MOTIVATION: One way to identify genes possibly associated with ageing is to build a classification model (from the machine learning field) capable of classifying genes as associated with multiple age-related diseases. To build this model, we use a pre-compiled list of human genes associated with age-related diseases and apply a novel Deep Neural Network (DNN) method to find associations between gene descriptors (e.g. Gene Ontology terms, protein-protein interaction data and biological pathway information) and age-related diseases. RESULTS: The novelty of our new DNN method is its modular architecture, which has the capability of combining several sources of biological data to predict which ageing-related diseases a gene is associated with (if any). Our DNN method achieves better predictive performance than standard DNN approaches, a Gradient Boosted Tree classifier (a strong baseline method) and a Logistic Regression classifier. Given the DNN model produced by our method, we use two approaches to identify human genes that are not known to be associated with age-related diseases according to our dataset. First, we investigate genes that are close to other disease-associated genes in a complex multi-dimensional feature space learned by the DNN algorithm. Second, using the class label probabilities output by our DNN approach, we identify genes with a high probability of being associated with age-related diseases according to the model. We provide evidence of these putative associations retrieved from the DNN model with literature support. AVAILABILITY AND IMPLEMENTATION: The source code and datasets can be found at: https://github.com/fabiofabris/Bioinfo2019. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

One of the leading approaches to collaborative filtering is to use matrix factorization to discover a set of latent factors that explain the pattern of preferences. In this paper, we apply a resilient stochastic gradient descent approach that uses only the sign of the gradient, similar to the R-Prop algorithm in neural network training, to matrix factorization for collaborative filtering. We evaluate the performance of our approach on the MovieLens 1M dataset, and find that test set accuracy markedly improves compared to standard gradient descent. As a follow-up experiment, we apply clustering to the learned item-factor matrix in factor space, and attempt to manually characterize each cluster of movies.

Instance-based learning (IBL) methods predict the class label of a new instance based directly on the distance between the new unlabeled instance and each labeled instance in the training set, without constructing a classification model in the training phase. In this paper, we introduce a novel cla ss-based feature weighting technique, in the context of instance-based distance methods, using the Ant Colony Optimization meta-heuristic. We address three different approaches of instance-based classification: k-Nearest Neighbours, distance-based Nearest Neighbours, and Gaussian Kernel Estimator. We present a multi-archive adaptation of the ACOℝ algorithm and apply it to the optimization of the key parameter in each IBL algorithm and of the class-based feature weights. We also propose an ensemble of classifiers approach that makes use of the archived populations of the ACOℝ algorithm. We empirically evaluate the performance of our proposed algorithms on 36 benchmark datasets, and compare them with conventional instance-based classification algorithms, using various parameter settings, as well as with a state-of-the-art coevolutionary algorithm for instance selection and feature weighting for Nearest Neighbours classifiers.

ACOℝis a fairly-recent Ant Colony Optimization (ACO) algorithm for continuous problem domains. ACOR's search width parameter £ controls the extent to which the search is concentrated around the best solutions encountered so far. In this paper, we propose a variation of ACOℝ, in which ACOℝ's search width parameter decays over time. This is analogous to the common strategy, in Particle Swarm Optimization, of decreasing the inertia parameter over time. We evaluate our proposal in the context of neural network training using 36 popular datasets. We find that our approach produces solutions that are better, to a statistically significant extent, than the standard ACOℝalgorithm.

In the field of data mining, classification is a supervised learning task whose purpose is to induce models (classifiers), using a set of labeled training data instances, to predict the class of new unlabeled instances. Data preparation is crucial to the data mining process, and its aim is to impro ve the fitness of the training data to allow learning algorithms to produce more effective classifiers. Two widely-applied data preparation methods are feature selection and instance selection, both of which fall under the umbrella of data reduction. In this paper, we present new ant colony optimization (ACO) algorithms for data reduction - via both feature and instance selection - to improve the predictive quality of the constructed classification models. Empirical evaluations on 43 benchmark datasets with five well-known classification algorithms show that our ACO algorithms improve the predictive quality of the produced classifiers. We also compare the performance of our proposed ACO algorithms to CIW-NN, a state-of-the-art co-evolutionary instance selection, instance weighting and feature weighting nearest-neighbour classifier, using a Friedman test of statistical significance.

Classification is a central problem in the fields of data mining and machine learning. Using a training set of labelled instances, the task is to build a model (classifier) that can be used to predict the class of new unlabelled instances. Data preparation is crucial to the data mining process, and its focus is to improve the fitness of the training data for the learning algorithms to produce more effective classifiers. Two widely applied data preparation methods are feature selection and instance selection, which fall under the umbrella of data reduction. In this paper, we introduce ADR-Miner, a novel data reduction algorithm that utilizes ant colony optimization (ACO). ADR-Miner is designed to perform instance selection to improve the predictive effectiveness of the constructed classification models. Empirical evaluations on 20 benchmark data sets with three well-known classification algorithms show that ADR-Miner improves the predictive quality of the produced classifiers. The non-parametric Wilcoxon signed-ranks test is employed to determine statistical significance.

Bayesian Multi-nets (BMNs) are a special kind of Bayesian network (BN) classifiers that consist of several local Bayesian networks, one for each predictable class, to model an asymmetric set of variable dependencies given each class value. Deterministic methods using greedy local search are the mos t frequently used methods for learning the structure of BMNs based on optimizing a scoring function. Ant Colony Optimization (ACO) is a meta-heuristic global search method for solving combinatorial optimization problems, inspired by the behavior of real ant colonies. In this paper, we propose two novel ACO-based algorithms with two different approaches to build BMN classifiers: ABC-Minerlmn and ABC-Minergmn. The former uses a local learning approach, in which the ACO algorithm completes the construction of one local BN at a time. The latter uses a global approach, which involves building a complete BMN classifier by each single ant in the colony. We experimentally evaluate the performance of our ant-based algorithms on 33 benchmark classification datasets, where our proposed algorithms are shown to be significantly better than other commonly used deterministic algorithms for learning various Bayesian classifiers in the literature, as well as competitive to other well-known classification algorithms.

Learning classifiers from datasets is a central problem in data mining and machine learning research. ABC-Miner is an Ant-based Bayesian Classification algorithm that employs the Ant Colony Optimization (ACO) meta-heuristics to learn the structure of Bayesian Augmented Naive-Bayes (BAN) Classifiers. One of the most important aspects of the ACO algorithm is the choice of the quality measure used to evaluate a candidate solution to update pheromone. In this paper, we explore the use of various classification quality measures for evaluating the BAN classifiers constructed by the ants. The aim of this investigation is to discover how the use of different evaluation measures affects the quality of the output classifier in terms of predictive accuracy. In our experiments, we use 6 different classification measures on 25 benchmark datasets. We found that the hypothesis that different measures produce different results is acceptable according to the Friedman's statistical test.

Bayesian Multi-nets (BMNs) are a special kind of Bayesian network (BN) classifiers that consist of several local networks, typically, one for each predictable class, to model an asymmetric set of variable dependencies given each class value. Alternatively, multi-nets can be learnt upon arbitrary partitions of a dataset, in which each partition holds more consistent variable dependencies given the data subset in the partition. This paper proposes two contributions to the approach that clusters the dataset into separate data subsets to build asymmetric local BN classifiers, one for each subset. First, we extend the K-modes algorithm, previously used by the Case-Based Bayesian Network Classifiers (CBBN) approach to create clusters before learning the BN classifiers. Second, we introduce the Ant-Clust-B algorithm that employs Ant Colony Optimization (ACO) to learn clustering-based BMNs. Ant-Clust-B uses ACO in the clustering step before learning the local BN classifiers. Empirical results are obtained from experiments on 18 UCI datasets.

Ant-Miner is a classification rule discovery algorithm that is based on Ant Colony Optimization (ACO) metaheuristic. cAnt-Miner is the extended version of the algorithm that handles continuous attributes on-the-fly during the rule construction process, while μAnt-Miner is an extension of the algorithm that selects the rule class prior to its construction, and utilizes multiple pheromone types, one for each permitted rule class. In this paper, we combine these two algorithms to derive a new approach for learning classification rules using ACO. The proposed approach is based on using the measure function for 1) computing the heuristics for rule term selection, 2) a criteria for discretizing continuous attributes, and 3) evaluating the quality of the constructed rule for pheromone update as well. We explore the effect of using different measure functions for on the output model in terms of predictive accuracy and model size. Empirical evaluations found that hypothesis of different functions produce different results are acceptable according to Friedman's statistical test.