimentally, delivering a remarkably improved champion PCE of 26.91% in PSCs.

Qingsi Lai, Fanjie Xu, Lin Yao et al.

Powder X-ray diffraction (PXRD) is a prevalent technique in materials characterization. While the analysis of PXRD often requires extensive human manual intervention, and most automated method only achieved at coarse-grained level. The more difficult and important task of fine-grained crystal structure prediction from PXRD remains unaddressed. This study introduces XtalNet, the first equivariant deep generative model for end-to-end crystal structure prediction from PXRD. Unlike previous crystal structure prediction methods that rely solely on composition, XtalNet leverages PXRD as an additional condition, eliminating ambiguity and enabling the generation of complex organic structures with up to 400 atoms in the unit cell. XtalNet comprises two modules: a Contrastive PXRD-Crystal Pretraining (CPCP) module that aligns PXRD space with crystal structure space, and a Conditional Crystal Structure Generation (CCSG) module that generates candidate crystal structures conditioned on PXRD patterns. Evaluation on two MOF datasets (hMOF-100 and hMOF-400) demonstrates XtalNet's effectiveness. XtalNet achieves a top-10 Match Rate of 90.2% and 79% for hMOF-100 and hMOF-400 in conditional crystal structure prediction task, respectively. XtalNet enables the direct prediction of crystal structures from experimental measurements, eliminating the need for manual intervention and external databases. This opens up new possibilities for automated crystal structure determination and the accelerated discovery of novel materials.

Fanmeng Wang, Wentao Guo, Qi Ou et al.

Polymer conformation generation is a critical task that enables atomic-level studies of diverse polymer materials. While significant advances have been made in designing conformation generation methods for small molecules and proteins, these methods struggle to generate polymer conformations due to their unique structural characteristics. Meanwhile, the scarcity of polymer conformation datasets further limits the progress, making this important area largely unexplored. In this work, we propose PolyConf, a pioneering tailored polymer conformation generation method that leverages hierarchical generative models to unlock new possibilities. Specifically, we decompose the polymer conformation into a series of local conformations (i.e., the conformations of its repeating units), generating these local conformations through an autoregressive model, and then generating their orientation transformations via a diffusion model to assemble them into the complete polymer conformation. Moreover, we develop the first benchmark with a high-quality polymer conformation dataset derived from molecular dynamics simulations to boost related research in this area. The comprehensive evaluation demonstrates that PolyConf consistently outperforms existing conformation generation methods, thus facilitating advancements in polymer modeling and simulation.

Guojiang Zhao, Sihang Li, Zixiang Lu et al.

Large Language Models(LLMs) have demonstrated remarkable performance across various domains, yet their capabilities in molecular reasoning remain insufficiently explored. Current approaches tend to rely heavily on general-purpose prompting, which lacks domain-specific molecular semantics, while those that use fine-tuning strategies often face challenges with interpretability and reasoning depth. To address these issues, we introduce MolReasoner, a two-stage framework designed to transition LLMs from memorization towards chemical reasoning. First, we propose Mol-SFT, which initializes the model's reasoning abilities via synthetic Chain-of-Thought(CoT) samples generated by GPT-4o and verified for chemical accuracy. Subsequently, Mol-RL applies reinforcement learning with specialized reward functions designed explicitly to align chemical structures with linguistic descriptions, thereby enhancing molecular reasoning capabilities. Our approach notably enhances interpretability, improving the model 's molecular understanding and enabling better generalization. Extensive experiments demonstrate that MolReasoner outperforms existing methods, and marking a significant shift from memorization-based outputs to robust chemical reasoning.

Hengxing Cai, Xiaochen Cai, Shuwen Yang et al.

In scientific research and its application, scientific literature analysis is crucial as it allows researchers to build on the work of others. However, the fast growth of scientific knowledge has led to a massive increase in scholarly articles, making in-depth literature analysis increasingly challenging and time-consuming. The emergence of Large Language Models (LLMs) has offered a new way to address this challenge. Known for their strong abilities in summarizing texts, LLMs are seen as a potential tool to improve the analysis of scientific literature. However, existing LLMs have their own limits. Scientific literature often includes a wide range of multimodal elements, such as tables, charts, and molecule, which are hard for text-focused LLMs to understand and analyze. This issue points to the urgent need for new solutions that can fully understand and analyze multimodal content in scientific literature. To answer this demand, we present \textbf{Uni-SMART} (Universal Science Multimodal Analysis and Research Transformer), an innovative model designed for in-depth understanding of multimodal scientific literature. Through rigorous quantitative evaluation across several domains, Uni-SMART demonstrates superior performance over other text-focused LLMs. Furthermore, our exploration extends to practical applications, including patent infringement detection and nuanced analysis of charts. These applications not only highlight Uni-SMART's adaptability but also its potential to revolutionize how we interact with scientific literature.

Fanmeng Wang, Shan Mei, Wentao Guo et al.

Polymers, macromolecules formed from covalently bonded monomers, underpin countless technologies and are indispensable to modern life. While deep learning is advancing polymer science, existing methods typically represent the whole polymer solely through monomer-level descriptors, overlooking the global structural information inherent in polymer conformations, which ultimately limits their practical performance. Moreover, this field still lacks a universal foundation model that can effectively support diverse downstream tasks, thereby severely constraining progress. To address these challenges, we introduce PolyConFM, the first polymer foundation model that unifies polymer modeling and design through conformation-centric generative pretraining. Recognizing that each polymer conformation can be decomposed into a sequence of local conformations (i.e., those of its repeating units), we pretrain PolyConFM under the conditional generation paradigm, reconstructing these local conformations via masked autoregressive (MAR) modeling and further generating their orientation transformations to recover the corresponding polymer conformation. Besides, we construct the first high-quality polymer conformation dataset via molecular dynamics simulations to mitigate data sparsity, thereby enabling conformation-centric pretraining. Experiments demonstrate that PolyConFM consistently outperforms representative task-specific methods on diverse downstream tasks, equipping polymer science with a universal and powerful tool.