Multi-label Classification for Tree and Directed Acyclic Graphs Hierarchies

Abstract. Hierarchical Multi-label Classification (HMC) is the task of assigning a set of classes to a single instance with the peculiarity that the classes are ordered in a predefined structure. We propose a novel HMC method for tree and Directed Acyclic Graphs (DAG) hierarchies. Using the combined predictions of locals classifiers and a weighting scheme according to the level in the hierarchy, we select the "best" single path for tree hierarchies, and multiple paths for DAG hierarchies. We developed a method that returns paths from the root down to a leaf node (Mandatory Leaf Node Prediction or MLNP) and an extension for Non Mandatory Leaf Node Prediction (NMLNP). For NMLNP we compared several pruning approaches varying the pruning direction, pruning time and pruning condition. Additionally, we propose a new evaluation metric for hierarchical classifiers, that avoids the bias of current measures which favor conservative approaches when using NMLNP. The proposed approach was experimentally evaluated with 10 tree and 8 DAG hierarchical datasets in the domain of protein function prediction. We concluded that our method works better for deep, DAG hierarchies and in general NMLNP improves MLNP

Machine Learning for Information Retrieval

In this thesis, we explore the use of machine learning techniques for information retrieval. More specifically, we focus on ad-hoc retrieval, which is concerned with searching large corpora to identify the documents relevant to user queries. Thisidentification is performed through a ranking task. Given a user query, an ad-hoc retrieval system ranks the corpus documents, so that the documents relevant to the query ideally appear above the others. In a machine learning framework, we are interested in proposing learning algorithms that can benefit from limited training data in order to identify a ranker likely to achieve high retrieval performance over unseen documents and queries. This problem presents novel challenges compared to traditional learning tasks, such as regression or classification. First, our task is a ranking problem, which means that the loss for a given query cannot be measured as a sum of an individual loss suffered for each corpus document. Second, most retrieval queries present a highly unbalanced setup, with a set of relevant documents accounting only for a very small fraction of the corpus. Third, ad-hoc retrieval corresponds to a kind of ``double'' generalization problem, since the learned model should not only generalize to new documents but also to new queries. Finally, our task also presents challenging efficiency constraints, since ad-hoc retrieval is typically applied to large corpora. % The main objective of this thesis is to investigate the discriminative learning of ad-hoc retrieval models. For that purpose, we propose different models based on kernel machines or neural networks adapted to different retrieval contexts. The proposed approaches rely on different online learning algorithms that allow efficient learning over large corpora. The first part of the thesis focus on text retrieval. In this case, we adopt a classical approach to the retrieval ranking problem, and order the text documents according to their estimated similarity to the text query. The assessment of semantic similarity between text items plays a key role in that setup and we propose a learning approach to identify an effective measure of text similarity. This identification is not performed relying on a set of queries with their corresponding relevant document sets, since such data are especially expensive to label and hence rare. Instead, we propose to rely on hyperlink data, since hyperlinks convey semantic proximity information that is relevant to similarity learning. This setup is hence a transfer learning setup, where we benefit from the proximity information encoded by hyperlinks to improve the performance over the ad-hoc retrieval task. We then investigate another retrieval problem, i.e. the retrieval of images from text queries. Our approach introduces a learning procedure optimizing a criterion related to the ranking performance. This criterion adapts our previous learning objective for learning textual similarity to the image retrieval problem. This yields an image ranking model that addresses the retrieval problem directly. This approach contrasts with previous research that rely on an intermediate image annotation task. Moreover, our learning procedure builds upon recent work on the online learning of kernel-based classifiers. This yields an efficient, scalable algorithm, which can benefit from recent kernels developed for image comparison. In the last part of the thesis, we show that the objective function used in the previous retrieval problems can be applied to the task of keyword spotting, i.e. the detection of given keywords in speech utterances. For that purpose, we formalize this problem as a ranking task: given a keyword, the keyword spotter should order the utterances so that the utterances containing the keyword appear above the others. Interestingly, this formulation yields an objective directly maximizing the area under the receiver operating curve, the most common keyword spotter evaluation measure. This objective is then used to train a model adapted to this intrinsically sequential problem. This model is then learned with a procedure derived from the algorithm previously introduced for the image retrieval task. To conclude, this thesis introduces machine learning approaches for ad-hoc retrieval. We propose learning models for various multi-modal retrieval setups, i.e. the retrieval of text documents from text queries, the retrieval of images from text queries and the retrieval of speech recordings from written keywords. Our approaches rely on discriminative learning and enjoy efficient training procedures, which yields effective and scalable models. In all cases, links with prior approaches were investigated and experimental comparisons were conducted

Novel approaches for hierarchical classification with case studies in protein function prediction

A very large amount of research in the data mining, machine learning, statistical pattern recognition and related research communities has focused on flat classification problems. However, many problems in the real world such as hierarchical protein function prediction have their classes naturally organised into hierarchies. The task of hierarchical classification, however, needs to be better defined as researchers into one application domain are often unaware of similar efforts developed in other research areas. The first contribution of this thesis is to survey the task of hierarchical classification across different application domains and present an unifying framework for the task. After clearly defining the problem, we explore novel approaches to the task. Based on the understanding gained by surveying the task of hierarchical classification, there are three major approaches to deal with hierarchical classification problems. The first approach is to use one of the many existing flat classification algorithms to predict only the leaf classes in the hierarchy. Note that, in the training phase, this approach completely ignores the hierarchical class relationships, i.e. the parent-child and sibling class relationships, but in the testing phase the ancestral classes of an instance can be inferred from its predicted leaf classes. The second approach is to build a set of local models, by training one flat classification algorithm for each local view of the hierarchy. The two main variations of this approach are: (a) training a local flat multi-class classifier at each non-leaf class node, where each classifier discriminates among the child classes of its associated class; or (b) training a local fiat binary classifier at each node of the class hierarchy, where each classifier predicts whether or not a new instance has the classifier’s associated class. In both these variations, in the testing phase a procedure is used to combine the predictions of the set of local classifiers in a coherent way, avoiding inconsistent predictions. The third approach is to use a global-model hierarchical classification algorithm, which builds one single classification model by taking into account all the hierarchical class relationships in the training phase. In the context of this categorization of hierarchical classification approaches, the other contributions of this thesis are as follows. The second contribution of this thesis is a novel algorithm which is based on the local classifier per parent node approach. The novel algorithm is the selective representation approach that automatically selects the best protein representation to use at each non-leaf class node. The third contribution is a global-model hierarchical classification extension of the well known naive Bayes algorithm. Given the good predictive performance of the global-model hierarchical-classification naive Bayes algorithm, we relax the Naive Bayes’ assumption that attributes are independent from each other given the class by using the concept of k dependencies. Hence, we extend the flat classification /¿-Dependence Bayesian network classifier to the task of hierarchical classification, which is the fourth contribution of this thesis. Both the proposed global-model hierarchical classification Naive Bayes and the proposed global-model hierarchical /¿-Dependence Bayesian network classifier have achieved predictive accuracies that were, overall, significantly higher than the predictive accuracies obtained by their corresponding local hierarchical classification versions, across a number of datasets for the task of hierarchical protein function prediction