Patrick Gallinari

The Wikipedia XML corpus

Wikipedia is a well known free content, multilingual encyclopedia written collaboratively by contributors around the world. Anybody can edit an article using a wiki markup language that offers a simplified alternative to HTML. This encyclopedia is composed of millions of articles in different languages.Wikipedia is a well known free content, multilingual encyclopedia written collaboratively by contributors around the world. Anybody can edit an article using a wiki markup language that offers a simplified alternative to HTML. This encyclopedia is composed of millions of articles in different languages.

The XML Wikipedia Corpus

Wikipedia is a well known free content, multilingual encyclopedia written collaboratively by contributors around the world. Anybody can edit an article using a wiki markup language that offers a simplified alternative to HTML. This encyclopedia is composed of millions of articles in different languages.Wikipedia is a well known free content, multilingual encyclopedia written collaboratively by contributors around the world. Anybody can edit an article using a wiki markup language that offers a simplified alternative to HTML. This encyclopedia is composed of millions of articles in different languages.

Improved performance in protein secondary structure prediction by inhomogeneous score combination.

MOTIVATION In many fields of pattern recognition, combination has proved efficient to increase the generalization performance of individual prediction methods. Numerous systems have been developed for protein secondary structure prediction, based on different principles. Finding better ensemble methods for this task may thus become crucial. Furthermore, efforts need to be made to help the biologist in the post-processing of the outputs. RESULTS An ensemble method has been designed to post-process the outputs of discriminant models, in order to obtain an improvement in prediction accuracy while generating class posterior probability estimates. Experimental results establish that it can increase the recognition rate of protein secondary structure prediction methods that provide inhomogeneous scores, even though their individual prediction successes are largely different. This combination thus constitutes a help for the biologist, who can use it confidently on top of any set of prediction methods. Moreover, the resulting estimates can be used in various ways, for instance to determine which areas in the sequence are predicted with a given level of reliability. AVAILABILITY The prediction is freely available over the Internet on the Network Protein Sequence Analysis (NPS@) WWW server at http://pbil.ibcp.fr/NPSA/npsa_server.ht ml. The source code of the combiner can be obtained on request for academic use.

Solving multiclass support vector machines with LaRank

Optimization algorithms for large margin multiclass recognizers are often too costly to handle ambitious problems with structured outputs and exponential numbers of classes. Optimization algorithms that rely on the full gradient are not effective because, unlike the solution, the gradient is not sparse and is very large. The LaRank algorithm sidesteps this difficulty by relying on a randomized exploration inspired by the perceptron algorithm. We show that this approach is competitive with gradient based optimizers on simple multiclass problems. Furthermore, a single LaRank pass over the training examples delivers test error rates that are nearly as good as those of the final solution.

Bayesian network model for semi-structured document classification

Recently, a new community has started to emerge around the development of new information research methods for searching and analyzing semi-structured and XML like documents. The goal is to handle both content and structural information, and to deal with different types of information content (text, image, etc.). We consider here the task of structured document classification. We propose a generative model able to handle both structure and content which is based on Bayesian networks. We then show how to transform this generative model into a discriminant classifier using the method of Fisher kernel. The model is then extended for dealing with different types of content information (here text and images). The model was tested on three databases: the classical webKB corpus composed of HTML pages, the new INEX corpus which has become a reference in the field of ad-hoc retrieval for XML documents, and a multimedia corpus of Web pages.

Ranking with ordered weighted pairwise classification

In ranking with the pairwise classification approach, the loss associated to a predicted ranked list is the mean of the pairwise classification losses. This loss is inadequate for tasks like information retrieval where we prefer ranked lists with high precision on the top of the list. We propose to optimize a larger class of loss functions for ranking, based on an ordered weighted average (OWA) (Yager, 1988) of the classification losses. Convex OWA aggregation operators range from the max to the mean depending on their weights, and can be used to focus on the top ranked elements as they give more weight to the largest losses. When aggregating hinge losses, the optimization problem is similar to the SVM for interdependent output spaces. Moreover, we show that OWA aggregates of margin-based classification losses have good generalization properties. Experiments on the Letor 3.0 benchmark dataset for information retrieval validate our approach.

Variable selection with neural networks

Abstract In this paper, we present 3 different neural network-based methods to perform variable selection . OCD — Optimal Cell Damage — is a pruning method, which evaluates the usefulness of a variable and prunes the least useful ones (it is related to the Optimal Brain Damage method of Le Cun et al.). Regularization theory proposes to constrain estimators by adding a term to the cost function used to train a neural network. In the Bayesian framework, this additional term can be interpreted as the log prior to the weights distribution. We propose to use two priors (a Gaussian and a Gaussian mixture) and show that this regularization approach allows to select efficient subsets of variables. Our methods are compared to conventional statistical selection procedures and are shown to significantly improve on that.

The use of unlabeled data to improve supervised learning for text summarization

With the huge amount of information available electronically, there is an increasing demand for automatic text summarization systems. The use of machine learning techniques for this task allows one to adapt summaries to the user needs and to the corpus characteristics. These desirable properties have motivated an increasing amount of work in this field over the last few years. Most approaches attempt to generate summaries by extracting sentence segments and adopt the supervised learning paradigm which requires to label documents at the text span level. This is a costly process, which puts strong limitations on the applicability of these methods. We investigate here the use of semi-supervised algorithms for summarization. These techniques make use of few labeled data together with a larger amount of unlabeled data. We propose new semi-supervised algorithms for training classification models for text summarization. We analyze their performances on two data sets - the Reuters news-wire corpus and the Computation and Language (cmp_lg) collection of TIPSTER SUMMAC. We perform comparisons with a baseline - non learning - system, and a reference trainable summarizer system.

An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition

BackgroundThis article provides an overview of the first BioASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BioASQ assesses the ability of systems to semantically index very large numbers of biomedical scientific articles, and to return concise and user-understandable answers to given natural language questions by combining information from biomedical articles and ontologies.ResultsThe 2013 BioASQ competition comprised two tasks, Task 1a and Task 1b. In Task 1a participants were asked to automatically annotate new PubMed documents with MeSH headings. Twelve teams participated in Task 1a, with a total of 46 system runs submitted, and one of the teams performing consistently better than the MTI indexer used by NLM to suggest MeSH headings to curators. Task 1b used benchmark datasets containing 29 development and 282 test English questions, along with gold standard (reference) answers, prepared by a team of biomedical experts from around Europe and participants had to automatically produce answers. Three teams participated in Task 1b, with 11 system runs. The BioASQ infrastructure, including benchmark datasets, evaluation mechanisms, and the results of the participants and baseline methods, is publicly available.ConclusionsA publicly available evaluation infrastructure for biomedical semantic indexing and QA has been developed, which includes benchmark datasets, and can be used to evaluate systems that: assign MeSH headings to published articles or to English questions; retrieve relevant RDF triples from ontologies, relevant articles and snippets from PubMed Central; produce “exact” and paragraph-sized “ideal” answers (summaries). The results of the systems that participated in the 2013 BioASQ competition are promising. In Task 1a one of the systems performed consistently better from the NLM’s MTI indexer. In Task 1b the systems received high scores in the manual evaluation of the “ideal” answers; hence, they produced high quality summaries as answers. Overall, BioASQ helped obtain a unified view of how techniques from text classification, semantic indexing, document and passage retrieval, question answering, and text summarization can be combined to allow biomedical experts to obtain concise, user-understandable answers to questions reflecting their real information needs.

Report on the XML mining track at INEX 2005 and INEX 2006: categorization and clustering of XML documents

This article is a report concerning the two years of the XML Mining track at INEX (2005 and 2006). We focus here on the classification and clustering of XML documents. We detail these two tasks and the corpus used for this challenge and then present a summary of the different methods proposed by the participants. We last compare the results obtained during the two years of the track.