AIMC Topic: Programming Languages

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Language models for biological research: a primer.

Nature methods Aug 9, 2024
Language models are playing an increasingly important role in many areas of artificial intelligence (AI) and computational biology. In this primer, we discuss the ways in which language models, both those based on natural language and those based on ...
Artificial Intelligence Computational Biology Humans Natural Language Processing Programming Languages
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Python tools for structural tasks in chemistry.

Molecular diversity May 14, 2024
In recent decades, the use of computational approaches and artificial intelligence in the scientific environment has become more widespread. In this regard, the popular and versatile programming language Python has attracted considerable attention fr...
Software Programming Languages Cheminformatics
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A systematic literature review on the applications of recurrent neural networks in code clone research.

PloS one Feb 2, 2024
Code clones, referring to code fragments that are either similar or identical and are copied and pasted within software systems, have negative effects on both software quality and maintenance. The objective of this work is to systematically review an...
Humans Semantics Neural Networks, Computer Software Programming Languages
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plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style.

BMC genomics Oct 3, 2023
BACKGROUND: The visual sequence logo has been a hot area in the development of bioinformatics tools. ggseqlogo written in R language has been the most popular API since it was published. With the popularity of artificial intelligence and deep learnin...
Artificial Intelligence Programming Languages Position-Specific Scoring Matrices Software Computational Biology
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MZA: A Data Conversion Tool to Facilitate Software Development and Artificial Intelligence Research in Multidimensional Mass Spectrometry.

Journal of proteome research Nov 22, 2022
Modern mass spectrometry-based workflows employing hybrid instrumentation and orthogonal separations collect multidimensional data, potentially allowing deeper understanding in omics studies through adoption of artificial intelligence methods. Howeve...
Artificial Intelligence Software Information Storage and Retrieval Mass Spectrometry Programming Languages
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GapPredict - A Language Model for Resolving Gaps in Draft Genome Assemblies.

IEEE/ACM transactions on computational biology and bioinformatics Dec 8, 2021
Short-read DNA sequencing instruments can yield over 10 bases per run, typically composed of reads 150 bases long. Despite this high throughput, de novo assembly algorithms have difficulty reconstructing contiguous genome sequences using short reads ...
High-Throughput Nucleotide Sequencing Genome, Human Natural Language Processing Programming Languages Humans Algorithms Genomics Deep Learning Sequence Analysis, DNA
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SpinSPJ: a novel NMR scripting system to implement artificial intelligence and advanced applications.

BMC bioinformatics Dec 7, 2021
BACKGROUND: Software for nuclear magnetic resonance (NMR) spectrometers offer general functionality of instrument control and data processing; these applications are often developed with non-scripting languages. NMR users need to flexibly integrate r...
Programming Languages Magnetic Resonance Spectroscopy Artificial Intelligence Software User-Computer Interface Magnetic Resonance Imaging
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A weighted patient network-based framework for predicting chronic diseases using graph neural networks.

Scientific reports Nov 19, 2021
Chronic disease prediction is a critical task in healthcare. Existing studies fulfil this requirement by employing machine learning techniques based on patient features, but they suffer from high dimensional data problems and a high level of bias. We...
Pulmonary Disease, Chronic Obstructive Programming Languages Male Machine Learning Cardiovascular Diseases Risk Software Data Interpretation, Statistical Female Chronic Disease Humans Algorithms Translational Research, Biomedical Reproducibility of Results Neural Networks, Computer Databases, Factual
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The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.

Journal of integrative bioinformatics Oct 5, 2021
Computational simulation experiments increasingly inform modern biological research, and bring with them the need to provide ways to annotate, archive, share and reproduce the experiments performed. These simulations increasingly require extensive co...
Programming Languages Systems Biology Language Models, Biological Ecosystem
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celldeath: A tool for detection of cell death in transmitted light microscopy images by deep learning-based visual recognition.

PloS one Jun 24, 2021
Cell death experiments are routinely done in many labs around the world, these experiments are the backbone of many assays for drug development. Cell death detection is usually performed in many ways, and requires time and reagents. However, cell dea...
Humans Programming Languages Deep Learning Cell Death Image Interpretation, Computer-Assisted MCF-7 Cells Microscopy
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