AIMC Topic: Computational Biology

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Protein Crystallization Identification via Fuzzy Model on Linear Neighborhood Representation.

IEEE/ACM transactions on computational biology and bioinformatics Oct 7, 2021
X-ray crystallography is the most popular approach for analyzing protein 3D structure. However, the success rate of protein crystallization is very low (2-10 percent). To reduce the cost of time and resources, lots of computation-based methods are de...
Algorithms Computational Biology Proteins Crystallization Support Vector Machine Fuzzy Logic
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MANORAA: A machine learning platform to guide protein-ligand design by anchors and influential distances.

Structure (London, England : 1993) Oct 5, 2021
The MANORAA platform uses structure-based approaches to provide information on drug design originally derived from mapping tens of thousands of amino acids on a grid. In-depth analyses of the pockets, frequently occurring atoms, influential distances...
COVID-19 SARS-CoV-2 Drug Design Protein Binding Humans Machine Learning Pandemics Models, Molecular Protein Domains Ligands Crystallography, X-Ray Computational Biology Proteins Databases, Protein Trimethoprim Tetrahydrofolate Dehydrogenase
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DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment.

PLoS computational biology Oct 5, 2021
Drug treatment induces cell type specific transcriptional programs, and as the number of combinations of drugs and cell types grows, the cost for exhaustive screens measuring the transcriptional drug response becomes intractable. We developed DeepCel...
Unsupervised Machine Learning MCF-7 Cells Gene Knockdown Techniques PC-3 Cells Antineoplastic Agents Humans Deep Learning Transcriptome Computational Biology
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WinBinVec: Cancer-Associated Protein-Protein Interaction Extraction and Identification of 20 Various Cancer Types and Metastasis Using Different Deep Learning Models.

IEEE journal of biomedical and health informatics Oct 5, 2021
Biophysical protein-protein interactions perform dominant roles in the initiation and progression of many cancer-related pathways. A protein-protein interaction might play different roles in diverse cancer types. Hence, prioritizing the PPIs in each ...
Humans Computational Biology Proteins Amino Acid Sequence Protein Interaction Mapping Neural Networks, Computer Neoplasms Deep Learning
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Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms.

Nature methods Oct 4, 2021
Deep learning using neural networks relies on a class of machine-learnable models constructed using 'differentiable programs'. These programs can combine mathematical equations specific to a particular domain of natural science with general-purpose, ...
Protein Conformation Biophysics Computational Chemistry Proteins Models, Chemical Pattern Recognition, Automated Deep Learning Neural Networks, Computer Computational Biology
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SCMAG: A Semisupervised Single-Cell Clustering Method Based on Matrix Aggregation Graph Convolutional Neural Network.

Computational and mathematical methods in medicine Oct 4, 2021
Clustering analysis is one of the most important technologies for single-cell data mining. It is widely used in the division of different gene sequences, the identification of functional genes, and the detection of new cell types. Although the tradit...
Cluster Analysis Single-Cell Analysis Humans Databases, Nucleic Acid Supervised Machine Learning RNA-Seq Neural Networks, Computer Data Mining Computational Biology Algorithms
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Classification of Alzheimer's Disease Using Gaussian-Based Bayesian Parameter Optimization for Deep Convolutional LSTM Network.

Computational and mathematical methods in medicine Oct 4, 2021
Alzheimer's disease (AD) is one of the most important causes of mortality in elderly people, and it is often challenging to use traditional manual procedures when diagnosing a disease in the early stages. The successful implementation of machine lear...
Imaging, Three-Dimensional Neuroimaging Computational Biology Neural Networks, Computer Normal Distribution Magnetic Resonance Imaging Bayes Theorem Prognosis Multimodal Imaging Case-Control Studies Alzheimer Disease Humans Deep Learning Early Diagnosis Cognitive Dysfunction
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Segmentation of Overlapping Cervical Cells with Mask Region Convolutional Neural Network.

Computational and mathematical methods in medicine Oct 4, 2021
The task of segmenting cytoplasm in cytology images is one of the most challenging tasks in cervix cytological analysis due to the presence of fuzzy and highly overlapping cells. Deep learning-based diagnostic technology has proven to be effective in...
Cytodiagnosis Image Interpretation, Computer-Assisted Cytoplasm Deep Learning Vaginal Smears Computational Biology Cervix Uteri Databases, Factual Female Uterine Cervical Neoplasms Humans Neural Networks, Computer
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Competency of Neural Networks for the Numerical Treatment of Nonlinear Host-Vector-Predator Model.

Computational and mathematical methods in medicine Oct 4, 2021
The aim of this work is to introduce a stochastic solver based on the Levenberg-Marquardt backpropagation neural networks (LMBNNs) for the nonlinear host-vector-predator model. The nonlinear host-vector-predator model is dependent upon five classes, ...
Animals Computational Biology Neural Networks, Computer Computer Simulation Stochastic Processes Predatory Behavior Disease Vectors Models, Biological Vector Borne Diseases Nonlinear Dynamics Plant Diseases
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Pancreatic Cancer Survival Prediction: A Survey of the State-of-the-Art.

Computational and mathematical methods in medicine Sep 30, 2021
Cancer early detection increases the chances of survival. Some cancer types, like pancreatic cancer, are challenging to diagnose or detect early, and the stages have a fast progression rate. This paper presents the state-of-the-art techniques used in...
Survival Analysis Early Detection of Cancer Pancreatic Neoplasms Carcinoma, Pancreatic Ductal Surveys and Questionnaires Computational Biology Support Vector Machine Humans Neural Networks, Computer Machine Learning Survival Rate Deep Learning Algorithms Prognosis
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