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Yue Gao

Publications and source records attributed to Yue Gao.

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Unfolding Scientific Papers into Multi-Turn Generation Trajectories for Continued Pre-Training

A recent line of synthetic-data work reconstructs the thinking behind existing text rather than rewriting the text itself, but it operates on short web passages, recovers only local thoughts, and leaves the structure of whole documents untouched. Scientific papers are written to a clear and largely uniform structure and make a natural substrate for lifting this paradigm to the document level. We present a pipeline that unfolds each paper into a multi-turn generation trajectory in which a teacher model reconstructs the writing process of the whole paper: a writing request, a global plan, and pre-writing deliberation for each section. All section texts and the abstract are kept verbatim from the source paper. We apply the pipeline to 1.8M quality-filtered arXiv papers and obtain a 60B-token corpus for continued pre-training (CPT) that is roughly twice the source text. The same reverse construction extends to instruction data and evaluation. We build an SFT dataset of 200K samples using answers derived from paper text. We also use held-out papers to construct PAW-Bench, a benchmark of 2,940 academic writing tasks with per-task rubrics and checklists. In controlled experiments, CPT on our corpus followed by SFT on public datasets improves writing performance while preserving general reasoning and improving long document reading. Replacing part of the writing SFT data with our synthetic instruction data further improves performance on PAW-Bench.

cs.CL

Hyper-Fold: Exploring the Expressive Limit of Sequence-Geometry Learning for Proteins via Hypergraph Modeling

Protein structure modeling rests on a single computational primitive: the interaction between what a residue is (sequence content) and where it sits (three-dimensional geometry). What is the expressive limit of this layer class? We show that the complete bilinear operator over content-geometry outer products--the sufficient statistic of all second-order interactions--is the expressive ceiling, while the additive message passing of mainstream geometric GNNs is provably blind to content-geometry binding. We then introduce Hyper-Fold, a rank-K separable convolutional backbone approaching this ceiling at message-passing cost: each radius neighborhood is organized into a sequence hyperedge and a contact hyperedge, modulated by an edge-conditioned matrix-valued operator factorized into K learned basis operators with geometry-generated coefficients. Across enzyme function prediction, fold classification, and ligand binding site detection, Hyper-Fold and its hierarchical variant Hyper-Fold-Deep achieve the best results among protein-specific structure encoders; Hyper-Fold-Pocket, an anchored set-prediction head, surpasses UniSite-3D on UniSite-DS and two zero-shot benchmarks with no sequence language model features, 68x fewer parameters, and 4.8x lower latency--suggesting that a sufficiently expressive 3D backbone recovers information that fusion architectures previously borrowed from evolution-scale pretraining.

cs.AI