Automated recognition and classification of bacteria species from microscopic images have significant importance in clinical microbiology. Bacteria classification is usually carried out manually by biologists using different shapes and morphologic characteristics of bacteria species. The manual taxonomy of bacteria typ…
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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…
Discriminative neural networks offer little or no performance guarantees when deployed on data not generated by the same process as the training distribution. On such out-of-distribution (OOD) inputs, the prediction may not only be erroneous, but confidently so, limiting the safe deployment of classifiers in real-world…
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…
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…
Supporting supervised learning in fungal Biosynthetic Gene Cluster discovery: new benchmark datasetsq-bio.GN
New datasets support supervised learning for fungal BGC discovery.
problem Lack of labeled data for fungal BGCs.
method Developed new publicly available datasets for supervised learning.
result Supervised learning outperforms data-driven methods in fungal BGC prediction.
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.
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…
New method provides reliable probabilistic bounds for VUR detection.
problem Detect VUR in children without radiation exposure.
method Machine learning with probabilistic bounds for conditional probability.
result Guaranteed bounds contain well-calibrated probabilities.
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…
We introduce a flexible, scalable Bayesian inference framework for nonlinear dynamical systems characterised by distinct and hierarchical variability at the individual, group, and population levels. Our model class is a generalisation of nonlinear mixed-effects (NLME) dynamical systems, the statistical workhorse for ma…
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…
DCENWCNet improves WBC classification with LIME-based explainability.
problem Classifying white blood cells from blood images with high accuracy and interpretability.
method Integrates three CNN architectures with different settings to balance feature learning and performance.
result Achieves highest mean accuracy on the Rabbin-WBC dataset, outperforming state-of-the-art networks.
Study tackles causal effects of close contact on MRSA infections from entangled treatment data.
problem Estimating causal effects of close contact on MRSA infections from observational data with entangled treatments.
method NEAT method that models treatment assignment mechanism and mitigates confounding biases.
result NEAT method effectively estimates causal effects from entangled treatment data.