Paper uses machine learning to identify key pathways for c-di-GMP in bacterial genomes.
problem Understanding pathways essential for c-di-GMP in bacterial cellulose production.
method Applied Lasso and Random Forests for feature selection and modeling gene count data.
result Bacterial chemotaxis is identified as the most essential pathway for c-di-GMP encoding domains.
Rapid identification of bacteria is essential to prevent the spread of infectious disease, help combat antimicrobial resistance, and improve patient outcomes. Raman optical spectroscopy promises to combine bacterial detection, identification, and antibiotic susceptibility testing in a single step. However, achieving cl…
Deep learning automates bacterial image classification.
problem Manual bacterial classification is time-consuming and error-prone.
method ResNet-50 pre-trained CNN architecture with transfer learning.
result Average classification accuracy of 99.2%.
Machine learning identifies key metabolic control circuits in bacterial pathways.
problem Identifying regulated metabolic pathways in bacteria.
method Machine learning approach analyzing multi-omics data.
result Identification of E. coli Glycolysis regulatory circuits.
Logistic regression with wavelets achieves bacterial infection detection accuracy.
problem Interpreting complex biomedical signal models for high-stakes decisions.
method Wavelet features and knockoff variables for feature selection.
result Logistic regression outperforms neural networks in bacterial infection detection.
We introduce a new method for estimating the support size of an unknown distribution which provably matches the performance bounds of the state-of-the-art techniques in the area and outperforms them in practice. In particular, we present both theoretical and computer simulation results that illustrate the utility and p…
Study uses machine learning to optimize antibiotic therapy for MRSA skin infections.
problem Optimizing antibiotic choice for MRSA skin infections due to reduced treatment options and side effects.
method Propensity score matching, machine learning models (SVM, RF, LASSO), counterfactual analysis.
result RF model shows stronger treatment heterogeneity and potential for therapy change.
Bayesian model fuses diverse microbiome data types.
problem Challenges in fusing different types of microbiome data.
method Flexible multinomial-Gaussian generative model with variational EM algorithm.
result Inferred latent variables provide common dimensionality reduction and predictive posterior distribution.
Modeling high-frequency speculative markets as auction search processes.
problem Understanding trading dynamics in high-frequency order-driven markets.
method Total order book model with diffusion-drift-reaction model, inspired by foraging and chemotaxis.
result Analytic and numerical analysis of trading performance in various search mechanisms.
Machine learning model diagnoses COVID-19 from routine blood tests.
problem Difficulty in diagnosing COVID-19 due to inconsistent blood parameter changes.
method Constructed a machine learning model using 5,333 patients with various infections and 160 COVID-19-positive patients.
result Cross-validated AUC of 0.97, sensitivity of 81.9%, specificity of 97.9%.
We consider the problem of joint modelling of metabolic signals and gene expression in systems biology applications. We propose an approach based on input-output factorial hidden Markov models and propose a structured variational inference approach to infer the structure and states of the model. We start from the class…
Derivative-free method uses deep neural nets for solving PDEs.
problem Solving elliptic partial differential equations (PDEs) without derivatives.
method Trains a deep neural network using reinforcement learning guided by a probabilistic PDE representation.
result Demonstrates effectiveness on various test problems.
Antimicrobial resistance is an important public health concern that has implications in the practice of medicine worldwide. Accurately predicting resistance phenotypes from genome sequences shows great promise in promoting better use of antimicrobial agents, by determining which antibiotics are likely to be effective i…
Increasingly complex generative models are being used across disciplines as they allow for realistic characterization of data, but a common difficulty with them is the prohibitively large computational cost to evaluate the likelihood function and thus to perform likelihood-based statistical inference. A likelihood-free…
Method identifies IPS governing equations from particle data efficiently.
problem Identify governing equations of interacting particle systems efficiently.
method Combines mean-field theory and WSINDy for large N and M. result Converges with rate O(N−1/2) for N≥100. Improved likelihood-free inference for high-dimensional models.
problem Challenges in likelihood-free inference for high-dimensional parameter spaces.
method Bayesian optimization-based approach with misspecification-robust characterisation.
result Efficient inference in 100-dimensional space with real data application.
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated expression of modules (and module groups) of functionally related genes across the gen…
Many complex ecosystems, such as those formed by multiple microbial taxa, involve intricate interactions amongst various sub-communities. The most basic relationships are frequently modeled as co-occurrence networks in which the nodes represent the various players in the community and the weighted edges encode levels o…
Deep learning ensembles improve COVID-19 detection from chest X-rays.
problem Detecting COVID-19 from chest X-rays using machine learning.
method Custom CNN and ImageNet models, transfer learning, iterative pruning, ensemble learning.
result 99.01% accuracy in detecting COVID-19 from chest X-rays.
Unified method for discovering biclusters and triclusters in longitudinal data.
problem High-dimensional, sparsely sampled, irregularly observed longitudinal data.
method Tri-SfSVD, a unified sparse functional Singular Value Decomposition framework.
result Identified localized structures at the subject, subject-feature, and subject-feature-time levels.
Bayesian deep learning ensemble improves pneumonia diagnosis accuracy.
problem Manual, time-consuming pneumonia diagnosis with high inter-observer variability.
method Multi-level ensemble classification system using Bayesian Deep Learning.
result Accuracy of 98.06% in differentiating four pathologies.
Proposes TPIS for early and low-cost TB vs. pneumonia diagnosis.
problem Challenges in differentiating TB from pneumonia.
method Two-step decision support system with stacked ensemble classifiers.
result TPIS outperforms other methods in early and final diagnosis.
CoroNet detects COVID-19 from chest X-rays with high accuracy.
problem Detecting COVID-19 from chest X-rays using limited testing kits.
method Proposes CoroNet, a deep neural network based on Xception architecture trained on a combined dataset of COVID-19 and pneumonia X-rays.
result CoroNet achieved an overall accuracy of 89.6% and precision/recall rates of 93%/98.2% for 4-class cases (COVID vs Pneumonia bacterial vs pneumonia viral vs normal).