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Identifying the relations between chemicals and proteins is an important text mining task. BioCreative VII track 1 DrugProt task aims to promote the development and evaluation of systems that can automatically detect relations between…
In this work, we present RePlaChem, a software library for reducing detailed large-scale plasma chemical mechanisms to smaller skeletal ones. The library parses a plasma chemical mechanism in the well-established format compatible with the…
Graph similarity search algorithms usually leverage the structural properties of a database. Hence, these algorithms are effective only on some structural variations of the data and are ineffective on other forms, which makes them hard to…
Improving the detailed understanding of the underlying properties and functions of biomolecules has recently attracted growing interest, enabled by the possibility of real-space imaging of single, intact macromolecules using Scanning…
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
In this uncertain world, data uncertainty is inherent in many applications and its importance is growing drastically due to the rapid development of modern technologies. Nowadays, researchers have paid more attention to mine patterns in…
This paper develops the first question answering dataset (DrugEHRQA) containing question-answer pairs from both structured tables and unstructured notes from a publicly available Electronic Health Record (EHR). EHRs contain patient records,…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
The integration of large-scale chemical databases represents a critical bottleneck in modern cheminformatics research, particularly for machine learning applications requiring high-quality, multi-source validated datasets. This paper…
Chemical structure extraction from documents remains a hard problem due to both false positive identification of structures during segmentation and errors in the predicted structures. Current approaches rely on handcrafted rules and…
A novel framework has recently been proposed for designing the molecular structure of chemical compounds with a desired chemical property, where design of novel drugs is an important topic in bioinformatics and chemo-informatics. The…
Reconstruction of biochemical reaction networks is a central topic in systems biology which raises crucial theoretical challenges in system identification. Nonlinear Ordinary Differential Equations (ODEs) that involve polynomial and…
While accurate protein structure predictions are now available for nearly every observed protein sequence, predicted structures lack much of the functional context offered by experimental structure determination. We address this gap with…
There will be a paradigm shift in chemical and biological research, to be enabled by autonomous, closed-loop, real-time self-directed decision-making experimentation. Spectrum-to-structure correlation, which is to elucidate molecular…
Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts.…
The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network…
Identifying potential drug targets using metabolic modeling requires integrating multiple modeling methods and heterogenous biological datasets, which can be challenging without sophisticated tools. We developed COMO, a user-friendly…
Modeling the relationship between chemical structure and molecular activity is a key goal in drug development. Many benchmark tasks have been proposed for molecular property prediction, but these tasks are generally aimed at specific,…
In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum…
Maintaining a legacy database is a difficult task especially when system documentation is poor written or even missing. Database reverse engineering is an attempt to recover high-level conceptual design from the existing database instances.…