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.
Study reduces complexity and uncertainty in human atrial cell models.
GPMI method interpolates uncertain atrial conduction velocity on non-Euclidean manifolds.
Left atrium shape has been shown to be an independent predictor of recurrence after atrial fibrillation (AF) ablation. Shape-based representation is imperative to such an estimation process, where correspondence-based representation offers the most flexibility and ease-of-computation for population-level shape statisti…
TIMELY improves consistency in labeling blood cell images.
Counting and classifying blood cells is an important diagnostic tool in medicine. Support Vector Machines are increasingly popular and efficient and could replace artificial neural network systems. Here a method to classify blood cells is proposed using SVM. A set of statistics on images are implemented in C++. The MPE…
We present a convolutional-recurrent neural network architecture with long short-term memory for real-time processing and classification of digital sensor data. The network implicitly performs typical signal processing tasks such as filtering and peak detection, and learns time-resolved embeddings of the input signal. …
We develop a latent variable model and an efficient spectral algorithm motivated by the recent emergence of very large data sets of chromatin marks from multiple human cell types. A natural model for chromatin data in one cell type is a Hidden Markov Model (HMM); we model the relationship between multiple cell types by…
We tackle the problem of classifying Electrocardiography (ECG) signals with the aim of predicting the onset of Paroxysmal Atrial Fibrillation (PAF). Atrial fibrillation is the most common type of arrhythmia, but in many cases PAF episodes are asymptomatic. Therefore, in order to help diagnosing PAF, it is important to …
Atrial fibrillation is a cardiac arrhythmia that affects an estimated 33.5 million people globally and is the potential cause of 1 in 3 strokes in people over the age of 60. Detection and diagnosis of atrial fibrillation (AFIB) is done noninvasively in the clinical environment through the evaluation of electrocardiogra…
New method extracts biological concepts from cell microscopy images.
In this work we apply variations of ResNet architecture to the task of atrial fibrillation classification. Variations differ in number of filter after first convolution, ResNet block layout, number of filters in block convolutions and number of ResNet blocks between downsampling operations. We have found a range of mod…
The development of new technology such as wearables that record high-quality single channel ECG, provides an opportunity for ECG screening in a larger population, especially for atrial fibrillation screening. The main goal of this study is to develop an automatic classification algorithm for normal sinus rhythm (NSR), …
New method classifies reticulocytes from red blood cells without labels.
Understanding cell identity is an important task in many biomedical areas. Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are not available for many cell types. A second approach is to use machine learning to discriminate cell types based on th…
Study shows GAN and GMM data augmentation improves AF signal classification accuracy.
Accurately predicting drug responses to cancer is an important problem hindering oncologists' efforts to find the most effective drugs to treat cancer, which is a core goal in precision medicine. The scientific community has focused on improving this prediction based on genomic, epigenomic, and proteomic datasets measu…
Difficult image segmentation problems, for instance left atrium MRI, can be addressed by incorporating shape priors to find solutions that are consistent with known objects. Nonetheless, a single multivariate Gaussian is not an adequate model in cases with significant nonlinear shape variation or where the prior distri…
Complex numbers have long been favoured for digital signal processing, yet complex representations rarely appear in deep learning architectures. RNNs, widely used to process time series and sequence information, could greatly benefit from complex representations. We present a novel complex gated recurrent cell, which i…
Determining the localization of specific protein in human cells is important for understanding cellular functions and biological processes of underlying diseases. Among imaging techniques, high-throughput fluorescence microscopy imaging is an efficient biotechnology to stain the protein of interest in a cell. In this w…
This technical note considers the problems of blind sparse learning and inference of electrogram (EGM) signals under atrial fibrillation (AF) conditions. First of all we introduce a mathematical model for the observed signals that takes into account the multiple foci typically appearing inside the heart during AF. Then…
A Deep Autoencoder based content retrieval algorithm is proposed for prediction and differentiation of cancer types based on the presence of epigenetic patterns of DNA methylation identified in genetic regions known as CpG islands. The developed deep learning system uses a CpG island state classification sub-system to …
We aim to produce predictive models that are not only accurate, but are also interpretable to human experts. Our models are decision lists, which consist of a series of if...then... statements (e.g., if high blood pressure, then stroke) that discretize a high-dimensional, multivariate feature space into a series of sim…
Analysis of flow cytometry data is an essential tool for clinical diagnosis of hematological and immunological conditions. Current clinical workflows rely on a manual process called gating to classify cells into their canonical types. This dependence on human annotation limits the rate, reproducibility, and complexity …
Recent efforts to improve the interpretability of deep neural networks use saliency to characterize the importance of input features to predictions made by models. Work on interpretability using saliency-based methods on Recurrent Neural Networks (RNNs) has mostly targeted language tasks, and their applicability to tim…
Classifying chemicals according to putative modes of action (MOAs) is of paramount importance in the context of risk assessment. However, current methods are only able to handle a very small proportion of the existing chemicals. We address this issue by proposing an integrative deep learning architecture that learns a …
Model predicts anti-cancer drug responses using gene and molecular data.
In this article, we propose a novel ECG classification framework for atrial fibrillation (AF) detection using spectro-temporal representation (i.e., time varying spectrum) and deep convolutional networks. In the first step we use a Bayesian spectro-temporal representation based on the estimation of time-varying coeffic…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient sharing of research material through community databases have opened up new view…
The article focuses on determining the predictive uncertainty of a model on the example of atrial fibrillation detection problem by a single-lead ECG signal. To this end, the model predicts parameters of the beta distribution over class probabilities instead of these probabilities themselves. It was shown that the desc…
Atrial Fibrillation (AF) is a common electro-physiological cardiac disorder that causes changes in the anatomy of the atria. A better characterization of these changes is desirable for the definition of clinical biomarkers, furthermore, thus there is a need for its fully automatic segmentation from clinical images. In …
CRL approach improves understanding of heterogeneous treatment effects in complex diseases.
Method infers TCR effects on disease using patient data.
The visual systems of many mammals, including humans, is able to integrate the geometric information of visual stimuli and to perform cognitive tasks already at the first stages of the cortical processing. This is thought to be the result of a combination of mechanisms, which include feature extraction at single cell l…
The aim of this paper is to construct a natural Riemann-Lagrange differential geometry on 1-jet spaces, in the sense of nonlinear connections, generalized Cartan connections, d-torsions, d-curvatures, jet electromagnetic fields and jet electromagnetic Yang-Mills energies, starting from some given nonlinear evolution OD…
Diagnosing basal cell carcinomas (BCC), one of the most common cutaneous malignancies in humans, is a task regularly performed by pathologists and dermato-pathologists. Improving histological diagnosis by providing diagnosis suggestions, i.e. computer-assisted diagnoses is actively researched to improve safety, quality…
We consider learning ancestral causal relationships in high dimensions. Our approach is driven by a supervised learning perspective, with discrete indicators of causal relationships treated as labels to be learned from available data. We focus on the setting in which some causal (ancestral) relationships are known (via…
A new method learns manifold-valued latents without an encoder.
A new method improves data representation for diverse tasks.
SRCA reduces high-dimensional data to lower dimensions while preserving geometric structures.
Independent component analysis (ICA) aims at decomposing an observed random vector into statistically independent variables. Deflation-based implementations, such as the popular one-unit FastICA algorithm and its variants, extract the independent components one after another. A novel method for deflationary ICA, referr…
ALPODS AI diagnoses high-dimensional biomedical data with human-understandable explanations.
Developing neural network image classification models often requires significant architecture engineering. In this paper, we study a method to learn the model architectures directly on the dataset of interest. As this approach is expensive when the dataset is large, we propose to search for an architectural building bl…
Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interact in vivo as components of larger molecular machines. Understanding how these high-order in…
Kernel testing compares cell states in single-cell data.
A novel method detects multiple mitosis events and mitigates annotation gaps in phase-contrast microscopy.
Cell detection and cell type classification from biomedical images play an important role for high-throughput imaging and various clinical application. While classification of single cell sample can be performed with standard computer vision and machine learning methods, analysis of multi-label samples (region containi…
Forest Fire Clustering discovers cell types from single-cell data.
Proposes CCCVAE for better single-cell clustering with cell-cell communication.