Study assesses linear classifiers for virus genotyping and subtyping.
problem Challenges in classifying viral sequences, especially in alignment-free methods.
method Comprehensive evaluation of linear classifiers on HCV genomes, varying parameters and sequence lengths.
result Several classifiers perform well under specific conditions, providing robust assessment.
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…
Multi-scanner Antivirus systems provide insightful information on the nature of a suspect application; however there is often a lack of consensus and consistency between different Anti-Virus engines. In this article, we analyze more than 250 thousand malware signatures generated by 61 different Anti-Virus engines after…
Study of influenza A virus spread using mathematical equations.
problem Understanding the spread of influenza A virus infection.
method Mathematical model and analysis of dynamical system.
result Surface trajectories and asymptotic behavior of the system.
As machine-learning (ML) based systems for malware detection become more prevalent, it becomes necessary to quantify the benefits compared to the more traditional anti-virus (AV) systems widely used today. It is not practical to build an agreed upon test set to benchmark malware detection systems on pure classification…
Enhanced Zika spread forecasting using topological data analysis.
problem Challenging prediction of Zika virus spread due to nonlinear spatio-temporal dependency and lack of historical records.
method Integrates topological data analysis, specifically persistent homology, into predictive machine learning models.
result Ensemble forecasting improves Zika spread predictions in Brazil.
The application of machine learning to bioinformatics problems is well established. Less well understood is the application of bioinformatics techniques to machine learning and, in particular, the representation of non-biological data as biosequences. The aim of this paper is to explore the effects of giving amino acid…
Study assesses sugar beet yields under EU's neonicotinoids ban and climate change.
problem Impact of yellow virus on sugar beet yields under neonicotinoids ban and climate change.
method Modeling using climate datasets and simulations of aphid flight and abundance.
result Reconstructs sugar beet yields using 'as if' approach without neonicotinoids.
MutaGAN predicts mutations of evolving protein populations using GANs.
problem Predicting mutations in evolving protein populations.
method Generative adversarial networks (GANs) with recurrent neural networks (RNNs).
result MutaGAN generates complete protein sequences with mutations.
Bayesian networks and ML improve COVID-19 symptom classification and severity analysis.
problem Understanding the relationship between COVID-19 symptoms and demographic variables.
method Bayesian network structure learning followed by unsupervised clustering and demographic symptom identification.
result 99.99% testing accuracy compared to 41.15% for a heuristic method.
This paper automates mining of COVID-19 scholarly articles using machine learning.
problem Time-consuming and impractical manual extraction of relevant COVID-19 research articles.
method Used machine learning approaches, specifically clustering and parallel one-class support vector machines (OCSVMs), on the CORD-19 dataset.
result Parallel OCSVMs outperform other methods for both original and reduced feature space.
Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with 12 corresponding packaging signals in three affinity bands. This whole genome/phenotype space consisting of 312 genomes has been explored via comp…
Icosahedral virus capsids are composed of symmetrons, organized arrangements of capsomers. There are three types of symmetrons: disymmetrons, trisymmetrons, and pentasymmetrons, which have different shapes and are centered on the icosahedral 2-fold, 3-fold and 5-fold axes of symmetry, respectively. In 2010 [Sinkovits &…
Optimizes lockdown strategies to balance economic activities and virus spread.
problem Balancing economic activities and virus spread during lockdowns.
method Modeling the pandemic as SEIR, applying Granovetter threshold model for social distancing, and using NSGA-II optimization.
result Optimal lockdown policies for ten weeks to minimize infections and economic impact.
We analyse the importance of international relations between countries on the financial stability. The contagion effect in the network is tested by implementing an epidemiological model, comprising a number of European countries and using bilateral data on foreign claims between them. Banking statistics of consolidated…
TinyBayes detects crop diseases from images on edge devices with high accuracy and minimal resources.
problem Automated disease detection for cocoa crops in resource-constrained settings.
method Combines YOLOv8-Nano for lesion localisation, MobileNetV3-Small for feature extraction, and Jacobi prior for Bayesian classification.
result Achieves 78.7% accuracy on Amini Cocoa Contamination Challenge dataset with 9.5 MB model size and 150 ms inference time.
Study uses machine learning to detect early COVID-19 from CT images.
problem Early detection of COVID-19 from CT images.
method Machine learning methods applied to patches of CT images, feature extraction (GLCM, LDP, GLRLM, GLSZM, DWT), SVM classification.
result Best classification accuracy of 99.68% with 10-fold cross-validation and GLSZM feature extraction.
Noisy Pooled PCR tests large groups more efficiently.
problem Efficiently test large populations for viral infections.
method Converts group testing to a linear inverse problem with a message passing algorithm.
result Estimates patient illness status with fewer pooled measurements.
DeepVir uses deep matrix factorization to predict antivirals for COVID-19.
problem Predicting effective antivirals for COVID-19 using known drug-virus associations.
method Graphical deep matrix factorization with HyPALM optimization.
result DeepVir outperforms state-of-the-art techniques in predicting antivirals for COVID-19.
This study analyzes the effects of lifting lockdowns on Brazil's COVID-19 spread.
problem Understanding the impact of lifting lockdowns on Brazil's COVID-19 spread.
method Extended SEIR model with on/off strategy and developed a neural regressor.
result Lifting lockdowns could lead to a more severe second wave of COVID-19.
DeepRC uses Hopfield networks and attention to classify immune repertoires.
problem Classifying the vast number of immunosequences of an individual.
method Integrates transformer-like attention into deep learning architectures.
result DeepRC outperforms other methods in predictive performance.
This paper tackles efficient testing strategies for COVID-19 by using a partially observable MDP approach.
problem Greedy testing strategies miss dormant virus areas, leading to inefficient use of testing resources.
method Develops efficient learning strategies based on policy iteration and look-ahead rules for a sequential learning-based resource allocation problem.
result Shows that the testing problem can be effectively managed using a partially observable MDP approach.
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…
Machine learning predicts mask mandates reduce COVID-19 deaths.
problem Effectiveness of mask mandates on reducing COVID-19 deaths.
method Machine learning classification algorithms applied to survey data.
result Mask mandates correlated with reduced death ratios in most counties.
Machine learning identifies potential drugs for COVID-19.
problem Finding effective treatments for COVID-19.
method Trained neural network models on virus protein sequences and antiviral drugs.
result Identified potential drug candidates for treating COVID-19.
DeCom predicts post-COVID RSV timing and intensity with NPI consideration.
problem Predicting RSV timing and intensity post-COVID with NPI impact.
method Deep coupled tensor factorization machine (DeCom) leveraging tensor factorization and residual modeling.
result DeCom achieves up to 46% lower RMSE and 49% lower MAE compared to baselines.
Develops geometric framework for uncertainty-aware multi-class classification.
problem Silent failure of AI models when uncertain, especially in multi-class settings.
method Geometric framework treating probability vectors as points on the (c−1)-dimensional probability simplex, using Fisher--Rao metric for calibration and uncertainty quantification. result Empirical validation shows 72.5% of errors captured while deferring 34.5% of ambiguous predictions, reducing automated decision error rates from 16.8% to 6.9%.
Information diffusion and virus propagation are fundamental processes taking place in networks. While it is often possible to directly observe when nodes become infected with a virus or adopt the information, observing individual transmissions (i.e., who infects whom, or who influences whom) is typically very difficult…
Mathematician summarizes protein geometry and mutation effects.
problem Understanding how proteins mutate and their structure-function relationship.
method Mathematical analysis of protein structures and functions, focusing on hydrogen bonds and secondary structure.
result Protein secondary structure regulates mutation by stabilizing or destabilizing regions.
Framework uses machine learning to distinguish major COVID-19 variants.
problem Discriminate and visualize associations between major COVID-19 variants based on genome sequences.
method Unsupervised machine learning methods, including k-mer analysis, PCA, t-SNE, UMAP, and agglomerative hierarchical clustering.
result Framework effectively distinguishes between major variants and identifies emerging variants.
This paper describes an approach for automatic construction of dictionaries for Named Entity Recognition (NER) using large amounts of unlabeled data and a few seed examples. We use Canonical Correlation Analysis (CCA) to obtain lower dimensional embeddings (representations) for candidate phrases and classify these phra…
New lattice path method for statistical inference of persistent diagrams.
problem Statistical inference on persistent diagrams.
method Lattice path representation and combinatorial enumerations.
result Topological changes observed in spike proteins of COVID-19 virus.
Study uses machine learning to analyze Twitter sentiments about COVID-19.
problem Examining public concerns and sentiments about COVID-19 from Twitter.
method Machine learning (Latent Dirichlet Allocation) to identify topics and sentiments.
result Identified 13 topics and categorized into five themes, revealing dominant fears and mixed feelings.
Paper proposes a hybrid AI method to optimize pandemic actions.
problem Optimizing government actions to balance public health and economy.
method Combines Deep Q-Learning and Genetic Algorithms for optimal sequences of actions.
result Deep Q-Learning outperforms Genetic Algorithms in optimizing action sequences.
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.
Novel method for estimating SIRD model parameters and forecasting COVID-19 deaths in Poland.
problem Estimating epidemiological parameters for SARS-CoV-2 spread in Poland.
method Modified SIRD model, GPU architecture for computation.
result Effectiveness of short-term forecasts (up to 2 weeks) and stability of the method.
This paper introduces a machine for sampling approximate model-X knockoffs for arbitrary and unspecified data distributions using deep generative models. The main idea is to iteratively refine a knockoff sampling mechanism until a criterion measuring the validity of the produced knockoffs is optimized; this criterion i…
We propose a solution to the image deconvolution problem where the convolution kernel or point spread function (PSF) is assumed to be only partially known. Small perturbations generated from the model are exploited to produce a few principal components explaining the PSF uncertainty in a high dimensional space. Unlike …
The study uses neural networks to classify and predict coronavirus data.
problem Classifying and predicting coronavirus data from input variables.
method Artificial neural networks with logcosh loss function to classify branches of set-valued mappings.
result Successfully classified and predicted coronavirus data for each German district.
Unsupervised learning identifies key factors for NYC COVID-19 spread.
problem Identify key factors for NYC COVID-19 spread.
method Unsupervised machine learning framework to cluster ZIP code areas.
result 9 interpretable categories of similar outbreak patterns identified.
ESOP uses Bayesian optimization to find optimal lock-down schedules.
problem Finding optimal lock-down schedules balancing health and economy.
method Bayesian optimization interacting with epidemiological models.
result ESOP schedules balance public health and economic impacts.
Lung segmentation from abnormal CXRs using data imputation.
problem Segmenting lungs from CXRs with high opacity caused by respiratory ailments.
method Modified CNN-based segmentation network with deep generative model for data imputation.
result The model can segment lungs from abnormal CXRs, extending to cases with extreme abnormalities.
Study reveals hidden infections and infection dynamics from early data.
problem Understanding early infection dynamics and hidden infections in COVID-19.
method Data-driven machine learning analysis focusing on infection counts over time.
result Significant asymptomatic infections, 10-day lag, and strong infectious force.
Neural networks model COVID-19 spread with partial isolation data.
problem Modeling the spread of COVID-19 with limited data.
method Semi-supervised neural networks solving inverse problems.
result Estimates optimal conditions for virus spread and passive population.
The global crisis of 2008 provoked a heightened interest among scientists to study the phenomenon, its propagation and negative consequences. The process of modelling the spread of a virus is commonly used in epidemiology. Conceptually, the spread of a disease among a population is similar to the contagion process in e…
Motivation: HIV is difficult to treat because its virus mutates at a high rate and mutated viruses easily develop resistance to existing drugs. If the relationships between mutations and drug resistances can be determined from historical data, patients can be provided personalized treatment according to their own mutat…
Researchers use clustering to differentiate COVID-19 lung scans.
problem Identifying infected individuals with COVID-19.
method Applied unsupervised clustering techniques using PCA, K-Means++, and RCC.
result KM++ and RCC algorithms improved in clustering COVID-19 lung scans.
Develops algorithm to find subgroups with different treatment effects in HIV patients.
problem Estimating treatment effects in EHR data with challenges like time-varying confounding.
method SDLD algorithm combining generalized interaction tree and longitudinal targeted maximum likelihood estimation.
result Identifies subgroups of HIV patients at higher risk of weight gain with dolutegravir-containing ARTs.