Siqi Fan

Xinrui Chen, Yizhen Luo, Siqi Fan et al.

De novo functional protein design aims to generate protein sequences that realize specified biochemical functions without relying on evolutionary templates, enabling broad applications in biotechnology and medicine. Existing approaches adopt either direct function-to-sequence mapping or decoupled structure-sequence generation strategies but often fail to achieve functionality and foldability simultaneously. To address this, we propose CodeFP, a Co-generative protein language model for de novo Functional Protein design that simultaneously decodes sequence and structure tokens, thereby enabling superior simultaneous realization of functionality and foldability. CodeFP utilizes functional local structures to enrich functional semantic encodings, overcoming the suboptimal translation of flat encodings into structure tokens, while introducing auxiliary functional supervision to alleviate training ambiguity stemming from the one-to-many structure-to-token mapping. Extensive experiments show that CodeFP consistently achieves average improvements of 6.1% in functional consistency and 3.2% in foldability over the strongest baseline.

Siqi Fan, Yuguang Xie, Bowen Cai et al.

Understanding the chemical structure from a graphical representation of a molecule is a challenging image caption task that would greatly benefit molecule-centric scientific discovery. Variations in molecular images and caption subtasks pose a significant challenge in both image representation learning and task modeling. Yet, existing methods only focus on a specific caption task that translates a molecular image into its graph structure, i.e., OCSR. In this paper, we propose the Optical Chemical Structure Understanding (OCSU) task, which extends low-level recognition to multilevel understanding and aims to translate chemical structure diagrams into readable strings for both machine and chemist. To facilitate the development of OCSU technology, we explore both OCSR-based and OCSR-free paradigms. We propose DoubleCheck to enhance OCSR performance via attentive feature enhancement for local ambiguous atoms. It can be cascaded with existing SMILES-based molecule understanding methods to achieve OCSU. Meanwhile, Mol-VL is a vision-language model end-to-end optimized for OCSU. We also construct Vis-CheBI20, the first large-scale OCSU dataset. Through comprehensive experiments, we demonstrate the proposed approaches excel at providing chemist-readable caption for chemical structure diagrams, which provide solid baselines for further research. Our code, model, and data are open-sourced at https://github.com/PharMolix/OCSU.

Siqi Fan, Bowen Qin, Peng Han et al.

Recent thinking models trained with reinforcement learning and backward-checking CoT often suffer from overthinking: they produce excessively long outputs even on simple problems, wasting computation. Existing evaluations, based on token efficiency, give an incomplete view as they neglect problem difficulty and intermediate computation costs. We formalize reasoning efficiency as a relative measure between thinking and instruct models, treating instruct models as the minimal-effort baseline. A systematic study across four thinking models and multiple benchmarks reveals two consistent patterns: (i) instruct models achieve higher efficiency overall, and (ii) problem difficulty affects efficiency, with thinking models wasting computation on easy problems but providing value on harder ones. Building on this insight, we propose COTHINK, a simple two-stage pipeline: an instruct model drafts a brief outline, and a thinking model expands it. On GSM8K, MATH500, and AIME24, COTHINK cuts token usage by 21.1% while keeping accuracy on four thinking models, and remains competitive with strong efficiency baselines.