ScInfoVAE: interpretable dimensional reduction of single cell transcription data with variational autoencoders and extended mutual information regularization
Single-cell RNA-sequencing (scRNA-seq) data can serve as a good indicator of cell-to-cell heterogeneity and can aid in the study of cell growth by identifying cell types. Recently, advances in Variational Auto... (Source: BioData Mining)
Source: BioData Mining - June 10, 2023 Category: Bioinformatics Authors: Weiquan Pan, Faning Long and Jian Pan Tags: Research Source Type: research
Changing word meanings in biomedical literature reveal pandemics and new technologies
While we often think of words as having a fixed meaning that we use to describe a changing world, words are also dynamic and changing. Scientific research can also be remarkably fast-moving, with new concepts ... (Source: BioData Mining)
Source: BioData Mining - May 5, 2023 Category: Bioinformatics Authors: David N. Nicholson, Faisal Alquaddoomi, Vincent Rubinetti and Casey S. Greene Tags: Software Source Type: research
A self-inspected adaptive SMOTE algorithm (SASMOTE) for highly imbalanced data classification in healthcare
In many healthcare applications, datasets for classification may be highly imbalanced due to the rare occurrence of target events such as disease onset. The SMOTE (Synthetic Minority Over-sampling Technique) a... (Source: BioData Mining)
Source: BioData Mining - April 25, 2023 Category: Bioinformatics Authors: Tanapol Kosolwattana, Chenang Liu, Renjie Hu, Shizhong Han, Hua Chen and Ying Lin Tags: Research Source Type: research
Automated quantitative trait locus analysis (AutoQTL)
Quantitative Trait Locus (QTL) analysis and Genome-Wide Association Studies (GWAS) have the power to identify variants that capture significant levels of phenotypic variance in complex traits. However, effort ... (Source: BioData Mining)
Source: BioData Mining - April 10, 2023 Category: Bioinformatics Authors: Philip J. Freda, Attri Ghosh, Elizabeth Zhang, Tianhao Luo, Apurva S. Chitre, Oksana Polesskaya, Celine L. St. Pierre, Jianjun Gao, Connor D. Martin, Hao Chen, Angel G. Garcia-Martinez, Tengfei Wang, Wenyan Han, Keita Ishiwari, Paul Meyer, Alexander Lampa Tags: Methodology Source Type: research
Reference-free phylogeny from sequencing data
Clustering of genetic sequences is one of the key parts of bioinformatics analyses. Resulting phylogenetic trees are beneficial for solving many research questions, including tracing the history of species, st... (Source: BioData Mining)
Source: BioData Mining - March 27, 2023 Category: Bioinformatics Authors: Petr Ry šavý and Filip Železný Tags: Research Source Type: research
Clinical assistant decision-making model of tuberculosis based on electronic health records
Tuberculosis is a dangerous infectious disease with the largest number of reported cases in China every year. Preventing missed diagnosis has an important impact on the prevention, treatment, and recovery of t... (Source: BioData Mining)
Source: BioData Mining - March 16, 2023 Category: Bioinformatics Authors: Mengying Wang, Cuixia Lee, Zhenhao Wei, Hong Ji, Yingyun Yang and Cheng Yang Tags: Research Source Type: research
Algorithm-based detection of acute kidney injury according to full KDIGO criteria including urine output following cardiac surgery: a descriptive analysis
Automated data analysis and processing has the potential to assist, improve and guide decision making in medical practice. However, by now it has not yet been fully integrated in a clinical setting. Herein we ... (Source: BioData Mining)
Source: BioData Mining - March 16, 2023 Category: Bioinformatics Authors: Nico Schmid, Mihnea Ghinescu, Moritz Schanz, Micha Christ, Severin Schricker, Markus Ketteler, Mark Dominik Alscher, Ulrich Franke and Nora Goebel Tags: Research Source Type: research
Unsupervised encoding selection through ensemble pruning for biomedical classification
Owing to the rising levels of multi-resistant pathogens, antimicrobial peptides, an alternative strategy to classic antibiotics, got more attention. A crucial part is thereby the costly identification and vali... (Source: BioData Mining)
Source: BioData Mining - March 16, 2023 Category: Bioinformatics Authors: Sebastian Sp änig, Alexander Michel and Dominik Heider Tags: Methodology Source Type: research
Genetics and precision health: the ecological fallacy and artificial intelligence solutions
(Source: BioData Mining)
Source: BioData Mining - March 13, 2023 Category: Bioinformatics Authors: Scott M. Williams and Jason H. Moore Tags: Editorial Source Type: research
Prediction of the risk of developing end-stage renal diseases in newly diagnosed type 2 diabetes mellitus using artificial intelligence algorithms
Type 2 diabetes mellitus (T2DM) imposes a great burden on healthcare systems, and these patients experience higher long-term risks for developing end-stage renal disease (ESRD). Managing diabetic nephropathy b... (Source: BioData Mining)
Source: BioData Mining - March 10, 2023 Category: Bioinformatics Authors: Shuo-Ming Ou, Ming-Tsun Tsai, Kuo-Hua Lee, Wei-Cheng Tseng, Chih-Yu Yang, Tz-Heng Chen, Pin-Jie Bin, Tzeng-Ji Chen, Yao-Ping Lin, Wayne Huey-Herng Sheu, Yuan-Chia Chu and Der-Cherng Tarng Tags: Research Source Type: research
Signature literature review reveals AHCY, DPYSL3, and NME1 as the most recurrent prognostic genes for neuroblastoma
Neuroblastoma is a childhood neurological tumor which affects hundreds of thousands of children worldwide, and information about its prognosis can be pivotal for patients, their families, and clinicians. One o... (Source: BioData Mining)
Source: BioData Mining - March 4, 2023 Category: Bioinformatics Authors: Davide Chicco, Tiziana Sanavia and Giuseppe Jurman Tags: Research Source Type: research
Ten simple rules for providing bioinformatics support within a hospital
Bioinformatics has become a key aspect of the biomedical research programmes of many hospitals ’ scientific centres, and the establishment of bioinformatics facilities within hospitals has become a common pract... (Source: BioData Mining)
Source: BioData Mining - February 23, 2023 Category: Bioinformatics Authors: Davide Chicco and Giuseppe Jurman Tags: Brief Report Source Type: research
iU-Net: a hybrid structured network with a novel feature fusion approach for medical image segmentation
In recent years, convolutional neural networks (CNNs) have made great achievements in the field of medical image segmentation, especially full convolutional neural networks based on U-shaped structures and ski... (Source: BioData Mining)
Source: BioData Mining - February 21, 2023 Category: Bioinformatics Authors: Yun Jiang, Jinkun Dong, Tongtong Cheng, Yuan Zhang, Xin Lin and Jing Liang Tags: Research Source Type: research
The Matthews correlation coefficient (MCC) should replace the ROC AUC as the standard metric for assessing binary classification
Binary classification is a common task for which machine learning and computational statistics are used, and the area under the receiver operating characteristic curve (ROC AUC) has become the common standard ... (Source: BioData Mining)
Source: BioData Mining - February 17, 2023 Category: Bioinformatics Authors: Davide Chicco and Giuseppe Jurman Tags: Methodology Source Type: research
LoFTK: a framework for fully automated calculation of predicted Loss-of-Function variants and genes
Loss-of-Function (LoF) variants in human genes are important due to their impact on clinical phenotypes and frequent occurrence in the genomes of healthy individuals. The association of LoF variants with compl... (Source: BioData Mining)
Source: BioData Mining - February 2, 2023 Category: Bioinformatics Authors: Abdulrahman Alasiri, Konrad J. Karczewski, Brian Cole, Bao-Li Loza, Jason H. Moore, Sander W. van der Laan, Folkert W. Asselbergs, Brendan J. Keating and Jessica van Setten Tags: Software Source Type: research
