AIMC Topic: Algorithms

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Quantitative Assessment of the Physiological Parameters Influencing QT Interval Response to Medication: Application of Computational Intelligence Tools.

Computational and mathematical methods in medicine Jan 4, 2018
Human heart electrophysiology is complex biological phenomenon, which is indirectly assessed by the measured ECG signal. ECG trace is further analyzed to derive interpretable surrogates including QT interval, QRS complex, PR interval, and T wave morp...
Programming Languages Myocytes, Cardiac Observer Variation Ions Sodium Electrophysiology Terfenadine Clinical Trials as Topic Cell Membrane Risk Regression Analysis Heart Potassium Anti-Arrhythmia Agents Calcium Arrhythmias, Cardiac Electrocardiography Action Potentials Models, Statistical Algorithms Reproducibility of Results Humans Artificial Intelligence Software
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A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia.

Nature communications Jan 3, 2018
Cancers that appear pathologically similar often respond differently to the same drug regimens. Methods to better match patients to drugs are in high demand. We demonstrate a promising approach to identify robust molecular markers for targeted treatm...
Humans Topoisomerase II Inhibitors Drug Resistance, Neoplasm Etoposide Antineoplastic Agents Precision Medicine DNA Helicases Biomarkers, Tumor Nuclear Proteins Leukemia, Myeloid, Acute Transcription Factors Cell Line Datasets as Topic Machine Learning Algorithms
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VAMPnets for deep learning of molecular kinetics.

Nature communications Jan 2, 2018
There is an increasing demand for computing the relevant structures, equilibria, and long-timescale kinetics of biomolecular processes, such as protein-drug binding, from high-throughput molecular dynamics simulations. Current methods employ transfor...
Neural Networks, Computer Machine Learning Molecular Dynamics Simulation Markov Chains Protein Folding Algorithms Protein Binding Kinetics
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Gene ontology concept recognition using named concept: understanding the various presentations of the gene functions in biomedical literature.

Database : the journal of biological databases and curation Jan 1, 2018
OBJECTIVE: A major challenge in precision medicine is the development of patient-specific genetic biomarkers or drug targets. The firsthand information of the genes associated with the pathologic pathways of interest is buried in the ocean of biomedi...
Semantics Reproducibility of Results Machine Learning Biomedical Research Algorithms Gene Ontology Publications
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Extracting chemical-protein relations using attention-based neural networks.

Database : the journal of biological databases and curation Jan 1, 2018
Relation extraction is an important task in the field of natural language processing. In this paper, we describe our approach for the BioCreative VI Task 5: text mining chemical-protein interactions. We investigate multiple deep neural network (DNN) ...
Databases, Chemical Neural Networks, Computer Algorithms Proteins Databases, Protein
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Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach.

Database : the journal of biological databases and curation Jan 1, 2018
The precision medicine (PM) initiative promises to identify individualized treatment depending on a patients' genetic profile and their related responses. In order to help health professionals and researchers in the PM endeavor, BioCreative VI organi...
Algorithms Protein Interaction Maps Neural Networks, Computer Mutation Databases, Protein
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Large-scale automated machine reading discovers new cancer-driving mechanisms.

Database : the journal of biological databases and curation Jan 1, 2018
PubMed, a repository and search engine for biomedical literature, now indexes >1 million articles each year. This exceeds the processing capacity of human domain experts, limiting our ability to truly understand many diseases. We present Reach, a sys...
Automation Algorithms Neoplasms Publications Humans Machine Learning
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An end-to-end deep learning architecture for extracting protein-protein interactions affected by genetic mutations.

Database : the journal of biological databases and curation Jan 1, 2018
The BioCreative VI Track IV (mining protein interactions and mutations for precision medicine) challenge was organized in 2017 with the goal of applying biomedical text mining methods to support advancements in precision medicine approaches. As part ...
Databases, Protein Machine Learning Neural Networks, Computer Mutation Algorithms Protein Interaction Maps
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Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling.

Database : the journal of biological databases and curation Jan 1, 2018
We present a system for automatically identifying a multitude of biomedical entities from the literature. This work is based on our previous efforts in the BioCreative VI: Interactive Bio-ID Assignment shared task in which our system demonstrated sta...
Algorithms Fuzzy Logic Molecular Sequence Annotation
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Hierarchical bi-directional attention-based RNNs for supporting document classification on protein-protein interactions affected by genetic mutations.

Database : the journal of biological databases and curation Jan 1, 2018
In this paper, we describe a hierarchical bi-directional attention-based Re-current Neural Network (RNN) as a reusable sequence encoder architecture, which is used as sentence and document encoder for document classification. The sequence encoder is ...
Databases, Protein Neural Networks, Computer Mutation Data Mining Protein Interaction Maps Models, Theoretical Support Vector Machine Algorithms Reproducibility of Results
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