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.
Bayesian model enhances phenotype discovery in asthma EHRs.
Tensor factorization models offer an effective approach to convert massive electronic health records into meaningful clinical concepts (phenotypes) for data analysis. These models need a large amount of diverse samples to avoid population bias. An open challenge is how to derive phenotypes jointly across multiple hospi…
This paper reviews methods for discovering patient subgroups from EHR data.
Understanding the phenotypic drug response on cancer cell lines plays a vital rule in anti-cancer drug discovery and re-purposing. The Genomics of Drug Sensitivity in Cancer (GDSC) database provides open data for researchers in phenotypic screening to test their models and methods. Previously, most research in these ar…
We develop a model to cluster time-series data with interval censoring, improving disease phenotyping.
Exponential growth in Electronic Healthcare Records (EHR) has resulted in new opportunities and urgent needs for discovery of meaningful data-driven representations and patterns of diseases in Computational Phenotyping research. Deep Learning models have shown superior performance for robust prediction in computational…
WEST uses EHRs and expert cases to improve rare disease phenotyping.
The increasing size and complexity of scientific data could dramatically enhance discovery and prediction for basic scientific applications. Realizing this potential, however, requires novel statistical analysis methods that are both interpretable and predictive. We introduce Union of Intersections (UoI), a flexible, m…
Method uses network biology to construct gene expression models for cancer.
Identifying measurable genetic indicators (or biomarkers) of a specific condition of a biological system is a key element of precision medicine. Indeed it allows to tailor diagnostic, prognostic and treatment choice to individual characteristics of a patient. In machine learning terms, biomarker discovery can be framed…
Characterization of a patient clinical phenotype is central to biomedical informatics. ICD codes, assigned to inpatient encounters by coders, is important for population health and cohort discovery when clinical information is limited. While ICD codes are assigned to patients by professionals trained and certified in c…
Given genetic variations and various phenotypical traits, such as Magnetic Resonance Imaging (MRI) features, we consider two important and related tasks in biomedical research: i)to select genetic and phenotypical markers for disease diagnosis and ii) to identify associations between genetic and phenotypical data. Thes…
Visual summarization of clinical data collected on patients contained within the electronic health record (EHR) may enable precise and rapid triage at the time of patient presentation to an emergency department (ED). The triage process is critical in the appropriate allocation of resources and in anticipating eventual …
Disease phenotyping algorithms process observational clinical data to identify patients with specific diseases. Supervised phenotyping methods require significant quantities of expert-labeled data, while unsupervised methods may learn non-disease phenotypes. To address these limitations, we propose the Semi-Supervised …
Electronic phenotyping is the task of ascertaining whether an individual has a medical condition of interest by analyzing their medical record and is foundational in clinical informatics. Increasingly, electronic phenotyping is performed via supervised learning. We investigate the effectiveness of multitask learning fo…
VBphenoR uses variational Bayes for EHR-based patient phenotyping.
It has been recently shown that sparse, nonnegative tensor factorization of multi-modal electronic health record data is a promising approach to high-throughput computational phenotyping. However, such approaches typically do not leverage available domain knowledge while extracting the phenotypes; hence, some of the su…
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…
The widely used genetic pleiotropic analysis of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high dimensional genotype (next-generation sequencing) data. To overcome these limitations, we …
Model identifies key problems in HIV patients' records.
Federated learning improves bioinformatics by sharing data legally.
Objective: We investigate whether deep learning techniques for natural language processing (NLP) can be used efficiently for patient phenotyping. Patient phenotyping is a classification task for determining whether a patient has a medical condition, and is a crucial part of secondary analysis of healthcare data. We ass…
Develops methods for GWAS of high dimensional phenotypes using summary statistics.
ODBAE detects complex phenotypes in biological data.
A looming question that must be solved before robotic plant phenotyping capabilities can have significant impact to crop improvement programs is scalability. High Throughput Phenotyping (HTP) uses robotic technologies to analyze crops in order to determine species with favorable traits, however, the current practices r…
The goal of feature selection is to identify important features that are relevant to explain an outcome variable. Most of the work in this domain has focused on identifying globally relevant features, which are features that are related to the outcome using evidence across the entire dataset. We study a more fine-grain…
Traditional anatomical analyses captured only a fraction of real phenomic information. Here, we apply deep learning to quantify total phenotypic similarity across 2468 butterfly photographs, covering 38 subspecies from the polymorphic mimicry complex of and . E…
SWoTTeD discovers hidden temporal patterns in EHR data.
OMTL uses ontology to learn from imbalanced EHR data.
Study develops electronic phenotypes of ICU patient acuity.
Acute Kidney Injury (AKI) is a common clinical syndrome characterized by the rapid loss of kidney excretory function, which aggravates the clinical severity of other diseases in a large number of hospitalized patients. Accurate early prediction of AKI can enable in-time interventions and treatments. However, AKI is hig…
Baseline injury categorization is important to traumatic brain injury (TBI) research and treatment. Current categorization is dominated by symptom-based scores that insufficiently capture injury heterogeneity. In this work, we apply unsupervised clustering to identify novel TBI phenotypes. Our approach uses a generaliz…
Phenotyping electronic health records (EHR) focuses on defining meaningful patient groups (e.g., heart failure group and diabetes group) and identifying the temporal evolution of patients in those groups. Tensor factorization has been an effective tool for phenotyping. Most of the existing works assume either a static …
The increased affordability of whole genome sequencing has motivated its use for phenotypic studies. We address the problem of learning interpretable models for discrete phenotypes from whole genomes. We propose a general approach that relies on the Set Covering Machine and a k-mer representation of the genomes. We sho…
Binary PheNorm extends phenotype labeling for EHRs using binary silver labels.
New method phenotypes sleep apnea patients using time series analysis.
Machine learning predicts plant phenotypes from soil microbiome data.
Study developed phenotypes for ICU patients' brain dysfunction states.
As an increasing number of genome-wide association studies reveal the limitations of attempting to explain phenotypic heritability by single genetic loci, there is growing interest for associating complex phenotypes with sets of genetic loci. While several methods for multi-locus mapping have been proposed, it is often…
The paper presents a systematic review of state-of-the-art approaches to identify patient cohorts using electronic health records. It gives a comprehensive overview of the most commonly de-tected phenotypes and its underlying data sets. Special attention is given to preprocessing of in-put data and the different modeli…
The paper tackles high-dimensional mixed linear regression with unknown parameters and proposes methods for estimation, confidence intervals, and hypothesis testing.
New algorithm improves plant breeding by clustering soybean genotypes more accurately and efficiently.
This work proposes a new algorithm for automated and simultaneous phenotyping of multiple co-occurring medical conditions, also referred as comorbidities, using clinical notes from the electronic health records (EHRs). A basic latent factor estimation technique of non-negative matrix factorization (NMF) is augmented wi…
The recent adoption of Electronic Health Records (EHRs) by health care providers has introduced an important source of data that provides detailed and highly specific insights into patient phenotypes over large cohorts. These datasets, in combination with machine learning and statistical approaches, generate new opport…
We propose a non-parametric regression methodology, Random Forests on Distance Matrices (RFDM), for detecting genetic variants associated to quantitative phenotypes representing the human brain's structure or function, and obtained using neuroimaging techniques. RFDM, which is an extension of decision forests, requires…
Fast and cheaper next generation sequencing technologies will generate unprecedentedly massive and highly-dimensional genomic and epigenomic variation data. In the near future, a routine part of medical record will include the sequenced genomes. A fundamental question is how to efficiently extract genomic and epigenomi…
With large volumes of health care data comes the research area of computational phenotyping, making use of techniques such as machine learning to describe illnesses and other clinical concepts from the data itself. The "traditional" approach of using supervised learning relies on a domain expert, and has two main limit…
We developed OmicsMapNet approach to take advantage of existing deep leaning frameworks to analyze high-dimensional omics data as 2-dimensional images. The omics data of individual samples were first rearranged into 2D images in which molecular features related in functions, ontologies, or other relationships were orga…