Jinfeng Zhang

Qingyu Chen, Alexis Allot, Robert Leaman et al.

The COVID-19 pandemic has been severely impacting global society since December 2019. Massive research has been undertaken to understand the characteristics of the virus and design vaccines and drugs. The related findings have been reported in biomedical literature at a rate of about 10,000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200,000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g., Diagnosis and Treatment) to the articles in LitCovid. Despite the continuing advances in biomedical text mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset, consisting of over 30,000 articles with manually reviewed topics, was created for training and testing. It is one of the largest multilabel classification datasets in biomedical scientific literature. 19 teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181, and 0.9394 for macro F1-score, micro F1-score, and instance-based F1-score, respectively. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development.

Han Yue, Eric Zhou, Alex Hu et al.

Biomedical question answering (QA) encompasses diverse question types, including yes/no, factoid, list, and summary questions, each requiring distinct forms of evidence and reasoning. However, most retrieval-augmented QA systems rely on a unified retrieval pipeline, regardless of the information needs of different question categories. This one-size-fits-all approach may limit the effectiveness of evidence acquisition and downstream answer generation. In this work, we propose an adaptive retrieval framework that selects retrieval and evidence aggregation strategies according to question type. The system combines query understanding, biomedical document retrieval, reranking, knowledge graph augmentation, document clustering, and large language model-based answer generation. For yes/no questions, it focuses on precise evidence retrieval; for factoid and list questions, it emphasizes entity-oriented retrieval and clustering; and for summary questions, it performs broader evidence collection and synthesis. We evaluate the proposed framework on the BioASQ benchmark and demonstrate that adaptive retrieval strategies improve evidence relevance and answer quality across multiple question types. Our results suggest that aligning retrieval mechanisms with question-specific information needs provides an effective direction for enhancing retrieval-augmented biomedical QA systems.

Qing Han, Shubo Tian, Jinfeng Zhang

As a major social media platform, Twitter publishes a large number of user-generated text (tweets) on a daily basis. Mining such data can be used to address important social, public health, and emergency management issues that are infeasible through other means. An essential step in many text mining pipelines is named entity recognition (NER), which presents some special challenges for tweet data. Among them are nonstandard expressions, extreme imbalanced classes, and lack of context information, etc. The track 3 of BioCreative challenge VII (BC7) was organized to evaluate methods for detecting medication mentions in tweets. In this paper, we report our work on BC7 track 3, where we explored a PubMedBERT-based classifier trained with a combination of multiple data augmentation approaches. Our method achieved an F1 score of 0.762, which is substantially higher than the mean of all submissions (0.696).

Jie Hao, Xing Wang, Shuming Shi et al.

Current state-of-the-art neural machine translation (NMT) uses a deep multi-head self-attention network with no explicit phrase information. However, prior work on statistical machine translation has shown that extending the basic translation unit from words to phrases has produced substantial improvements, suggesting the possibility of improving NMT performance from explicit modeling of phrases. In this work, we present multi-granularity self-attention (Mg-Sa): a neural network that combines multi-head self-attention and phrase modeling. Specifically, we train several attention heads to attend to phrases in either n-gram or syntactic formalism. Moreover, we exploit interactions among phrases to enhance the strength of structure modeling - a commonly-cited weakness of self-attention. Experimental results on WMT14 English-to-German and NIST Chinese-to-English translation tasks show the proposed approach consistently improves performance. Targeted linguistic analysis reveals that Mg-Sa indeed captures useful phrase information at various levels of granularities.

Jie Hao, Xing Wang, Shuming Shi et al.

Recent studies have shown that a hybrid of self-attention networks (SANs) and recurrent neural networks (RNNs) outperforms both individual architectures, while not much is known about why the hybrid models work. With the belief that modeling hierarchical structure is an essential complementary between SANs and RNNs, we propose to further enhance the strength of hybrid models with an advanced variant of RNNs - Ordered Neurons LSTM (ON-LSTM), which introduces a syntax-oriented inductive bias to perform tree-like composition. Experimental results on the benchmark machine translation task show that the proposed approach outperforms both individual architectures and a standard hybrid model. Further analyses on targeted linguistic evaluation and logical inference tasks demonstrate that the proposed approach indeed benefits from a better modeling of hierarchical structure.

Jie Hao, Xing Wang, Baosong Yang et al.

Recently, the Transformer model that is based solely on attention mechanisms, has advanced the state-of-the-art on various machine translation tasks. However, recent studies reveal that the lack of recurrence hinders its further improvement of translation capacity. In response to this problem, we propose to directly model recurrence for Transformer with an additional recurrence encoder. In addition to the standard recurrent neural network, we introduce a novel attentive recurrent network to leverage the strengths of both attention and recurrent networks. Experimental results on the widely-used WMT14 English-German and WMT17 Chinese-English translation tasks demonstrate the effectiveness of the proposed approach. Our studies also reveal that the proposed model benefits from a short-cut that bridges the source and target sequences with a single recurrent layer, which outperforms its deep counterpart.

Albert Steppi, Jinchan Qu, Minjing Tao et al.

The increasing volume of scientific publications and grant proposals has generated an unprecedentedly high workload to scientific communities. Consequently, review quality has been decreasing and review outcomes have become less correlated with the real merits of the papers and proposals. A novel distributed peer review (DPR) approach has recently been proposed to address these issues. The new approach assigns principal investigators (PIs) who submitted proposals (or papers) to the same program as reviewers. Each PI reviews and ranks a small number (such as seven) of other PIs' proposals. The individual rankings are then used to estimate a global ranking of all proposals using the Modified Borda Count (MBC). In this study, we perform simulation studies to investigate several parameters important for the decision making when adopting this new approach. We also propose a new method called Concordance Index-based Global Ranking (CIGR) to estimate global ranking from individual rankings. An efficient simulated annealing algorithm is designed to search the optimal Concordance Index (CI). Moreover, we design a new balanced review assignment procedure, which can result in significantly better performance for both MBC and CIGR methods. We found that CIGR performs better than MBC when the review quality is relatively high. As review quality and review difficulty are tightly correlated, we constructed a boundary in the space of review quality vs review difficulty that separates the CIGR-superior and MBC-superior regions. Finally, we propose a multi-stage DPR strategy based on CIGR, which has the potential to substantially improve the overall review performance while reducing the review workload.