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Multiple Sequences Alignment (MSA) of biological sequences is a fundamental problem in computational biology due to its critical significance in wide ranging applications including haplotype reconstruction, sequence homology, phylogenetic…
The exponential growth of scientific production makes secondary literature abridgements increasingly demanding. We introduce a new open-source framework for systematic reviews that significantly reduces time and workload for collecting and…
We study the task of automatically finding evidence relevant to hypotheses in biomedical papers. Finding relevant evidence is an important step when researchers investigate scientific hypotheses. We introduce EvidenceBench to measure models…
We support scientific writers in determining whether a written sentence is scientific, to which section it belongs, and suggest paraphrasings to improve the sentence. Firstly, we propose a regression model trained on a corpus of scientific…
Citation content analysis seeks to understand citations based on the language used during the making of a citation. A key issue in citation content analysis is looking for linguistic structures that characterize distinct classes of…
The selection of features is an essential data preprocessing stage in data mining. The core principle of feature selection seems to be to pick a subset of possible features by excluding features with almost no predictive information as well…
Retrieval-augmented generation (RAG) grounds large language models in external medical knowledge, yet standard retrievers frequently surface hard negatives that are semantically close to the query but describe clinically distinct…
Graph classification is a highly impactful task that plays a crucial role in a myriad of real-world applications such as molecular property prediction and protein function prediction.Aiming to handle the new classes with limited labeled…
Protein structure prediction is one of the most important problems in computational biology. The most successful computational approach, also called template-based modeling, identifies templates with solved crystal structures for the query…
Context: Citations are a key measure of scientific performance in most fields, including software engineering. However, there is limited research that studies which characteristics of articles' metadata (title, abstract, keywords, and…
Citation graphs can be helpful in generating high-quality summaries of scientific papers, where references of a scientific paper and their correlations can provide additional knowledge for contextualising its background and main…
In this paper, we study the importance of context in predicting the citation worthiness of sentences in scholarly articles. We formulate this problem as a sequence labeling task solved using a hierarchical BiLSTM model. We contribute a new…
Scientific papers make claims about prior work backed by citations. Verifying those citations at scale (that each cited paper exists, says what the citation claims, and is itself reliable) is structurally beyond what human review can…
A systematic review identifies and collates various clinical studies and compares data elements and results in order to provide an evidence based answer for a particular clinical question. The process is manual and involves lot of time. A…
With the tremendous growth in the number of scientific papers being published, searching for references while writing a scientific paper is a time-consuming process. A technique that could add a reference citation at the appropriate place…
Learning semantically meaningful representations from scientific documents can facilitate academic literature search and improve performance of recommendation systems. Pre-trained language models have been shown to learn rich textual…
The medical image processing field often encounters the critical issue of scarce annotated data. Transfer learning has emerged as a solution, yet how to select an adequate source task and effectively transfer the knowledge to the target…
Accurate parsing of citations is necessary for machine-readable scholarly infrastructure. But, despite sustained interest in this problem, existing evaluation techniques are often not generalizable, based on synthetic data, or not publicly…
A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…
Given a data set, misleading conclusions can be drawn from it by cherry-picking selected samples. One important class of conclusions is a trend derived from a data set of values over time. Our goal is to evaluate whether the 'trends'…