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A range of studies have proven the feasibility of TM for extracting structured information from clinical narratives such as those found in pathology or radiology reports. In this article, we provide a critical overview of the current state of the art for TM related to cancer. The review highlighted a strong bias towards symbolic methods, e.g. named entity recognition (NER) based on dictionary lookup and information extraction (IE) relying on pattern matching. The F-measure of NER ranges between 80% and 90%, while that of IE for simple tasks is in the high 90s. To further improve the performance, TM approaches need to deal effectively with idiosyncrasies of the clinical sublanguage such as non-standard abbreviations as well as a high degree of spelling and grammatical errors. This requires a shift from rule-based methods to machine learning following the success of similar trends in biological applications of TM. Machine learning approaches require large training datasets, but clinical narratives are not readily available for TM research due to privacy and confidentiality concerns. This issue remains the main bottleneck for progress in this area. In addition, there is a need for a comprehensive cancer ontology that would enable semantic representation of textual information found in narrative reports.

The epidemiological question of concern here is "can young children at risk of obesity be identified from their early growth records?" Pilot work using logistic regression to predict overweight and obese children demonstrated relatively limited success. Hence we investigate the incorporation of non-linear interactions to help improve accuracy of prediction; by comparing the result of logistic regression with those of six mature data mining techniques.The contributions of this paper are as follows: a) a comparison of logistic regression with six data mining techniques: specifically, for the prediction of overweight and obese children at 3 years using data recorded at birth, 6 weeks, 8 months and 2 years respectively; b) improved accuracy of prediction: prediction at 8 months accuracy is improved very slightly, in this case by using neural networks, whereas for prediction at 2 years obtained accuracy is improved by over 10%, in this case by using Bayesian methods. It has also been shown that incorporation of non-linear interactions could be important in epidemiological prediction, and that data mining techniques are becoming sufficiently well established to offer the medical research community a valid alternative to logistic regression.

BackgroundNeurofibromatosis 1 (NF1) is a monogenic model for syndromic autism. Statins rescue the social and cognitive phenotype in animal knockout models, but translational trials with subjects > 8 years using cognition/behaviour outcomes have shown mixed results. This trial breaks new ground by studying statin effects for the first time in younger children with NF1 and co-morbid autism and by using multiparametric imaging outcomes.MethodsA single-site triple-blind RCT of simvastatin vs. placebo was done. Assessment (baseline and 12-week endpoint) included peripheral MAPK assay, awake magnetic resonance imaging spectroscopy (MRS; GABA and glutamate+glutamine (Glx)), arterial spin labelling (ASL), apparent diffusion coefficient (ADC), resting state functional MRI, and autism behavioural outcomes (Aberrant Behaviour Checklist and Clinical Global Impression).ResultsThirty subjects had a mean age of 8.1 years (SD 1.8). Simvastatin was well tolerated. The amount of imaging data varied by test. Simvastatin treatment was associated with (i) increased frontal white matter MRS GABA (t(12) = − 2.12, p = .055), GABA/Glx ratio (t(12) = − 2.78, p = .016), and reduced grey nuclei Glx (ANCOVA p < 0.05, Mann-Whitney p < 0.01); (ii) increased ASL perfusion in ventral diencephalon (Mann-Whitney p < 0.01); and (iii) decreased ADC in cingulate gyrus (Mann-Whitney p < 0.01). Machine-learning classification of imaging outcomes achieved 79% (p < .05) accuracy differentiating groups at endpoint against chance level (64%, p = 0.25) at baseline. Three of 12 (25%) simvastatin cases compared to none in placebo met ‘clinical responder’ criteria for behavioural outcome.ConclusionsWe show feasibility of peripheral MAPK assay and autism symptom measurement, but the study was not powered to test effectiveness. Multiparametric imaging suggests possible simvastatin effects in brain areas previously associated with NF1 pathophysiology and the social brain network.Trial registrationEU Clinical Trial Register (EudraCT) 2012-005742-38 (www.clinicaltrialsregister.eu)Electronic supplementary materialThe online version of this article (10.1186/s13229-018-0190-z) contains supplementary material, which is available to authorized users.