arXiv:2405.16041v4 Announce Type: replace-cross Abstract: Providing explainable molecular property predictions is critical for many scientific domains, such as drug discovery and material science. Though transformer-based language models have shown great potential in accurate molecular property prediction, they neither provide chemically meaningful explanations nor faithfully reveal the molecular structure-property relationships. In this work, we develop a framework for explainable molecular property prediction based on language models, dubbed as Lamole, which can provide chemical concepts-aligned explanations. We take a string-based molecular representation -- Group SELFIES -- as input tokens to pretrain and fine-tune our Lamole, as it provides chemically meaningful semantics. By disentangling the information flows of Lamole, we propose combining self-attention weights and gradients for better quantification of each chemically meaningful substructure's impact on the model's output. To make the explanations more faithfully respect the structure-property relationship, we then carefully craft a marginal loss to explicitly optimize the explanations to be able to align with the chemists' annotations. We bridge the manifold hypothesis with the elaborated marginal loss to prove that the loss can align the explanations with the tangent space of the data manifold, leading to concept-aligned explanations. Experimental results over six mutagenicity datasets and one hepatotoxicity dataset demonstrate Lamole can achieve comparable classification accuracy and boost the explanation accuracy by up to 14.3%, being the state-of-the-art in explainable molecular property prediction.

arXiv:2510.24701v1 Announce Type: cross Abstract: We present Tongyi DeepResearch, an agentic large language model, which is specifically designed for long-horizon, deep information-seeking research tasks. To incentivize autonomous deep research agency, Tongyi DeepResearch is developed through an end-to-end training framework that combines agentic mid-training and agentic post-training, enabling scalable reasoning and information seeking across complex tasks. We design a highly scalable data synthesis pipeline that is fully automatic, without relying on costly human annotation, and empowers all training stages. By constructing customized environments for each stage, our system enables stable and consistent interactions throughout. Tongyi DeepResearch, featuring 30.5 billion total parameters, with only 3.3 billion activated per token, achieves state-of-the-art performance across a range of agentic deep research benchmarks, including Humanity's Last Exam, BrowseComp, BrowseComp-ZH, WebWalkerQA, xbench-DeepSearch, FRAMES and xbench-DeepSearch-2510. We open-source the model, framework, and complete solutions to empower the community.

Cell Death Discovery, Published online: 14 March 2024; doi:10.1038/s41420-024-01896-6

Purine salvage–associated metabolites as biomarkers for early diagnosis of esophageal squamous cell carcinoma: a diagnostic model–based study

Nature, Published online: 20 December 2023; doi:10.1038/s41586-023-06857-0

Mitochondria have a pivotal role in the transport of dietary lipids in enterocytes, a finding that might have relevance to understanding the aberrant gastrointestinal function in patients with mitochondrial disorders.