Reading is a complex cognitive process, errors in which may assume diverse forms. In this study, introducing a novel approach, we use two families of probabilistic graphical models to analyze patterns of reading errors made by dyslexic people: an LDA-based model and two Naëve Bayes models which differ by their assumptions about the generation process of reading errors. The models are trained on a large corpus of reading errors. Results show that a Naëve Bayes model achieves highest accuracy compared to labels given by clinicians (AUC = 0.801 ± 0.05), thus providing the first automated and objective diagnosis tool for dyslexia which is solely based on reading errors data. Results also show that the LDA-based model best captures patterns of reading errors and could therefore contribute to the understanding of dyslexia and to future improvement of the diagnostic procedure. Finally, we draw on our results to shed light on a theoretical debate about the definition and heterogeneity of dyslexia. Our results support a model assuming multiple dyslexia subtypes, that of a heterogeneous view of dyslexia.

Chronic diseases constitute the leading cause of mortality in the western world, have a major impact on the patients' quality of life, and comprise the bulk of healthcare costs. Nowadays, healthcare data management systems integrate large amounts of medical information on patients, including diagnoses, medical procedures, lab test results, and more. Sophisticated analysis methods are needed for utilizing these data to assist in patient management and to enhance treatment quality at reduced costs. In this study, we take a first step towards better disease management of diabetic patients by applying state-of-the art methods to anticipate the patient's future health condition and to identify patients at high risk. Two relevant outcome measures are explored: the need for emergency care services and the probability of the treatment producing a sub-optimal result, as defined by domain experts. By identifying the high-risk patients our prediction system can be used by healthcare providers to prepare both financially and logistically for the patient needs. To demonstrate a potential downstream application for the identified high-risk patients, we explore the association between the physician treating these patients and the treatment outcome, and propose a system that can assist healthcare providers in optimizing the match between a patient and a physician.

We propose an unsupervised learning technique for extracting information about authors and topics from large text collections. We model documents as if they were generated by a two-stage stochastic process. An author is represented by a probability distribution over topics, and each topic is represented as a probability distribution over words. The probability distribution over topics in a multi-author paper is a mixture of the distributions associated with the authors. The topic-word and author-topic distributions are learned from data in an unsupervised manner using a Markov chain Monte Carlo algorithm. We apply the methodology to three large text corpora: 150,000 abstracts from the CiteSeer digital library, 1740 papers from the Neural Information Processing Systems (NIPS) Conferences, and 121,000 emails from the Enron corporation. We discuss in detail the interpretation of the results discovered by the system including specific topic and author models, ranking of authors by topic and topics by author, parsing of abstracts by topics and authors, and detection of unusual papers by specific authors. Experiments based on perplexity scores for test documents and precision-recall for document retrieval are used to illustrate systematic differences between the proposed author-topic model and a number of alternatives. Extensions to the model, allowing for example, generalizations of the notion of an author, are also briefly discussed.

MOTIVATION: Optimizing HIV therapies is crucial since the virus rapidly develops mutations to evade drug pressure. Recent studies have shown that genotypic information might not be sufficient for the design of therapies and that other clinical and demographical factors may play a role in therapy failure. This study is designed to assess the improvement in prediction achieved when such information is taken into account. We use these factors to generate a prediction engine using a variety of machine learning methods and to determine which clinical conditions are most misleading in terms of predicting the outcome of a therapy. RESULTS: Three different machine learning techniques were used: generative-discriminative method, regression with derived evolutionary features, and regression with a mixture of effects. All three methods had similar performances with an area under the receiver operating characteristic curve (AUC) of 0.77. A set of three similar engines limited to genotypic information only achieved an AUC of 0.75. A straightforward combination of the three engines consistently improves the prediction, with significantly better prediction when the full set of features is employed. The combined engine improves on predictions obtained from an online state-of-the-art resistance interpretation system. Moreover, engines tend to disagree more on the outcome of failure therapies than regarding successful ones. Careful analysis of the differences between the engines revealed those mutations and drugs most closely associated with uncertainty of the therapy outcome. AVAILABILITY: The combined prediction engine will be available from July 2008, see http://engine.euresist.org.

A standard method for approximating averages in probabilistic models is to construct a Markov chain in the product space of the random variables with the desired equilibrium distribution. Since the number of configurations in this space grows exponentially with the number of random variables we often need to represent the distribution with samples. In this paper we show that if one is interested in averages over single variables only, an alternative Markov chain defined on the much smaller "union space", which can be evolved exactly, becomes feasible. The transition kernel of this Markov chain is based on conditional distributions for pairs of variables and we present ways to approximate them using approximate inference algorithms such as mean field, factorized neighbors and belief propagation. Robustness to these approximations and error bounds on the estimates follow from stability analysis for Markov chains. We also present ideas on a new class of algorithms that iterate between increasingly accurate estimates for conditional and marginal distributions. Experiments validate the proposed methods.

We propose a new unsupervised learning technique for extracting information from large text collections. We model documents as if they were generated by a two-stage stochastic process. Each author is represented by a probability distribution over topics, and each topic is represented as a probability distribution over words for that topic. The words in a multi-author paper are assumed to be the result of a mixture of each authors' topic mixture. The topic-word and author-topic distributions are learned from data in an unsupervised manner using a Markov chain Monte Carlo algorithm. We apply the methodology to a large corpus of 160,000 abstracts and 85,000 authors from the well-known CiteSeer digital library, and learn a model with 300 topics. We discuss in detail the interpretation of the results discovered by the system including specific topic and author models, ranking of authors by topic and topics by author, significant trends in the computer science literature between 1990 and 2002, parsing of abstracts by topics and authors and detection of unusual papers by specific authors. An online query interface to the model is also discussed that allows interactive exploration of author-topic models for corpora such as CiteSeer.

Directed graphical models with one layer of observed random variables and one or more layers of hidden random variables have been the dom- inant modelling paradigm in many research fields. Although this ap- proach has met with considerable success, the causal semantics of these models can make it difficult to infer the posterior distribution over the hidden variables. In this paper we propose an alternative two-layer model based on exponential family distributions and the semantics of undi- rected models. Inference in these “exponential family harmoniums” is fast while learning is performed by minimizing contrastive divergence. A member of this family is then studied as an alternative probabilistic model for latent semantic indexing. In experiments it is shown that they perform well on document retrieval tasks and provide an elegant solution to searching with keywords.