Related papers: Sentence Simplification Aids Protein-Protein Inter…
Eukaryotic cells transmit information by signaling through complex networks of interacting proteins. Here we develop a theoretical and computational framework that relates the biophysics of protein-protein interactions (PPIs) within a…
Aberrant protein-protein interactions (PPIs) underpin a plethora of human diseases, and disruption of these harmful interactions constitute a compelling treatment avenue. Advances in computational approaches to PPI prediction have closely…
We present data augmentation techniques for process extraction tasks in scientific publications. We cast the process extraction task as a sequence labeling task where we identify all the entities in a sentence and label them according to…
Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language…
Prompt-based fine-tuning for pre-trained models has proven effective for many natural language processing tasks under few-shot settings in general domain. However, tuning with prompt in biomedical domain has not been investigated…
We present the first sentence simplification model that learns explicit edit operations (ADD, DELETE, and KEEP) via a neural programmer-interpreter approach. Most current neural sentence simplification systems are variants of…
We advance the state of the art in biomolecular interaction extraction with three contributions: (i) We show that deep, Abstract Meaning Representations (AMR) significantly improve the accuracy of a biomolecular interaction extraction…
Drug-drug interaction (DDI) is a vital information when physicians and pharmacists intend to co-administer two or more drugs. Thus, several DDI databases are constructed to avoid mistakenly combined use. In recent years, automatically…
Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…
Proteins interact with other proteins within biological pathways, forming connected subgraphs in the protein-protein interactome (PPI). Proteins are often involved in multiple biological pathways which complicates interpretation of…
Automatic relationship extraction (RE) from biomedical literature is critical for managing the vast amount of scientific knowledge produced each year. In recent years, utilizing pre-trained language models (PLMs) has become the prevalent…
Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere…
Accessing medical literature is difficult for laypeople as the content is written for specialists and contains medical jargon. Automated text simplification methods offer a potential means to address this issue. In this work, we propose a…
Relation extraction is a core problem for natural language processing in the biomedical domain. Recent research on relation extraction showed that prompt-based learning improves the performance on both fine-tuning on full training set and…
We participated, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of the BioCreative III Challenge. For the ACT, we pursued an extensive testing of…
For both human readers and pre-trained language models (PrLMs), lexical diversity may lead to confusion and inaccuracy when understanding the underlying semantic meanings of given sentences. By substituting complex words with simple…
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…
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…
The rapid growth in published clinical trials makes it difficult to maintain up-to-date systematic reviews, which requires finding all relevant trials. This leads to policy and practice decisions based on out-of-date, incomplete, and biased…
Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated…