Random forests with random projections of the output space for high dimensional multi-label classification

We adapt the idea of random projections applied to the output space, so as to enhance tree-based ensemble methods in the context of multi-label classification. We show how learning time complexity can be reduced without affecting computational complexity and accuracy of predictions. We also show that random output space projections may be used in order to reach different bias-variance tradeoffs, over a broad panel of benchmark problems, and that this may lead to improved accuracy while reducing significantly the computational burden of the learning stage

Hyperbolic Interaction Model For Hierarchical Multi-Label Classification

Different from the traditional classification tasks which assume mutual exclusion of labels, hierarchical multi-label classification (HMLC) aims to assign multiple labels to every instance with the labels organized under hierarchical relations. Besides the labels, since linguistic ontologies are intrinsic hierarchies, the conceptual relations between words can also form hierarchical structures. Thus it can be a challenge to learn mappings from word hierarchies to label hierarchies. We propose to model the word and label hierarchies by embedding them jointly in the hyperbolic space. The main reason is that the tree-likeness of the hyperbolic space matches the complexity of symbolic data with hierarchical structures. A new Hyperbolic Interaction Model (HyperIM) is designed to learn the label-aware document representations and make predictions for HMLC. Extensive experiments are conducted on three benchmark datasets. The results have demonstrated that the new model can realistically capture the complex data structures and further improve the performance for HMLC comparing with the state-of-the-art methods. To facilitate future research, our code is publicly available

Many Local Pattern Texture Features: Which Is Better for Image-Based Multilabel Human Protein Subcellular Localization Classification?

Human protein subcellular location prediction can provide critical knowledge for understanding a protein’s function. Since significant progress has been made on digital microscopy, automated image-based protein subcellular location classification is urgently needed. In this paper, we aim to investigate more representative image features that can be effectively used for dealing with the multilabel subcellular image samples. We prepared a large multilabel immunohistochemistry (IHC) image benchmark from the Human Protein Atlas database and tested the performance of different local texture features, including completed local binary pattern, local tetra pattern, and the standard local binary pattern feature. According to our experimental results from binary relevance multilabel machine learning models, the completed local binary pattern, and local tetra pattern are more discriminative for describing IHC images when compared to the traditional local binary pattern descriptor. The combination of these two novel local pattern features and the conventional global texture features is also studied. The enhanced performance of final binary relevance classification model trained on the combined feature space demonstrates that different features are complementary to each other and thus capable of improving the accuracy of classification

How is a data-driven approach better than random choice in label space division for multi-label classification?

We propose using five data-driven community detection approaches from social networks to partition the label space for the task of multi-label classification as an alternative to random partitioning into equal subsets as performed by RAkELd: modularity-maximizing fastgreedy and leading eigenvector, infomap, walktrap and label propagation algorithms. We construct a label co-occurence graph (both weighted an unweighted versions) based on training data and perform community detection to partition the label set. We include Binary Relevance and Label Powerset classification methods for comparison. We use gini-index based Decision Trees as the base classifier. We compare educated approaches to label space divisions against random baselines on 12 benchmark data sets over five evaluation measures. We show that in almost all cases seven educated guess approaches are more likely to outperform RAkELd than otherwise in all measures, but Hamming Loss. We show that fastgreedy and walktrap community detection methods on weighted label co-occurence graphs are 85-92% more likely to yield better F1 scores than random partitioning. Infomap on the unweighted label co-occurence graphs is on average 90% of the times better than random paritioning in terms of Subset Accuracy and 89% when it comes to Jaccard similarity. Weighted fastgreedy is better on average than RAkELd when it comes to Hamming Loss

Multitask Protein Function Prediction Through Task Dissimilarity

Automated protein function prediction is a challenging problem with distinctive features, such as the hierarchical organization of protein functions and the scarcity of annotated proteins for most biological functions. We propose a multitask learning algorithm addressing both issues. Unlike standard multitask algorithms, which use task (protein functions) similarity information as a bias to speed up learning, we show that dissimilarity information enforces separation of rare class labels from frequent class labels, and for this reason is better suited for solving unbalanced protein function prediction problems. We support our claim by showing that a multitask extension of the label propagation algorithm empirically works best when the task relatedness information is represented using a dissimilarity matrix as opposed to a similarity matrix. Moreover, the experimental comparison carried out on three model organism shows that our method has a more stable performance in both "protein-centric" and "function-centric" evaluation settings

Nuevos Modelos de Aprendizaje Híbrido para Clasificación y Ordenamiento Multi-Etiqueta

En la última década, el aprendizaje multi-etiqueta se ha convertido en una importante tarea de investigación, debido en gran parte al creciente número de problemas reales que contienen datos multi-etiqueta. En esta tesis se estudiaron dos problemas sobre datos multi-etiqueta, la mejora del rendimiento de los algoritmos en datos multi-etiqueta complejos y la mejora del rendimiento de los algoritmos a partir de datos no etiquetados. El primer problema fue tratado mediante métodos de estimación de atributos. Se evaluó la efectividad de los métodos de estimación de atributos propuestos en la mejora del rendimiento de los algoritmos de vecindad, mediante la parametrización de las funciones de distancias empleadas para recuperar los ejemplos más cercanos. Además, se demostró la efectividad de los métodos de estimación en la tarea de selección de atributos. Por otra parte, se desarrolló un algoritmo de vecindad inspirado en el enfoque de clasifcación basada en gravitación de datos. Este algoritmo garantiza un balance adecuado entre eficiencia y efectividad en su solución ante datos multi-etiqueta complejos. El segundo problema fue resuelto mediante técnicas de aprendizaje activo, lo cual permite reducir los costos del etiquetado de datos y del entrenamiento de un mejor modelo. Se propusieron dos estrategias de aprendizaje activo. La primer estrategia resuelve el problema de aprendizaje activo multi-etiqueta de una manera efectiva y eficiente, para ello se combinaron dos medidas que representan la utilidad de un ejemplo no etiquetado. La segunda estrategia propuesta se enfocó en la resolución del problema de aprendizaje activo multi-etiqueta en modo de lotes, para ello se formuló un problema multi-objetivo donde se optimizan tres medidas, y el problema de optimización planteado se resolvió mediante un algoritmo evolutivo. Como resultados complementarios derivados de esta tesis, se desarrolló una herramienta computacional que favorece la implementación de métodos de aprendizaje activo y la experimentación en esta tarea de estudio. Además, se propusieron dos aproximaciones que permiten evaluar el rendimiento de las técnicas de aprendizaje activo de una manera más adecuada y robusta que la empleada comunmente en la literatura. Todos los métodos propuestos en esta tesis han sido evaluados en un marco experimental adecuado, se utilizaron numerosos conjuntos de datos y se compararon los rendimientos de los algoritmos frente a otros métodos del estado del arte. Los resultados obtenidos, los cuales fueron verificados mediante la aplicación de test estadísticos no paramétricos, demuestran la efectividad de los métodos propuestos y de esta manera comprueban las hipótesis planteadas en esta tesis.In the last decade, multi-label learning has become an important area of research due to the large number of real-world problems that contain multi-label data. This doctoral thesis is focused on the multi-label learning paradigm. Two problems were studied, rstly, improving the performance of the algorithms on complex multi-label data, and secondly, improving the performance through unlabeled data. The rst problem was solved by means of feature estimation methods. The e ectiveness of the feature estimation methods proposed was evaluated by improving the performance of multi-label lazy algorithms. The parametrization of the distance functions with a weight vector allowed to recover examples with relevant label sets for classi cation. It was also demonstrated the e ectiveness of the feature estimation methods in the feature selection task. On the other hand, a lazy algorithm based on a data gravitation model was proposed. This lazy algorithm has a good trade-o between e ectiveness and e ciency in the resolution of the multi-label lazy learning. The second problem was solved by means of active learning techniques. The active learning methods allowed to reduce the costs of the data labeling process and training an accurate model. Two active learning strategies were proposed. The rst strategy e ectively solves the multi-label active learning problem. In this strategy, two measures that represent the utility of an unlabeled example were de ned and combined. On the other hand, the second active learning strategy proposed resolves the batch-mode active learning problem, where the aim is to select a batch of unlabeled examples that are informative and the information redundancy is minimal. The batch-mode active learning was formulated as a multi-objective problem, where three measures were optimized. The multi-objective problem was solved through an evolutionary algorithm. This thesis also derived in the creation of a computational framework to develop any active learning method and to favor the experimentation process in the active learning area. On the other hand, a methodology based on non-parametric tests that allows a more adequate evaluation of active learning performance was proposed. All methods proposed were evaluated by means of extensive and adequate experimental studies. Several multi-label datasets from di erent domains were used, and the methods were compared to the most signi cant state-of-the-art algorithms. The results were validated using non-parametric statistical tests. The evidence showed the e ectiveness of the methods proposed, proving the hypotheses formulated at the beginning of this thesis

Identification of functionally related enzymes by learning-to-rank methods

Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored. In this work we show that rankings of that kind can be substantially improved by applying kernel-based learning algorithms. This approach enables the detection of statistical dependencies between similarities of the active cleft and the biological function of annotated enzymes. This is in contrast to search-based approaches, which do not take annotated training data into account. Similarity measures based on the active cleft are known to outperform sequence-based or structure-based measures under certain conditions. We consider the Enzyme Commission (EC) classification hierarchy for obtaining annotated enzymes during the training phase. The results of a set of sizeable experiments indicate a consistent and significant improvement for a set of similarity measures that exploit information about small cavities in the surface of enzymes