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We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (IAS), discovery of protein pairs (IPS) and text passages…

Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical…

When used in high-stakes settings, AI systems are expected to produce decisions that are transparent, interpretable and auditable, a requirement increasingly expected by regulations. Decision trees such as CART provide clear and verifiable…

The Biocreative VII Track-2 challenge consists of named entity recognition, entity-linking (or entity-normalization), and topic indexing tasks -- with entities and topics limited to chemicals for this challenge. Named entity recognition is…

In recent years, the number of biomedical publications has steadfastly grown, resulting in a rich source of untapped new knowledge. Most biomedical facts are however not readily available, but buried in the form of unstructured text, and…

Protein-protein interactions (PPIs) are fundamental to cellular function and disease mechanisms. Current learning-based PPI predictors focus on learning powerful protein representations but neglect designing specialized classification…

Identifying interactions between proteins is important to understand underlying biological processes. Extracting a protein-protein interaction (PPI) from the raw text is often very difficult. Previous supervised learning methods have used…

In the digital era, the exponential growth of scientific publications has made it increasingly difficult for researchers to efficiently identify and access relevant work. This paper presents an automated framework for research article…

In recent years, the rise of large language models (LLMs) has made it possible to directly achieve named entity recognition (NER) without any demonstration samples or only using a few samples through in-context learning (ICL). However,…

In this research, we present our work participation for the DrugProt task of BioCreative VII challenge. Drug-target interactions (DTIs) are critical for drug discovery and repurposing, which are often manually extracted from the…

Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and…

Due to their architecture and vast pre-training data, large language models (LLMs) demonstrate strong text classification performance. However, LLM output - here, the category assigned to a text - depends heavily on the wording of the…

This study is dedicated to exploring the application of prompt learning methods to advance Named Entity Recognition (NER) within the medical domain. In recent years, the emergence of large-scale models has driven significant progress in NER…

Entity relationship classification remains a challenging task in information extraction, especially in scenarios with limited labeled data and complex relational structures. In this study, we conduct a comparative analysis of three distinct…

Prompt learning is a new paradigm for utilizing pre-trained language models and has achieved great success in many tasks. To adopt prompt learning in the NER task, two kinds of methods have been explored from a pair of symmetric…

Item Response Theory (IRT) aims to assess latent abilities of respondents based on the correctness of their answers in aptitude test items with different difficulty levels. In this paper, we propose the $\beta^3$-IRT model, which models…

In this paper, we report our method for the Information Extraction task in 2019 Language and Intelligence Challenge. We incorporate BERT into the multi-head selection framework for joint entity-relation extraction. This model extends…

This study presents an ensemble approach that addresses the challenges of identification and analysis of research articles in rapidly evolving fields, using the field of Artificial Intelligence (AI) as a case study. Our approach included…

Large Language Models (LLMs) often do not perform well on queries that require the aggregation of information across texts. To better evaluate this setting and facilitate modeling efforts, we introduce TACT - Text And Calculations through…

Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier…