Tong Bao

Tong Bao, Heng Zhang, Chengzhi Zhang

Abstractive summarization of scientific papers has always been a research focus, yet existing methods face two main challenges. First, most summarization models rely on Encoder-Decoder architectures that treat papers as sequences of words, thus fail to fully capture the structured information inherent in scientific papers. Second, existing research often use keyword mapping or feature engineering to identify the structural information, but these methods struggle with the structural flexibility of scientific papers and lack robustness across different disciplines. To address these challenges, we propose a two-stage abstractive summarization framework that leverages automatic recognition of structural functions within scientific papers. In the first stage, we standardize chapter titles from numerous scientific papers and construct a large-scale dataset for structural function recognition. A classifier is then trained to automatically identify the key structural components (e.g., Background, Methods, Results, Discussion), which provides a foundation for generating more balanced summaries. In the second stage, we employ Longformer to capture rich contextual relationships across sections and generating context-aware summaries. Experiments conducted on two domain-specific scientific paper summarization datasets demonstrate that our method outperforms advanced baselines, and generates more comprehensive summaries. The code and dataset can be accessed at https://github.com/tongbao96/code-for-SFR-AS.

Wenqing Wu, Chengzhi Zhang, Tong Bao et al.

Novelty is a core component of academic papers, and there are multiple perspectives on the assessment of novelty. Existing methods often focus on word or entity combinations, which provide limited insights. The content related to a paper's novelty is typically distributed across different core sections, e.g., Introduction, Methodology and Results. Therefore, exploring the optimal combination of sections for evaluating the novelty of a paper is important for advancing automated novelty assessment. In this paper, we utilize different combinations of sections from academic papers as inputs to drive language models to predict novelty scores. We then analyze the results to determine the optimal section combinations for novelty score prediction. We first employ natural language processing techniques to identify the sectional structure of academic papers, categorizing them into introduction, methods, results, and discussion (IMRaD). Subsequently, we used different combinations of these sections (e.g., introduction and methods) as inputs for pretrained language models (PLMs) and large language models (LLMs), employing novelty scores provided by human expert reviewers as ground truth labels to obtain prediction results. The results indicate that using introduction, results and discussion is most appropriate for assessing the novelty of a paper, while the use of the entire text does not yield significant results. Furthermore, based on the results of the PLMs and LLMs, the introduction and results appear to be the most important section for the task of novelty score prediction. The code and dataset for this paper can be accessed at https://github.com/njust-winchy/SC4ANM.

Fei Wang, Xinye Zheng, Kun Li et al.

Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number ($k_\text{cat}$), Michaelis constant ($K_\text{m}$), and inhibition constant ($K_\text{i}$) depend jointly on the enzyme sequence, the substrate chemistry, and the conformational adaptation of the active site during binding. Many learning pipelines simplify this process to a static compatibility problem between the enzyme and substrate, fusing their representations through shallow operations and regressing a single value. Such formulations overlook the staged nature of catalysis, which involves both substrate recognition and conformational adaptation. In this regard, we reformulate kinetic prediction as a staged multimodal conditional modeling problem and introduce the Enzyme-Reaction Bridging Adapter (ERBA), which injects cross-modal information via fine-tuning into Protein Language Models (PLMs) while preserving their biochemical priors. ERBA performs conditioning in two stages: Molecular Recognition Cross-Attention (MRCA) first injects substrate information into the enzyme representation to capture specificity; Geometry-aware Mixture-of-Experts (G-MoE) then integrates active-site structure and routes samples to pocket-specialized experts to reflect induced fit. To maintain semantic fidelity, Enzyme-Substrate Distribution Alignment (ESDA) enforces distributional consistency within the PLM manifold in a reproducing kernel Hilbert space. Experiments across three kinetic endpoints and multiple PLM backbones, ERBA delivers consistent gains and stronger out-of-distribution performance compared with sequence-only and shallow-fusion baselines, offering a biologically grounded route to scalable kinetic prediction and a foundation for adding cofactors, mutations, and time-resolved structural cues.