arXiv subjects

Li S. Yifei

Publications and source records attributed to Li S. Yifei.

3 recordsLinked to original sources

arXiv2026

Self-Driving Datasets: From 20 Million Papers to Nuanced Biomedical Knowledge at Scale

Manually curated biomedical repositories -- spanning bioactivity, genomics, and chemistry -- are expensive to maintain, lag behind primary literature, and discard experimental context, obscuring nuances needed to assess data correctness and coverage. We show that PubMed itself can be autonomously and cost-effectively turned into structured datasets that are larger, more nuanced, and more accurate than the curated databases they replace. We present three coupled contributions: (1) an LLM-based entity-tagging pipeline, grounded in nine biomedical ontologies, that tags 4.5B entities across 19 categories in a 22.5M-paper, 2.5T-token PubMed corpus; (2) hybrid sparse-dense retrieval supporting entity-filtered semantic queries over the tagged corpus; and (3) Starling, a multi-agent deep research system that, given only a natural-language task description, designs precision- and recall-targeted retrieval filters, induces an extraction schema, and emits structured records with nuance-rich fields and supporting passages. Across six tasks -- blood-brain barrier permeability, oral bioavailability, acute toxicity (LD50), gene-disease associations, protein subcellular localization, and chemical reactions -- Starling produces ~6.3M records (91K-3M per task); several are, to our knowledge, the largest public datasets for their property. Frontier-model rejection of our extractions is 0.6-7.7% across tasks, far below error rates we measure on widely used curated counterparts (e.g., 16.5% on BBB_Martins, 7.3% on Bioavailability_Ma). Beyond scale and accuracy, the supporting passages carry nuance tabular databases discard -- e.g., oral bioavailability may depend on fed vs. fasted state. Together, the corpus, retrieval, and agent establish a foundation for AI-driven therapeutic design. Code and datasets: https://github.com/starling-labs/starling.

cs.LG↗

arXiv2025

ResearchQA: Evaluating Scholarly Question Answering at Scale Across 75 Fields with Survey-Mined Questions and Rubrics

Evaluating long-form responses to research queries heavily relies on expert annotators, restricting attention to areas like AI where researchers can conveniently enlist colleagues. Yet, research expertise is abundant: survey articles consolidate knowledge spread across the literature. We introduce ResearchQA, a resource for evaluating LLM systems by distilling survey articles from 75 research fields into 21K queries and 160K rubric items. Queries and rubrics are jointly derived from survey sections, where rubric items list query-specific answer evaluation criteria, i.e., citing papers, making explanations, and describing limitations. 31 Ph.D. annotators in 8 fields judge that 90% of queries reflect Ph.D. information needs and 87% of rubric items warrant emphasis of a sentence or longer. We leverage ResearchQA to evaluate 18 systems in 7.6K head-to-heads. No parametric or retrieval-augmented system we evaluate exceeds 70% on covering rubric items, and the highest-ranking system shows 75% coverage. Error analysis reveals that the highest-ranking system fully addresses less than 11% of citation rubric items, 48% of limitation items, and 49% of comparison items. We release our data to facilitate more comprehensive multi-field evaluations.

cs.CL↗

arXiv2023

Conceptor-Aided Debiasing of Large Language Models

Pre-trained large language models (LLMs) reflect the inherent social biases of their training corpus. Many methods have been proposed to mitigate this issue, but they often fail to debias or they sacrifice model accuracy. We use conceptors--a soft projection method--to identify and remove the bias subspace in LLMs such as BERT and GPT. We propose two methods of applying conceptors (1) bias subspace projection by post-processing by the conceptor NOT operation; and (2) a new architecture, conceptor-intervened BERT (CI-BERT), which explicitly incorporates the conceptor projection into all layers during training. We find that conceptor post-processing achieves state-of-the-art (SoTA) debiasing results while maintaining LLMs' performance on the GLUE benchmark. Further, it is robust in various scenarios and can mitigate intersectional bias efficiently by its AND operation on the existing bias subspaces. Although CI-BERT's training takes all layers' bias into account and can beat its post-processing counterpart in bias mitigation, CI-BERT reduces the language model accuracy. We also show the importance of carefully constructing the bias subspace. The best results are obtained by removing outliers from the list of biased words, combining them (via the OR operation), and computing their embeddings using the sentences from a cleaner corpus.

cs.CL↗