BowSaw: inferring higher-order trait interactions associated with complex biological phenotypes

Machine learning is helping the interpretation of biological complexity by enabling the inference and classification of cellular, organismal and ecological phenotypes based on large datasets, e.g. from genomic, transcriptomic and metagenomic analyses. A number of available algorithms can help search these datasets to uncover patterns associated with specific traits, including disease-related attributes. While, in many instances, treating an algorithm as a black box is sufficient, it is interesting to pursue an enhanced understanding of how system variables end up contributing to a specific output, as an avenue towards new mechanistic insight. Here we address this challenge through a suite of algorithms, named BowSaw, which takes advantage of the structure of a trained random forest algorithm to identify combinations of variables (“rules”) frequently used for classification. We first apply BowSaw to a simulated dataset, and show that the algorithm can accurately recover the sets of variables used to generate the phenotypes through complex Boolean rules, even under challenging noise levels. We next apply our method to data from the integrative Human Microbiome Project and find previously unreported high-order combinations of microbial taxa putatively associated with Crohn’s disease. By leveraging the structure of trees within a random forest, BowSaw provides a new way of using decision trees to generate testable biological hypotheses.Accepted manuscrip

Incremental learning of independent, overlapping, and graded concept descriptions with an instance-based process framework

Supervised learning algorithms make several simplifying assumptions concerning the characteristics of the concept descriptions to be learned. For example, concepts are often assumed to be (1) defined with respect to the same set of relevant attributes, (2) disjoint in instance space, and (3) have uniform instance distributions. While these assumptions constrain the learning task, they unfortunately limit an algorithm's applicability. We believe that supervised learning algorithms should learn attribute relevancies independently for each concept, allow instances to be members of any subset of concepts, and represent graded concept descriptions. This paper introduces a process framework for instance-based learning algorithms that exploit only specific instance and performance feedback information to guide their concept learning processes. We also introduce Bloom, a specific instantiation of this framework. Bloom is a supervised, incremental, instance-based learning algorithm that learns relative attribute relevancies independently for each concept, allows instances to be members of any subset of concepts, and represents graded concept memberships. We describe empirical evidence to support our claims that Bloom can learn independent, overlapping, and graded concept descriptions

A survey on utilization of data mining approaches for dermatological (skin) diseases prediction

Due to recent technology advances, large volumes of medical data is obtained. These data contain valuable information. Therefore data mining techniques can be used to extract useful patterns. This paper is intended to introduce data mining and its various techniques and a survey of the available literature on medical data mining. We emphasize mainly on the application of data mining on skin diseases. A categorization has been provided based on the different data mining techniques. The utility of the various data mining methodologies is highlighted. Generally association mining is suitable for extracting rules. It has been used especially in cancer diagnosis. Classification is a robust method in medical mining. In this paper, we have summarized the different uses of classification in dermatology. It is one of the most important methods for diagnosis of erythemato-squamous diseases. There are different methods like Neural Networks, Genetic Algorithms and fuzzy classifiaction in this topic. Clustering is a useful method in medical images mining. The purpose of clustering techniques is to find a structure for the given data by finding similarities between data according to data characteristics. Clustering has some applications in dermatology. Besides introducing different mining methods, we have investigated some challenges which exist in mining skin data