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 identifies 30 common bacterial pathogens from Raman spectra.
Deep learning automates bacterial image classification.
Detection of protein-protein interactions (PPIs) plays a vital role in molecular biology. Particularly, infections are caused by the interactions of host and pathogen proteins. It is important to identify host-pathogen interactions (HPIs) to discover new drugs to counter infectious diseases. Conventional wet lab PPI pr…
MutaGAN predicts mutations of evolving protein populations using GANs.
Approximate Bayesian computation (ABC) can be used for model fitting when the likelihood function is intractable but simulating from the model is feasible. However, even a single evaluation of a complex model may take several hours, limiting the number of model evaluations available. Modelling the discrepancy between t…
The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and pathogenic processes, thus being a priority for the identification of vital compon…
Method corrects deep generative model likelihood scores for OOD detection.
Study identifies COVID-19 pneumonia from chest X-rays.
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs," which are communities of bacteria administered to patients for specific therapeuti…
New datasets support supervised learning for fungal BGC discovery.
New algorithm improves GAN stability and quality.
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…
Machine learning identifies key metabolic control circuits in bacterial pathways.
The presence of bacteria or fungi in the bloodstream of patients is abnormal and can lead to life-threatening conditions. A computational model based on a bidirectional long short-term memory artificial neural network, is explored to assist doctors in the intensive care unit to predict whether examination of blood cult…
We address the problem of estimating a sparse low-rank matrix from its noisy observation. We propose an objective function consisting of a data-fidelity term and two parameterized non-convex penalty functions. Further, we show how to set the parameters of the non-convex penalty functions, in order to ensure that the ob…
Avian Influenza breakouts cause millions of dollars in damage each year globally, especially in Asian countries such as China and South Korea. The impact magnitude of a breakout directly correlates to time required to fully understand the influenza virus, particularly the interspecies pathogenicity. The procedure requi…
The Set Covering Machine (SCM) is a greedy learning algorithm that produces sparse classifiers. We extend the SCM for datasets that contain a huge number of features. The whole genetic material of living organisms is an example of such a case, where the number of feature exceeds 10^7. Three human pathogens were used to…
We present a framework for online inference in the presence of a nonexhaustively defined set of classes that incorporates supervised classification with class discovery and modeling. A Dirichlet process prior (DPP) model defined over class distributions ensures that both known and unknown class distributions originate …
GeNet classifies metagenomic sequences with less memory and comparable recall to state-of-the-art methods.
Paper presents IPRC for robust tumor recognition using sparse representation.
New method provides reliable probabilistic bounds for VUR detection.
Whilst there are many approaches to detecting changes in mean for a univariate time-series, the problem of detecting multiple changes in slope has comparatively been ignored. Part of the reason for this is that detecting changes in slope is much more challenging. For example, simple binary segmentation procedures do no…
QA-Token improves tokenization for noisy data, boosting model performance.
Novel method identifies proteomic risk markers for Alzheimer disease.
Deep neural networks predict B-cell epitopes for SARS-CoV and SARS-CoV-2.
Flexible Bayesian inference for complex dynamical systems.
New method designs antimicrobial peptides with high potency and low toxicity.
A framework infers causal direction from symbolic sequences using compression measures.
In tropical regions, populations continue to suffer morbidity and mortality from malaria and arboviral diseases. In Kedougou (Senegal), these illnesses are all endemic due to the climate and its geographical position. The co-circulation of malaria parasites and arboviruses can explain the observation of coinfected case…
Study assesses linear classifiers for virus genotyping and subtyping.
Populations of species in ecosystems are often constrained by availability of resources within their environment. In effect this means that a growth of one population, needs to be balanced by comparable reduction in populations of others. In neutral models of biodiversity all populations are assumed to change increment…
Study investigates how preprocessing, feature selection, and model selection affect performance on imbalanced genetic data.
DCENWCNet improves WBC classification with LIME-based explainability.
Infectious diseases are studied to understand their spreading mechanisms, to evaluate control strategies and to predict the risk and course of future outbreaks. Because people only interact with a small number of individuals, and because the structure of these interactions matters for spreading processes, the pairwise …
Market trade-routes can support infectious-disease transmission, impacting biological populations and even disrupting causal trade. Epidemiological models increasingly account for reductions in infectious contact, such as risk-aversion behaviour in response to pathogen outbreaks. However, market dynamics clearly differ…
Method detects batch heterogeneity in genomic data.
Major histocompatibility complex class two (MHC-II) molecules are trans-membrane proteins and key components of the cellular immune system. Upon recognition of foreign peptides expressed on the MHC-II binding groove, helper T cells mount an immune response against invading pathogens. Therefore, mechanistic identificati…
Study tackles causal effects of close contact on MRSA infections from entangled treatment data.
Network medicine predicts repurposable drugs for COVID-19.
Study predicts coastal water quality using machine learning, identifying salinity as key factor.