Machine learning enables detection of early-stage colorectal cancer by whole-genome sequencing of plasma cell-free DNA.

Background: Blood-based methods using cell-free DNA (cfDNA) are under development as an alternative to existing screening tests. However, early-stage detection of cancer using tumor-derived cfDNA has proven challenging because of the small proportion of cfDNA derived from tumor tissue in early-stage disease. A machine learning approach to discover signatures in cfDNA, potentially reflective of both tumor and non-tumor contributions, may represent a promising direction for the early detection of cancer.

Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data.

Motivation: Correct and rapid determination of Mycobacterium tuberculosis (MTB) resistance against available tuberculosis (TB) drugs is essential for the control and management of TB. Conventional molecular diagnostic test assumes that the presence of any well-studied single nucleotide polymorphisms is sufficient to cause resistance, which yields low sensitivity for resistance classification.

Summary: Given the availability of DNA sequencing data from MTB, we developed machine learning models for a cohort of 1839 UK bacterial isolates to classify MTB resistance against eight anti-TB drugs (isoniazid, rifampicin, ethambutol, pyrazinamide, ciprofloxacin, moxifloxacin, ofloxacin, streptomycin) and to classify multi-drug resistance.

Machine Learning and Decision Support in Critical Care.

Clinical data management systems typically provide caregiver teams with useful information, derived from large, sometimes highly heterogeneous, data sources that are often changing dynamically. Over the last decade there has been a significant surge in interest in using these data sources, from simply re-using the standard clinical databases for event prediction or decision support, to including dynamic and patient-specific information into clinical monitoring and prediction problems. However, in most cases, commercial clinical databases have been designed to document clinical activity for reporting, liability and billing reasons, rather than for developing new algorithms.

Phenotypic characterisation of Crohn's disease severity.

Crohn's disease (CD) is a highly heterogeneous disease, with great variation in patient severity. Using supervised machine learning techniques to predict severity from common laboratory and clinical measurements, we found that high levels of C-reactive protein and low levels of lymphocytes and albumin are important predictive factors. Building upon this knowledge, we used extreme value theory to create a probabilistic model that combines information about behaviour in the extremes of these lab measurements to produce a single risk score over time.

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.

Background: Diagnosing drug-resistance remains an obstacle to the elimination of tuberculosis. Phenotypic drug-susceptibility testing is slow and expensive, and commercial genotypic assays screen only common resistance-determining mutations. We used whole-genome sequencing to characterise common and rare mutations predicting drug resistance, or consistency with susceptibility, for all first-line and second-line drugs for tuberculosis.

First steps in using machine learning on fMRI data to predict intrusive memories of traumatic film footage.

After psychological trauma, why do some only some parts of the traumatic event return as intrusive memories while others do not? Intrusive memories are key to cognitive behavioural treatment for post-traumatic stress disorder, and an aetiological understanding is warranted. We present here analyses using multivariate pattern analysis (MVPA) and a machine learning classifier to investigate whether peri-traumatic brain activation was able to predict later intrusive memories (i.e.

Risk of cardiovascular disease from antiretroviral therapy for HIV: a systematic review.

Background: Recent studies suggest certain antiretroviral therapy (ART) drugs are associated with increases in cardiovascular disease.

Purpose: We performed a systematic review and meta-analysis to summarize the available evidence, with the goal of elucidating whether specific ART drugs are associated with an increased risk of myocardial infarction (MI).

Data Sources: We searched Medline, Web of Science, the Cochrane Library, and abstract archives from the Conference on Retroviruses and Opportunistic Infections and International AIDS Society up to June 2011 to identify published articles and abstracts.