A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Deep learning model explains breast cancer subtypes using logistic regression.
We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likel…
Due to the complexity of cancer, clustering algorithms have been used to disentangle the observed heterogeneity and identify cancer subtypes that can be treated specifically. While kernel based clustering approaches allow the use of more than one input matrix, which is an important factor when considering a multidimens…
Personalized treatment of patients based on tissue-specific cancer subtypes has strongly increased the efficacy of the chosen therapies. Even though the amount of data measured for cancer patients has increased over the last years, most cancer subtypes are still diagnosed based on individual data sources (e.g. gene exp…
New method clusters disease subtypes from model explanations.
New framework distinguishes lung cancer subtypes using MALDI mass spectrometry.
Precision medicine aims for personalized prognosis and therapeutics by utilizing recent genome-scale high-throughput profiling techniques, including next-generation sequencing (NGS). However, translating NGS data faces several challenges. First, NGS count data are often overdispersed, requiring appropriate modeling. Se…
Paper proposes scalable method for analyzing multi-omic data.
In many applications, multivariate samples may harbor previously unrecognized heterogeneity at the level of conditional independence or network structure. For example, in cancer biology, disease subtypes may differ with respect to subtype-specific interplay between molecular components. Then, both subtype discovery and…
Bayesian model clusters diverse 'omics data for disease subtyping.
Unlike common cancers, such as those of the prostate and breast, tumor grading in rare cancers is difficult and largely undefined because of small sample sizes, the sheer volume of time needed to undertake on such a task, and the inherent difficulty of extracting human-observed patterns. One of the most challenging exa…
We present a novel method for extracting cancer signatures by applying statistical risk models (http://ssrn.com/abstract=2732453) from quantitative finance to cancer genome data. Using 1389 whole genome sequenced samples from 14 cancers, we identify an "overall" mode of somatic mutational noise. We give a prescription …
Study identifies biomarkers for lung cancer in female non-smokers.
Diverse applications - particularly in tumour subtyping - have demonstrated the importance of integrative clustering techniques for combining information from multiple data sources. Cluster-Of-Clusters Analysis (COCA) is one such approach that has been widely applied in the context of tumour subtyping. However, the pro…
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 Neural Networks (DNNs) that is capable of simultaneous inference of various properti…
VICatMix clusters categorical biomedical data efficiently and selects relevant variables.
The medical research facilitates to acquire a diverse type of data from the same individual for particular cancer. Recent studies show that utilizing such diverse data results in more accurate predictions. The major challenge faced is how to utilize such diverse data sets in an effective way. In this paper, we introduc…
Many researches demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish different subtypes of the tumor. However, the conventional statistical methods …
Multi-view data, that is matched sets of measurements on the same subjects, have become increasingly common with advances in multi-omics technology. Often, it is of interest to find associations between the views that are related to the intrinsic class memberships. Existing association methods cannot directly incorpora…
OPAL optimizes labeling strategy for precise inference from uncertain models.
A hybrid method clusters and characterizes cancer data efficiently.
The task of clustering a set of objects based on multiple sources of data arises in several modern applications. We propose an integrative statistical model that permits a separate clustering of the objects for each data source. These separate clusterings adhere loosely to an overall consensus clustering, and hence the…
Many real-world tasks such as classification of digital histopathology images and 3D object detection involve learning from a set of instances. In these cases, only a group of instances or a set, collectively, contains meaningful information and therefore only the sets have labels, and not individual data instances. In…
The ability to accurately classify disease subtypes is of vital importance, especially in oncology where this capability could have a life saving impact. Here we report a classification between two subtypes of non-small cell lung cancer, namely Adeno- carcinoma vs Squamous cell carcinoma. The data consists of approxima…
ERICA assesses replicability of cluster analysis results.
Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists' capability to discover functional relevance of their experiment design. While elucidating gene set individually, inter gene sets association is rarely taken into co…
We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. This framework is designed to enable detection of clusters of data in the presence of structural requirements which we encode as algebraic constraints in a linear program. Our cluste…
We introduce a new discriminant analysis method (Empirical Discriminant Analysis or EDA) for binary classification in machine learning. Given a dataset of feature vectors, this method defines an empirical feature map transforming the training and test data into new data with components having Gaussian empirical distrib…
CN-SBM clusters cancer samples and regions based on copy number variants.
Integrative analysis of disparate data blocks measured on a common set of experimental subjects is a major challenge in modern data analysis. This data structure naturally motivates the simultaneous exploration of the joint and individual variation within each data block resulting in new insights. For instance, there i…
Flow cytometry is often used to characterize the malignant cells in leukemia and lymphoma patients, traced to the level of the individual cell. Typically, flow cytometric data analysis is performed through a series of 2-dimensional projections onto the axes of the data set. Through the years, clinicians have determined…
Study identifies five AD subtypes using graph diffusion and similarity learning.
Machine learning models for medical image analysis often suffer from poor performance on important subsets of a population that are not identified during training or testing. For example, overall performance of a cancer detection model may be high, but the model still consistently misses a rare but aggressive cancer su…
Efficient algorithm for Bayesian networks reduces marginal probability distribution computation.
Study proposes a model to improve patient subtyping from EHR data.
Exact hierarchical clustering algorithms for data analysis.
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of phenotypes makes high-throughput phenotype profiling a very difficult and labor…
Patient subtyping based on temporal observations can lead to significantly nuanced subtyping that acknowledges the dynamic characteristics of diseases. Existing methods for subtyping trajectories treat the evolution of clinical observations as a homogeneous process or employ data available at regular intervals. In real…
While developing their software, professional object-oriented (OO) software developers keep in their minds an image of the subtyping relation between types in their software. The goal of this paper is to present an observation about the graph of the subtyping relation in Java, namely the observation that, after the add…
Unsupervised method selects genes for tumor subtype discovery.
The fundamental aim of clustering algorithms is to partition data points. We consider tasks where the discovered partition is allowed to vary with some covariate such as space or time. One approach would be to use fragmentation-coagulation processes, but these, being Markov processes, are restricted to linear or tree s…
We present a global optimization approach for solving the maximum a-posteriori (MAP) clustering problem under the Gaussian mixture model.Our approach can accommodate side constraints and it preserves the combinatorial structure of the MAP clustering problem by formulating it asa mixed-integer nonlinear optimization pro…
We consider high-dimensional regression over subgroups of observations. Our work is motivated by biomedical problems, where disease subtypes, for example, may differ with respect to underlying regression models, but sample sizes at the subgroup-level may be limited. We focus on the case in which subgroup-specific model…
We release the largest public ECG dataset of continuous raw signals for representation learning containing 11 thousand patients and 2 billion labelled beats. Our goal is to enable semi-supervised ECG models to be made as well as to discover unknown subtypes of arrhythmia and anomalous ECG signal events. To this end, we…
We introduce a general framework for estimation of inverse covariance, or precision, matrices from heterogeneous populations. The proposed framework uses a Laplacian shrinkage penalty to encourage similarity among estimates from disparate, but related, subpopulations, while allowing for differences among matrices. We p…
Alzheimer's disease (AD) is a degenerative brain disease impairing a person's ability to perform day to day activities. The clinical manifestations of Alzheimer's disease are characterized by heterogeneity in age, disease span, progression rate, impairment of memory and cognitive abilities. Due to these variabilities, …
MAGIC uncovers disease heterogeneity across brain scales.
Smile-GANs clusters brain MRI scans to reveal disease subtypes and progression.