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The assessment of diversity and similarity is relevant in monitoring the status of ecosystems. The respective indicators are based on the taxonomic composition of biological communities of interest, currently estimated through the…
MicroRNAs (miRNAs) are small non-coding RNAs that function as regulators of gene expression. In recent years, there has been a tremendous and growing interest among researchers to investigate the role of miRNAs in normal cellular as well as…
In cancer research, high-throughput profiling has been extensively conducted. In recent studies, the integrative analysis of data on multiple cancer patient groups/subgroups has been conducted. Such analysis has the potential to reveal the…
Heterogeneity is a hallmark of complex diseases. Regression-based heterogeneity analysis, which is directly concerned with outcome-feature relationships, has led to a deeper understanding of disease biology. Such an analysis identifies the…
A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor reoccurs. Genome sequencing and…
High throughput technologies have become the practice of choice for comparative studies in biomedical applications. Limited number of sample points due to sequencing cost or access to organisms of interest necessitates the development of…
Biopsies are the gold standard for breast cancer diagnosis. This task can be improved by the use of Computer Aided Diagnosis (CAD) systems, reducing the time of diagnosis and reducing the inter and intra-observer variability. The advances…
Recent technological advancements have enabled detailed investigation of associations between the molecular architecture and tumor heterogeneity, through multi-source integration of radiological imaging and genomic (radiogenomic) data. In…
The cellular composition of the tumor microenvironment can directly impact cancer progression and the efficacy of therapeutics. Understanding immune cell activity, the body's natural defense mechanism, in the vicinity of cancerous cells is…
Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and…
It is well known that tumors originating from the same tissue have different prognosis and sensitivity to treatments. Over the last decade, cancer genomics consortia like the Cancer Genome Atlas (TCGA) have been generating thousands of…
We present a machine learning method capable of accurately detecting chromosome abnormalities that cause blood cancers directly from microscope images of the metaphase stage of cell division. The pipeline is built on a series of fine-tuned…
Advance in medical imaging is an important part in deep learning research. One of the goals of computer vision is development of a holistic, comprehensive model which can identify tumors from histology slides obtained via biopsies. A major…
Risk stratification is a key tool in clinical decision-making, yet current approaches often fail to translate sophisticated survival analysis into actionable clinical criteria. We present a novel method for unsupervised machine learning…
Cancer survival prediction is important for developing personalized treatments and inducing disease-causing mechanisms. Multi-omics data integration is attracting widespread interest in cancer research for providing information for…
Targeted amplicon panels are widely used in oncology diagnostics, but providing per-gene performance guarantees for copy number variant (CNV) detection remains challenging due to amplification artifacts, process-mismatch heterogeneity, and…
Bayesian Neural Networks (BNNs) provide a tool to estimate the uncertainty of a neural network by considering a distribution over weights and sampling different models for each input. In this paper, we propose a method for uncertainty…
The appropriateness of the Poisson model is frequently challenged when examining spatial count data marked by unbalanced distributions, over-dispersion, or under-dispersion. Moreover, traditional parametric models may inadequately capture…
Despite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep…
Heterogeneity in characteristics from one region (sub-population) to another, commonly observed in complex systems, such as glasses and a collection of cells, is hard to describe theoretically. In the context of cancer, intra-tumor…