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.
Machine learning predicts plant phenotypes from soil microbiome data.
New algorithm improves plant breeding by clustering soybean genotypes more accurately and efficiently.
Interpretable neural network for plant traits and species identification.
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…
Framework generates realistic crop images for growth modeling.
While linear mixed model (LMM) has shown a competitive performance in correcting spurious associations raised by population stratification, family structures, and cryptic relatedness, more challenges are still to be addressed regarding the complex structure of genotypic and phenotypic data. For example, geneticists hav…
We consider multi-response and multitask regression models, where the parameter matrix to be estimated is expected to have an unknown grouping structure. The groupings can be along tasks, or features, or both, the last one indicating a bi-cluster or "checkerboard" structure. Discovering this grouping structure along wi…
Inferring predictive maps between multiple input and multiple output variables or tasks has innumerable applications in data science. Multi-task learning attempts to learn the maps to several output tasks simultaneously with information sharing between them. We propose a novel multi-task learning framework for sparse l…
Deep neural networks have shown excellent performances in many real-world applications. Unfortunately, they may show "Clever Hans"-like behavior -- making use of confounding factors within datasets -- to achieve high performance. In this work, we introduce the novel learning setting of "explanatory interactive learning…
Availability of an explainable deep learning model that can be applied to practical real world scenarios and in turn, can consistently, rapidly and accurately identify specific and minute traits in applicable fields of biological sciences, is scarce. Here we consider one such real world example viz., accurate identific…
Motion planning for robots of high degrees-of-freedom (DOFs) is an important problem in robotics with sampling-based methods in configuration space C as one popular solution. Recently, machine learning methods have been introduced into sampling-based motion planning methods, which train a classifier to distinguish coll…
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 …
Bayesian model enhances phenotype discovery in asthma EHRs.
Model identifies key problems in HIV patients' records.
This paper reviews methods for discovering patient subgroups from EHR data.
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…
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…
Develops methods for GWAS of high dimensional phenotypes using summary statistics.
ODBAE detects complex phenotypes in biological data.
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.
WEST uses EHRs and expert cases to improve rare disease phenotyping.
OMTL uses ontology to learn from imbalanced EHR data.
We develop a model to cluster time-series data with interval censoring, improving disease phenotyping.
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 …
A new framework detects changepoints in complex data.
Spectral algorithms solve optimal community detection and related problems.
Exact partitioning of high-order planted models achieved through convex optimization.
The paper uses VGG-19 for plant species classification from leaf images.
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.
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…
New method phenotypes sleep apnea patients using time series analysis.
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…
New insights link diverse statistical problems via secret leakage planted clique.
Tackles the computational hardness of HPC detection, conjecturing equivalence to PC detection.
Plants monitor their surrounding environment and control their physiological functions by producing an electrical response. We recorded electrical signals from different plants by exposing them to Sodium Chloride (NaCl), Ozone (O3) and Sulfuric Acid (H2SO4) under laboratory conditions. After applying pre-processing tec…
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…