Machine learning classification of surgical pathology reports and chunk recognition for information extraction noise reduction

Background and aims: Machine learning techniques for the text mining of cancer-related clinical documents have not been sufficiently explored. Here some techniques are presented for the pre-processing of free-text breast cancer pathology reports, with the aim of facilitating the extraction of information relevant to cancer staging.

Materials and methods: The first technique was implemented using the freely available software RapidMiner to classify the reports according to their general layout: ‘semi-structured’ and ‘unstructured’. The second technique was developed using the open source language engineering framework GATE and aimed at the prediction of chunks of the report text containing information pertaining to the cancer morphology, the tumour size, its hormone receptor status and the number of positive nodes. The classifiers were trained and tested respectively on sets of 635 and 163 manually classified or annotated reports, from the Northern Ireland Cancer Registry.

Results: The best result of 99.4% accuracy – which included only one semi-structured report predicted as unstructured – was produced by the layout classifier with the k nearest algorithm, using the binary term occurrence word vector type with stopword filter and pruning. For chunk recognition, the best results were found using the PAUM algorithm with the same parameters for all cases, except for the prediction of chunks containing cancer morphology. For semi-structured reports the performance ranged from 0.97 to 0.94 and from 0.92 to 0.83 in precision and recall, while for unstructured reports performance ranged from 0.91 to 0.64 and from 0.68 to 0.41 in precision and recall. Poor results were found when the classifier was trained on semi-structured reports but tested on unstructured.

Conclusions: These results show that it is possible and beneficial to predict the layout of reports and that the accuracy of prediction of which segments of a report may contain certain information is sensitive to the report layout and the type of information sought.

Joint Analysis of Multiple Algorithms and Performance Measures

There has been an increasing interest in the development of new methods using Pareto optimality to deal with multi-objective criteria (for example, accuracy and time complexity). Once one has developed an approach to a problem of interest, the problem is then how to compare it with the state of art. In machine learning, algorithms are typically evaluated by comparing their performance on different data sets by means of statistical tests. Standard tests used for this purpose are able to consider jointly neither performance measures nor multiple competitors at once. The aim of this paper is to resolve these issues by developing statistical procedures that are able to account for multiple competing measures at the same time and to compare multiple algorithms altogether. In particular, we develop two tests: a frequentist procedure based on the generalized likelihood-ratio test and a Bayesian procedure based on a multinomial-Dirichlet conjugate model. We further extend them by discovering conditional independences among measures to reduce the number of parameters of such models, as usually the number of studied cases is very reduced in such comparisons. Data from a comparison among general purpose classifiers is used to show a practical application of our tests.

A Machine Learning Analysis of Twitter Sentiment to the Sandy Hook Shootings

Gun related violence is a complex issue and accounts for a large proportion of violent incidents. In the research reported in this paper, we set out to investigate the pro-gun and anti-gun sentiments expressed on a social media platform, namely Twitter, in response to the 2012 Sandy Hook Elementary School shooting in Connecticut, USA. Machine learning techniques are applied to classify a data corpus of over 700,000 tweets. The sentiments are captured using a public sentiment score that considers the volume of tweets as well as population. A web-based interactive tool is developed to visualise the sentiments and is available at this http://www.gunsontwitter.com. The key findings from this research are: (i) There are elevated rates of both pro-gun and anti-gun sentiments on the day of the shooting. Surprisingly, the pro-gun sentiment remains high for a number of days following the event but the anti-gun sentiment quickly falls to pre-event levels. (ii) There is a different public response from each state, with the highest pro-gun sentiment not coming from those with highest gun ownership levels but rather from California, Texas and New York.

Random Forest Based Approach for Concept-Drift Handling

Algorithms for concept drift handling are important for various applications including video analysis and smart grids. In this paper we present decision tree ensemble classication method based on the Random Forest algorithm for concept drift. The weighted majority voting ensemble aggregation rule is employed based on the ideas of Accuracy Weighted Ensemble (AWE) method. Base learner weight in our case is computed for each sample evaluation using base learners accuracy and intrinsic proximity measure of Random Forest. Our algorithm exploits both temporal weighting of samples and ensemble pruning as a forgetting strategy. We present results of empirical comparison of our method with îriginal random forest with incorporated replace-the-looser forgetting andother state-of-the-art concept-drift classiers like AWE2.