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

A MapReduce solution for associative classification of big data

Associative classifiers have proven to be very effective in classification problems. Unfortunately, the algorithms used for learning these classifiers are not able to adequately manage big data because of time complexity and memory constraints. To overcome such drawbacks, we propose a distributed association rule-based classification scheme shaped according to the MapReduce programming model. The scheme mines classification association rules (CARs) using a properly enhanced, distributed version of the well-known FP-Growth algorithm. Once CARs have been mined, the proposed scheme performs a distributed rule pruning. The set of survived CARs is used to classify unlabeled patterns. The memory usage and time complexity for each phase of the learning process are discussed, and the scheme is evaluated on seven real-world big datasets on the Hadoop framework, characterizing its scalability and achievable speedup on small computer clusters. The proposed solution for associative classifiers turns to be suitable to practically address big datasets even with modest hardware support. Comparisons with two state-of-the-art distributed learning algorithms are also discussed in terms of accuracy, model complexity, and computation time

Exploiting natural language structures in software informal documentation

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Communication means, such as issue trackers, mailing lists, Q&A forums, and app reviews, are premier means of collaboration among developers, and between developers and end-users. Analyzing such sources of information is crucial to build recommenders for developers, for example suggesting experts, re-documenting source code, or transforming user feedback in maintenance and evolution strategies for developers. To ease this analysis, in previous work we proposed DECA (Development Emails Content Analyzer), a tool based on Natural Language Parsing that classifies with high precision development emails' fragments according to their purpose. However, DECA has to be trained through a manual tagging of relevant patterns, which is often effort-intensive, error-prone and requires specific expertise in natural language parsing. In this paper, we first show, with a study involving Master's and Ph.D. students, the extent to which producing rules for identifying such patterns requires effort, depending on the nature and complexity of patterns. Then, we propose an approach, named NEON (Nlp-based softwarE dOcumentation aNalyzer), that automatically mines such rules, minimizing the manual effort. We assess the performances of NEON in the analysis and classification of mobile app reviews, developers discussions, and issues. NEON simplifies the patterns' identification and rules' definition processes, allowing a savings of more than 70% of the time otherwise spent on performing such activities manually. Results also show that NEON-generated rules are close to the manually identified ones, achieving comparable recall

Pac-Bayesian Supervised Classification: The Thermodynamics of Statistical Learning

This monograph deals with adaptive supervised classification, using tools borrowed from statistical mechanics and information theory, stemming from the PACBayesian approach pioneered by David McAllester and applied to a conception of statistical learning theory forged by Vladimir Vapnik. Using convex analysis on the set of posterior probability measures, we show how to get local measures of the complexity of the classification model involving the relative entropy of posterior distributions with respect to Gibbs posterior measures. We then discuss relative bounds, comparing the generalization error of two classification rules, showing how the margin assumption of Mammen and Tsybakov can be replaced with some empirical measure of the covariance structure of the classification model.We show how to associate to any posterior distribution an effective temperature relating it to the Gibbs prior distribution with the same level of expected error rate, and how to estimate this effective temperature from data, resulting in an estimator whose expected error rate converges according to the best possible power of the sample size adaptively under any margin and parametric complexity assumptions. We describe and study an alternative selection scheme based on relative bounds between estimators, and present a two step localization technique which can handle the selection of a parametric model from a family of those. We show how to extend systematically all the results obtained in the inductive setting to transductive learning, and use this to improve Vapnik's generalization bounds, extending them to the case when the sample is made of independent non-identically distributed pairs of patterns and labels. Finally we review briefly the construction of Support Vector Machines and show how to derive generalization bounds for them, measuring the complexity either through the number of support vectors or through the value of the transductive or inductive margin.Comment: Published in at http://dx.doi.org/10.1214/074921707000000391 the IMS Lecture Notes Monograph Series (http://www.imstat.org/publications/lecnotes.htm) by the Institute of Mathematical Statistics (http://www.imstat.org

Interpretable multiclass classification by MDL-based rule lists

Interpretable classifiers have recently witnessed an increase in attention from the data mining community because they are inherently easier to understand and explain than their more complex counterparts. Examples of interpretable classification models include decision trees, rule sets, and rule lists. Learning such models often involves optimizing hyperparameters, which typically requires substantial amounts of data and may result in relatively large models. In this paper, we consider the problem of learning compact yet accurate probabilistic rule lists for multiclass classification. Specifically, we propose a novel formalization based on probabilistic rule lists and the minimum description length (MDL) principle. This results in virtually parameter-free model selection that naturally allows to trade-off model complexity with goodness of fit, by which overfitting and the need for hyperparameter tuning are effectively avoided. Finally, we introduce the Classy algorithm, which greedily finds rule lists according to the proposed criterion. We empirically demonstrate that Classy selects small probabilistic rule lists that outperform state-of-the-art classifiers when it comes to the combination of predictive performance and interpretability. We show that Classy is insensitive to its only parameter, i.e., the candidate set, and that compression on the training set correlates with classification performance, validating our MDL-based selection criterion

Relatedness Measures to Aid the Transfer of Building Blocks among Multiple Tasks

Multitask Learning is a learning paradigm that deals with multiple different tasks in parallel and transfers knowledge among them. XOF, a Learning Classifier System using tree-based programs to encode building blocks (meta-features), constructs and collects features with rich discriminative information for classification tasks in an observed list. This paper seeks to facilitate the automation of feature transferring in between tasks by utilising the observed list. We hypothesise that the best discriminative features of a classification task carry its characteristics. Therefore, the relatedness between any two tasks can be estimated by comparing their most appropriate patterns. We propose a multiple-XOF system, called mXOF, that can dynamically adapt feature transfer among XOFs. This system utilises the observed list to estimate the task relatedness. This method enables the automation of transferring features. In terms of knowledge discovery, the resemblance estimation provides insightful relations among multiple data. We experimented mXOF on various scenarios, e.g. representative Hierarchical Boolean problems, classification of distinct classes in the UCI Zoo dataset, and unrelated tasks, to validate its abilities of automatic knowledge-transfer and estimating task relatedness. Results show that mXOF can estimate the relatedness reasonably between multiple tasks to aid the learning performance with the dynamic feature transferring.Comment: accepted by The Genetic and Evolutionary Computation Conference (GECCO 2020

IVTURS: A linguistic fuzzy rule-based classification system based on a new interval-valued fuzzy reasoning method with tuning and rule selection

Interval-valued fuzzy sets have been shown to be a useful tool for dealing with the ignorance related to the definition of the linguistic labels. Specifically, they have been successfully applied to solve classification problems, performing simple modifications on the fuzzy reasoning method to work with this representation and making the classification based on a single number. In this paper we present IVTURS, a new linguistic fuzzy rule-based classification method based on a new completely interval-valued fuzzy reasoning method. This inference process uses interval-valued restricted equivalence functions to increase the relevance of the rules in which the equivalence of the interval membership degrees of the patterns and the ideal membership degrees is greater, which is a desirable behaviour. Furthermore, their parametrized construction allows the computation of the optimal function for each variable to be performed, which could involve a potential improvement in the system’s behaviour. Additionally, we combine this tuning of the equivalence with rule selection in order to decrease the complexity of the system. In this paper we name our method IVTURS-FARC, since we use the FARC-HD method to accomplish the fuzzy rule learning process. The experimental study is developed in three steps in order to ascertain the quality of our new proposal. First, we determine both the essential role that interval-valued fuzzy sets play in the method and the need for the rule selection process. Next, we show the improvements achieved by IVTURS-FARC with respect to the tuning of the degree of ignorance when it is applied in both an isolated way and when combined with the tuning of the equivalence. Finally, the significance of IVTURS-FARC is further depicted by means of a comparison by which it is proved to outperform the results of FARC-HD and FURIA, which are two high performing fuzzy classification algorithms.This work was supported in part by the Spanish Ministry of Science and Technology under projects TIN2011-28488 and TIN2010-15055 and the Andalusian Research Plan P10-TIC-6858 and P11-TIC-7765