Yulong Li, Rong Xia, Yuxuan Zhang, Jianxu Chen, Xiwei Liu, Haochen Xue, Maosheng Li, Yuhang Liu 等 15 位作者
We introduce DoAtlas-2, a foundation for self-evolving causal biomedical discovery that organizes knowledge around causal mechanisms and advances through external evidence from human populations. DoAtlas-2 integrates 771 research resources covering more than 720,000 participants in 48 countries, from longitudinal clinical phenotypes, medical imaging, and continuous physiological signals to eight molecular layers, together with an evidence network of approximately 4.7 million literature-derived records over 93,566 concepts and 149,383 candidate causal relations. DoAtlas-2 autonomously formulates research questions from evidence gaps and unresolved mechanisms, prespecifies their causal designs, and generates validated analyses. Supporting, challenging, and unresolved results continuously revise mechanistic interpretations, the causal evidence state, and the discovery frontier, so that DoAtlas-2 self-evolves within a closed loop of hypothesis generation, empirical testing, and renewed discovery. DoAtlas-2 has systematically evaluated 2,031 research questions. In the Human Phenotype Project (HPP), it formulated 4,014 candidate pathway questions across vascular, early-glycemic, and hepatic-metabolic systems, and screening of the first 1,079 yielded statistical support for 756. Representative studies identify blood pressure as a convergence node linking adiposity, hepatic, and lipid phenotypes to vascular outcomes, and show that an adiposity-inflammation-blood-pressure pathway is largely attenuated by joint adjustment for body mass index (BMI) and smoking. The discovered vascular network constitutes a completely interpretable predictive foundation, admitting exact attribution of every prediction and closed-form mediation effects. DoAtlas-2 thereby unifies causal mechanism discovery, population-evidence testing, and interpretable prediction within one continuously evolving foundation.
Haochen Xue, Anastasia Godneva, Yulong Li, Qi Cao, Zhaodong Wu, Kaiyu Liang, Jionglong Su, Eran Segal 等 9 位作者
Existing gut microbiome foundation models typically use flat taxon representations, limiting their ability to exploit known taxonomic hierarchies. We introduce TaxoMFM, a microbiome foundation model that integrates taxonomic structure into self-supervised learning. TaxoMFM jointly learns abundance patterns across taxonomic ranks and relative proportions within groups through taxonomy-aware encoding and hierarchical compositional reconstruction. We further construct TaxoGut-HPP, comprising 100,806 gut microbiome profiles from 231 source cohorts and covering 40 classification and 8 regression tasks. TaxoMFM achieves competitive performance across disease, gut health, host trait, and liver ultrasound phenotype prediction. In cross-cohort zero-shot transfer, where target cohorts are excluded from both pretraining and downstream adaptation, TaxoMFM achieves AUROCs of 0.838, 0.736, and 0.722 for colorectal cancer, type 2 diabetes, and inflammatory bowel disease, respectively. Further analyses show that TaxoMFM recovers community changes across taxonomic scales, while preserving community information and producing consistent representations under database updates and species-vocabulary shifts. Our code is available at https://anonymous.4open.science/r/TaxoMFM-F16D/.
Linh Tran, Yulong Li, Radu Florian, Stacy Patterson, Ana Milanova, Wei Sun
The strong zero-shot and long-context capabilities of recent Large Language Models (LLMs) have paved the way for highly effective re-ranking systems. Attention-based re-rankers leverage attention weights from transformer heads to produce relevance scores, but not all heads are created equally: many contribute noise and redundancy, thus limiting performance. To address this, we introduce CoRe heads, a small set of retrieval heads identified via a contrastive scoring metric that explicitly rewards high attention heads that correlate with relevant documents, while downplaying nodes with higher attention that correlate with irrelevant documents. This relative ranking criterion isolates the most discriminative heads for re-ranking and yields a state-of-the-art list-wise re-ranker. Extensive experiments with three LLMs show that aggregated signals from CoRe heads, constituting less than 1% of all heads, substantially improve re-ranking accuracy over strong baselines. We further find that CoRe heads are concentrated in middle layers, and pruning the computation of final 50% of model layers preserves accuracy while significantly reducing inference time and memory usage.