AIMC Topic: Software

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BL-FlowSOM: Consistent and Highly Accelerated FlowSOM Based on Parallelized Batch Learning.

Cytometry. Part A : the journal of the International Society for Analytical Cytology Apr 17, 2025
The recent increase in the dimensionality of cytometry data has led to the development of various computational analysis methods. FlowSOM is one of the best-performing clustering methods but has room for improvement in terms of the consistency and sp...
Principal Component Analysis Flow Cytometry Machine Learning Software Humans Computational Biology Cluster Analysis Algorithms
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Geometric deep learning framework for de novo genome assembly.

Genome research Apr 14, 2025
The critical stage of every de novo genome assembler is identifying paths in assembly graphs that correspond to the reconstructed genomic sequences. The existing algorithmic methods struggle with this, primarily due to repetitive regions causing comp...
Software Algorithms Deep Learning Humans Genome Genomics Sequence Analysis, DNA
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PoseidonQ: A Free Machine Learning Platform for the Development, Analysis, and Validation of Efficient and Portable QSAR Models for Drug Discovery.

Journal of chemical information and modeling Apr 9, 2025
The advent of powerful machine learning algorithms as well as the availability of high volume of pharmacological data has given new fuel to QSAR, opening new unprecedented options for deriving highly predictive models for assisting the rationale desi...
Drug Discovery Machine Learning Quantitative Structure-Activity Relationship Software
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DTreePred: an online viewer based on machine learning for pathogenicity prediction of genomic variants.

BMC bioinformatics Apr 9, 2025
BACKGROUND: A significant challenge in precision medicine is confidently identifying mutations detected in sequencing processes that play roles in disease treatment or diagnosis. Furthermore, the lack of representativeness of single nucleotide varian...
Genomics Software Decision Trees Mutation Humans Algorithms Genetic Variation Machine Learning
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MIDAA: deep archetypal analysis for interpretable multi-omic data integration based on biological principles.

Genome biology Apr 8, 2025
High-throughput multi-omic molecular profiling allows the probing of biological systems at unprecedented resolution. However, integrating and interpreting high-dimensional, sparse, and noisy multimodal datasets remains challenging. Deriving new biolo...
Multiomics Deep Learning Genomics Computational Biology Humans Software
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DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations.

BMC bioinformatics Apr 8, 2025
Gene expression is the basis for cells to achieve various functions, while DNA methylation constitutes a critical epigenetic mechanism governing gene expression regulation. Here we propose DeepMethyGene, an adaptive recursive convolutional neural net...
Deep Learning Computational Biology Epigenesis, Genetic DNA Methylation Neural Networks, Computer Humans Software Transcription Initiation Site
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Data splitting to avoid information leakage with DataSAIL.

Nature communications Apr 8, 2025
Information leakage is an increasingly important topic in machine learning research for biomedical applications. When information leakage happens during a model's training, it risks memorizing the training data instead of learning generalizable prope...
Algorithms Machine Learning Humans Software
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Subtractive genomics approach: A guide to unveiling therapeutic targets across pathogens.

Journal of microbiological methods Apr 7, 2025
Subtractive genomics is an adaptable bioinformatics technique that is used to identify potential therapeutic targets by differentiating essential genes in pathogens and non-pathogenic genes. Since, identification of therapeutic targets and understand...
Humans Software Bacteria Drug Discovery Computational Biology Genomics Genome, Bacterial
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scAMZI: attention-based deep autoencoder with zero-inflated layer for clustering scRNA-seq data.

BMC genomics Apr 7, 2025
BACKGROUND: Clustering scRNA-seq data plays a vital role in scRNA-seq data analysis and downstream analyses. Many computational methods have been proposed and achieved remarkable results. However, there are several limitations of these methods. First...
Sequence Analysis, RNA Cluster Analysis Autoencoder Single-Cell Gene Expression Analysis Computational Biology Single-Cell Analysis RNA-Seq Humans Algorithms Deep Learning Software
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CGLoop: a neural network framework for chromatin loop prediction.

BMC genomics Apr 5, 2025
BACKGROUND: Chromosomes of species exhibit a variety of high-dimensional organizational features, and chromatin loops, which are fundamental structures in the three-dimensional (3D) structure of the genome. Chromatin loops are visible speckled patter...
Deep Learning Computational Biology Neural Networks, Computer Software Chromatin Humans
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