Related papers: ChemRecon: a Consolidated Meta-Database Platform f…
Motivation: An essential step in developing computational tools for the inference, optimization, and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks.…
Prediction of complete step-by-step chemical reaction mechanisms (CRMs) remains a major challenge. Whereas the traditional approaches in CRM tasks rely on expert-driven experiments or costly quantum chemical computations, contemporary deep…
Chemistry research has both high material and computational costs to conduct experiments. Institutions thus consider chemical data to be valuable and there have been few efforts to construct large public datasets for machine learning.…
Data commons collate data with cloud computing infrastructure and commonly used software services, tools and applications to create biomedical resources for the large-scale management, analysis, harmonization, and sharing of biomedical…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Any cutting-edge scientific research project requires a myriad of computational tools for data generation, management, analysis and visualization. Python is a flexible and extensible scientific programming platform that offered the perfect…
In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about…
Creating a single unified interatomic potential capable of attaining ab initio accuracy across all chemistry remains a long-standing challenge in computational chemistry and materials science. This work introduces a training protocol for…
Automated knowledge discovery from trending chemical literature is essential for more efficient biomedical research. How to extract detailed knowledge about chemical reactions from the core chemistry literature is a new emerging challenge…
Quantum-chemical subsystem and embedding methods require complex workflows that may involve multiple quantum-chemical program packages. Moreover, such workflows require the exchange of voluminous data that goes beyond simple quantities such…
This paper presents a novel method for parsing and vectorizing semi-structured data to enhance the functionality of Retrieval-Augmented Generation (RAG) within Large Language Models (LLMs). We developed a comprehensive pipeline for…
One of the major challenges providing large databases like the WFCAM Science Archive (WSA) is to minimize ingest times for pixel/image metadata and catalogue data. In this article we describe how the pipeline processed data are ingested…
Resolving coreference and bridging relations in chemical patents is important for better understanding the precise chemical process, where chemical domain knowledge is very critical. We proposed an approach incorporating external knowledge…
Functional groups and moieties are chemical descriptors of biomolecules that can be used to interpret their properties and functions, leading to the understanding of chemical or biological mechanisms. These chemical building blocks, or…
Previous research on radiology report generation has made significant progress in terms of increasing the clinical accuracy of generated reports. In this paper, we emphasize another crucial quality that it should possess, i.e., inter-report…
The pretraining-finetuning paradigm has powered major advances in domains such as natural language processing and computer vision, with representative examples including masked language modeling and next-token prediction. In molecular…
The identification of metabolites from complex biological samples often involves matching experimental mass spectrometry data to signatures of compounds derived from massive chemical databases. However, misidentifications may result due to…
Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
Data organization is a difficult and essential component in cultural heritage applications. Over the years, a great amount of archaeological ceramic data have been created and processed by various methods and devices. Such ceramic data are…