The proliferation of online information sources has led to an increased use of wrappers for extracting data from Web sources. While most of the previous research has focused on quick and efficient generation of wrappers, the development of tools for wrapper maintenance has received less attention. This is an important research problem because Web sources often change in ways that prevent the wrappers from extracting data correctly. We present an efficient algorithm that learns structural information about data from positive examples alone. We describe how this information can be used for two wrapper maintenance applications: wrapper verification and reinduction. The wrapper verification system detects when a wrapper is not extracting correct data, usually because the Web source has changed its format. The reinduction algorithm automatically recovers from changes in the Web source by identifying data on Web pages so that a new wrapper may be generated for this source. To validate our approach, we monitored 27 wrappers over a period of a year. The verification algorithm correctly discovered 35 of the 37 wrapper changes, and made 16 mistakes, resulting in precision of 0.73 and recall of 0.95. We validated the reinduction algorithm on ten Web sources. We were able to successfully reinduce the wrappers, obtaining precision and recall values of 0.90 and 0.80 on the data extraction task.

We develop, analyze, and evaluate a novel, supervised, specific-to-general learner for a simple temporal logic and use the resulting algorithm to learn visual event definitions from video sequences. First, we introduce a simple, propositional, temporal, event-description language called AMA that is sufficiently expressive to represent many events yet sufficiently restrictive to support learning. We then give algorithms, along with lower and upper complexity bounds, for the subsumption and generalization problems for AMA formulas. We present a positive-examples--only specific-to-general learning method based on these algorithms. We also present a polynomial-time--computable ``syntactic'' subsumption test that implies semantic subsumption without being equivalent to it. A generalization algorithm based on syntactic subsumption can be used in place of semantic generalization to improve the asymptotic complexity of the resulting learning algorithm. Finally, we apply this algorithm to the task of learning relational event definitions from video and show that it yields definitions that are competitive with hand-coded ones.

For large, real-world inductive learning problems, the number of training examples often must be limited due to the costs associated with procuring, preparing, and storing the training examples and/or the computational costs associated with learning from them. In such circumstances, one question of practical importance is: if only n training examples can be selected, in what proportion should the classes be represented? In this article we help to answer this question by analyzing, for a fixed training-set size, the relationship between the class distribution of the training data and the performance of classification trees induced from these data. We study twenty-six data sets and, for each, determine the best class distribution for learning. The naturally occurring class distribution is shown to generally perform well when classifier performance is evaluated using undifferentiated error rate (0/1 loss). However, when the area under the ROC curve is used to evaluate classifier performance, a balanced distribution is shown to perform well. Since neither of these choices for class distribution always generates the best-performing classifier, we introduce a budget-sensitive progressive sampling algorithm for selecting training examples based on the class associated with each example. An empirical analysis of this algorithm shows that the class distribution of the resulting training set yields classifiers with good (nearly-optimal) classification performance.

Elucidating the genetic basis of human diseases is a central goal of genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide long lists of tens or hundreds of disease gene candidates, the identification of disease genes among the candidates remains time-consuming and expensive. Efficient computational methods are therefore needed to prioritize genes within the list of candidates, by exploiting the wealth of information available about the genes in various databases. Here we propose ProDiGe, a novel algorithm for Prioritization of Disease Genes. ProDiGe implements a novel machine learning strategy based on learning from positive and unlabeled examples, which allows to integrate various sources of information about the genes, to share information about known disease genes across diseases, and to perform genome-wide searches for new disease genes. Experiments on real data show that ProDiGe outperforms state-of-the-art methods for the prioritization of genes in human diseases.

Computational approaches to transcription factor binding site identification have been actively researched for the past decade. Negative examples have long been utilized in de novo motif discovery and have been shown useful in transcription factor binding site search as well. However, understanding of the roles of negative examples in binding site search is still very limited. We propose the 2-centroid and optimal discriminating vector methods, taking into account negative examples. Cross-validation results on E. coli transcription factors show that the proposed methods benefit from negative examples, outperforming the centroid and position-specific scoring matrix methods. We further show that our proposed methods perform better than a state-of-the-art method. We characterize the proposed methods in the context of the other compared methods and show that, coupled with motif subtype identification, the proposed methods can be effectively applied to a wide range of transcription factors. Finally, we argue that the proposed methods are well-suited for eukaryotic transcription factors as well. Software tools are available at: http://biogrid.engr.uconn.edu/tfbs_search/.

The fundamental assumption being, any hypothesis found to approximate well over a sufficiently large Surface Electromyogram (SEMG) signals are physiological set of training examples will also approximate well over signals processed to assess the intensity of activity and the other unobserved examples (Mitchell 1997), belonging to fatigue state of the muscles, non-invasively (Kumar, Pah, the same distribution as the training data. But if this basic and Bradley 2003; Georgakis, Stergioulas, and Giakas 2003; assumption is violated as in the case of SEMG data over Koumantakis et al. 2001; Gerdle, Larsson, and Karlsson multiple subjects, direct application of traditional data mining 2000). However researches observed significant difference and machine learning methods would not work. Figure 1 between the data collected from different subjects shows a typical distribution of SEMG data for three different though they performed the same activity under similar experimental subjects, collected over a fatiguing exercise at varying speed conditions (Contessa, Adam, and Luca 2009; representing the four physiological phases corresponding to Gerdle, Larsson, and Karlsson 2000). Because of their four classes (l) low intensity of activity and low fatigue, (2) highly subject specific nature the SEMG based fatigue assessment high intensity of activity and moderate fatigue, (3) low intensity requires subject specific calibration and are hence of activity and moderate fatigue and (4) high intensity confined to clinical environments related to training and rehabilitation. of activity and high fatigue.

Sequential prediction problems such as imitation learning, where future observations depend on previous predictions (actions), violate the common i.i.d. assumptions made in statistical learning. This leads to poor performance in theory and often in practice. Some recent approaches provide stronger guarantees in this setting, but remain somewhat unsatisfactory as they train either non-stationary or stochastic policies and require a large number of iterations. In this paper, we propose a new iterative algorithm, which trains a stationary deterministic policy, that can be seen as a no regret algorithm in an online learning setting. We show that any such no regret algorithm, combined with additional reduction assumptions, must find a policy with good performance under the distribution of observations it induces in such sequential settings. We demonstrate that this new approach outperforms previous approaches on two challenging imitation learning problems and a benchmark sequence labeling problem.

Traditional learning-based coreference resolvers operate by training the mention-pair model for determining whether two mentions are coreferent or not. Though conceptually simple and easy to understand, the mention-pair model is linguistically rather unappealing and lags far behind the heuristic-based coreference models proposed in the pre-statistical NLP era in terms of sophistication. Two independent lines of recent research have attempted to improve the mention-pair model, one by acquiring the mention-ranking model to rank preceding mentions for a given anaphor, and the other by training the entity-mention model to determine whether a preceding cluster is coreferent with a given mention. We propose a cluster-ranking approach to coreference resolution, which combines the strengths of the mention-ranking model and the entity-mention model, and is therefore theoretically more appealing than both of these models. In addition, we seek to improve cluster rankers via two extensions: (1) lexicalization and (2) incorporating knowledge of anaphoricity by jointly modeling anaphoricity determination and coreference resolution. Experimental results on the ACE data sets demonstrate the superior performance of cluster rankers to competing approaches as well as the effectiveness of our two extensions.

We combine random forest (RF) and conditional random field (CRF) into a new computational framework, called random forest random field (RF)^2. Inference of (RF)^2 uses the Swendsen-Wang cut algorithm, characterized by Metropolis-Hastings jumps. A jump from one state to another depends on the ratio of the proposal distributions, and on the ratio of the posterior distributions of the two states. Prior work typically resorts to a parametric estimation of these four distributions, and then computes their ratio. Our key idea is to instead directly estimate these ratios using RF. RF collects in leaf nodes of each decision tree the class histograms of training examples. We use these class histograms for a non-parametric estimation of the distribution ratios. We derive the theoretical error bounds of a two-class (RF)^2. (RF)^2 is applied to a challenging task of multiclass object recognition and segmentation over a random field of input image regions. In our empirical evaluation, we use only the visual information provided by image regions (e.g., color, texture, spatial layout), whereas the competing methods additionally use higher-level cues about the horizon location and 3D layout of surfaces in the scene. Nevertheless, (RF)^2 outperforms the state of the art on benchmark datasets, in terms of accuracy and computation time.

Most current image categorization methods require large collections of manually annotated training examples to learn accurate visual recognition models. The time-consuming human labeling effort effectively limits these approaches to recognition problems involving a small number of different object classes. In order to address this shortcoming, in recent years several authors have proposed to learn object classifiers from weakly-labeled Internet images, such as photos retrieved by keyword-based image search engines. While this strategy eliminates the need for human supervision, the recognition accuracies of these methods are considerably lower than those obtained with fully-supervised approaches, because of the noisy nature of the labels associated to Web data. In this paper we investigate and compare methods that learn image classifiers by combining very few manually annotated examples (e.g., 1-10 images per class) and a large number of weakly-labeled Web photos retrieved using keyword-based image search. We cast this as a domain adaptation problem: given a few strongly-labeled examples in a target domain (the manually annotated examples) and many source domain examples (the weakly-labeled Web photos), learn classifiers yielding small generalization error on the target domain. Our experiments demonstrate that, for the same number of strongly-labeled examples, our domain adaptation approach produces significant recognition rate improvements over the best published results (e.g., 65% better when using 5 labeled training examples per class) and that our classifiers are one order of magnitude faster to learn and to evaluate than the best competing method, despite our use of large weakly-labeled data sets.