BioData Mining

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Assessment of emerging pretraining strategies in interpretable multimodal deep learning for cancer prognostication
BioData Mining - Tập 16 - Trang 1-24 - 2023
Zarif L. Azher, Anish Suvarna, Ji-Qing Chen, Ze Zhang, Brock C. Christensen, Lucas A. Salas, Louis J. Vaickus, Joshua J. Levy
Deep learning models can infer cancer patient prognosis from molecular and anatomic pathology information. Recent studies that leveraged information from complementary multimodal data improved prognostication, further illustrating the potential utility of such methods. However, current approaches: 1) do not comprehensively leverage biological and histomorphological relationships and 2) make use of...... hiện toàn bộ
A comparison of methods for interpreting random forest models of genetic association in the presence of non-additive interactions
BioData Mining - - 2021
Alena Orlenko, Jason H. Moore
Abstract Background Non-additive interactions among genes are frequently associated with a number of phenotypes, including known complex diseases such as Alzheimer’s, diabetes, and cardiovascular disease. Detecting interactions requires careful selection of analytical methods, and some machine learn...... hiện toàn bộ
Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation
BioData Mining - Tập 14 - Trang 1-25 - 2021
Mila Glavaški, Lazar Velicki
Biomedical knowledge is dispersed in scientific literature and is growing constantly. Curation is the extraction of knowledge from unstructured data into a computable form and could be done manually or automatically. Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease, with genotype–phenotype associations still incompletely understood. We compared human- and machine-cura...... hiện toàn bộ
Data mining and the evolution of biological complexity
BioData Mining - Tập 4 - Trang 1-2 - 2011
Davnah Urbach, Jason H Moore
Molecular network analysis of human microRNA targetome: from cancers to Alzheimer’s disease
BioData Mining - Tập 5 - Trang 1-22 - 2012
Jun-ichi Satoh
MicroRNAs (miRNAs), a class of endogenous small noncoding RNAs, mediate posttranscriptional regulation of protein-coding genes by binding chiefly to the 3’ untranslated region of target mRNAs, leading to translational inhibition, mRNA destabilization or degradation. A single miRNA concurrently downregulates hundreds of target mRNAs designated “targetome”, and thereby fine-tunes gene expression inv...... hiện toàn bộ
Xác định các chất hoạt động và cơ chế của gừng trong điều trị ung thư đại tràng dựa trên dược lý mạng và mô phỏng docking phân tử Dịch bởi AI
BioData Mining - Tập 14 Số 1 - 2021
Mengmeng Zhang, Dan Wang, Liang Feng, Rong Zhao, Xun Ye, Lin He, Li Ai, Chunjie Wu
Tóm tắt Đặt vấn đề và mục tiêu Ung thư đại tràng đang gia tăng với tỷ lệ cao và gừng (Zingiber officinale), như một loại thuốc thảo dược thông dụng, được gợi ý là một tác nhân tiềm năng cho ung thư đại tràng. Nghiên cứu này nhằm xác định các thành phần sinh học hoạt tính v...... hiện toàn bộ
CardioGxE, a catalog of gene-environment interactions for cardiometabolic traits
BioData Mining - Tập 7 - Trang 1-20 - 2014
Laurence D Parnell, Britt A Blokker, Hassan S Dashti, Paula-Dene Nesbeth, Brittany Elle Cooper, Yiyi Ma, Yu-Chi Lee, Ruixue Hou, Chao-Qiang Lai, Kris Richardson, José M Ordovás
Genetic understanding of complex traits has developed immensely over the past decade but remains hampered by incomplete descriptions of contribution to phenotypic variance. Gene-environment (GxE) interactions are one of these contributors and in the guise of diet and physical activity are important modulators of cardiometabolic phenotypes and ensuing diseases. We mined the scientific literature to...... hiện toàn bộ
A comparison and evaluation of five biclustering algorithms by quantifying goodness of biclusters for gene expression data
BioData Mining - Tập 5 - Trang 1-10 - 2012
Li Li, Yang Guo, Wenwu Wu, Youyi Shi, Jian Cheng, Shiheng Tao
Several biclustering algorithms have been proposed to identify biclusters, in which genes share similar expression patterns across a number of conditions. However, different algorithms would yield different biclusters and further lead to distinct conclusions. Therefore, some testing and comparisons between these algorithms are strongly required. In this study, five biclustering algorithms (i.e. BI...... hiện toàn bộ
Joint analysis of multiple high-dimensional data types using sparse matrix approximations of rank-1 with applications to ovarian and liver cancer
BioData Mining - Tập 9 - Trang 1-28 - 2016
Gordon Okimoto, Ashkan Zeinalzadeh, Tom Wenska, Michael Loomis, James B. Nation, Tiphaine Fabre, Maarit Tiirikainen, Brenda Hernandez, Owen Chan, Linda Wong, Sandi Kwee
Technological advances enable the cost-effective acquisition of Multi-Modal Data Sets (MMDS) composed of measurements for multiple, high-dimensional data types obtained from a common set of bio-samples. The joint analysis of the data matrices associated with the different data types of a MMDS should provide a more focused view of the biology underlying complex diseases such as cancer that would no...... hiện toàn bộ
Genetic variants and their interactions in disease risk prediction – machine learning and network perspectives
BioData Mining - Tập 6 - Trang 1-16 - 2013
Sebastian Okser, Tapio Pahikkala, Tero Aittokallio
A central challenge in systems biology and medical genetics is to understand how interactions among genetic loci contribute to complex phenotypic traits and human diseases. While most studies have so far relied on statistical modeling and association testing procedures, machine learning and predictive modeling approaches are increasingly being applied to mining genotype-phenotype relationships, al...... hiện toàn bộ
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