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This paper presents a novel method for unsupervised segmentation of pathology images. Staging of lung cancer is a major factor of prognosis. Measuring the maximum dimensions of the invasive component in a pathology images is an essential…

Feature selection methods have an important role on the readability of data and the reduction of complexity of learning algorithms. In recent years, a variety of efforts are investigated on feature selection problems based on unsupervised…

We consider the problem of segmenting an image into superpixels in the context of $k$-means clustering, in which we wish to decompose an image into local, homogeneous regions corresponding to the underlying objects. Our novel approach…

This paper proposes an efficient unsupervised method for detecting relevant changes between two temporally different images of the same scene. A convolutional neural network (CNN) for semantic segmentation is implemented to extract…

Background: Current research suggests that a small set of "driver" mutations are responsible for tumorigenesis while a larger body of "passenger" mutations occurs in the tumor but does not progress the disease. Due to recent pharmacological…

Background and purpose: Heart disease has been one of the most important causes of death in the last 10 years, so the use of classification methods to diagnose and predict heart disease is very important. If this disease is predicted before…

We present an algorithm for multi-scale tumor (chimeric cell) detection in high resolution slide scans. The broad range of tumor sizes in our dataset pose a challenge for current Convolutional Neural Networks (CNN) which often fail when…

Subspace clustering methods based on data self-expression have become very popular for learning from data that lie in a union of low-dimensional linear subspaces. However, the applicability of subspace clustering has been limited because…

Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…

We develop a novel algorithm, Predictive Hierarchical Clustering (PHC), for agglomerative hierarchical clustering of current procedural terminology (CPT) codes. Our predictive hierarchical clustering aims to cluster subgroups, not…

Accurate cell type annotation is a crucial step in analyzing single-cell RNA sequencing (scRNA-seq) data, which provides valuable insights into cellular heterogeneity. However, due to the high dimensionality and prevalence of zero elements…

We consider detecting objects in an image by iteratively selecting from a set of arbitrarily shaped candidate regions. Our generic approach, which we term visual chunking, reasons about the locations of multiple object instances in an image…

Clustering, like covariate selection for classification, is an important step to compress and interpret the data. However, clustering of covariates is often performed independently of the classification step, which can lead to undesirable…

Medical ultrasound image segmentation presents a formidable challenge in the realm of computer vision. Traditional approaches rely on Convolutional Neural Networks (CNNs) and Transformer-based methods to address the intricacies of medical…

Semi-supervised learning has made significant strides in the medical domain since it alleviates the heavy burden of collecting abundant pixel-wise annotated data for semantic segmentation tasks. Existing semi-supervised approaches enhance…

DNA methylation is a significant driver of cell-type heterogeneity and has been implicated in various regulatory processes ranging from cell differentiation to imprinting. As the methyl group is embedded in the DNA molecule, assessing DNA…

Mixed communities of organisms are found in many environments (from the human gut to marine ecosystems) and can have profound impact on human health and the environment. Metagenomics studies the genomic material of such communities through…

Colorectal cancer remains a major global health concern, with early detection being pivotal for improving patient outcomes. In this study, we leveraged high throughput methylation profiling of cellfree DNA to identify and validate…

We present a convex approach to probabilistic segmentation and modeling of time series data. Our approach builds upon recent advances in multivariate total variation regularization, and seeks to learn a separate set of parameters for the…

This paper presents a simple yet effective two-stage framework for semi-supervised medical image segmentation. Unlike prior state-of-the-art semi-supervised segmentation methods that predominantly rely on pseudo supervision directly on…