Entity linking maps name mentions in the documents to entries in a knowledge base through resolving the name variations and ambiguities. In this paper, we propose three advancements for entity linking. Firstly, expanding acronyms can effectively reduce the ambiguity of the acronym mentions. However, only rule-based approaches relying heavily on the presence of text markers have been used for entity linking. In this paper, we propose a supervised learning algorithm to expand more complicated acronyms encountered, which leads to 15.1% accuracy improvement over state-of-the-art acronym expansion methods. Secondly, as entity linking annotation is expensive and labor intensive, to automate the annotation process without compromise of accuracy, we propose an instance selection strategy to effectively utilize the automatically generated annotation. In our selection strategy, an informative and diverse set of instances are selected for effective disambiguation. Lastly, topic modeling is used to model the semantic topics of the articles. These advancements give statistical significant improvement to entity linking individually. Collectively they lead the highest performance on KBP-2010 task.

Multi-label learning deals with the problem where each training example is represented by a single instance while associated with a set of class labels. For an unseen example, existing approaches choose to determine the membership of each possible class label to it based on identical feature set, i.e. the very instance representation of the unseen example is employed in the discrimination processes of all labels. However, this commonly-used strategy might be suboptimal as different class labels usually carry specific characteristics of their own, and it could be beneficial to exploit different feature sets for the discrimination of different labels. Based on the above reflection, we propose a new strategy to multi-label learning by leveraging label-specific features, where a simple yet effective algorithm named LIFT is presented. Briefly, LIFT constructs features specific to each label by conducting clustering analysis on its positive and negative instances, and then performs training and testing by querying the clustering results. Extensive experiments across sixteen diversified data sets clearly validate the superiority of LIFT against other well-established multi-label learning algorithms.

In many real-world applications of the time series classification problem, not only could the negative training instances be missing, the number of positive instances available for learning may also be rather limited. This has motivated the development of new classification algorithms that can learn from a small set P of labeled seed positive instances augmented with a set U of unlabeled instances (i.e. PU learning algorithms). However, existing PU learning algorithms for time series classification have less than satisfactory performance as they are unable to identify the class boundary between positive and negative instances accurately. In this paper, we propose a novel PU learning algorithm LCLC (Learning from Common Local Clusters) for time series classification. LCLC is designed to effectively identify the ground truths’ positive and negative boundaries, resulting in more accurate classifiers than those constructed using existing methods. We have applied LCLC to classify time series data from different application domains; the experimental results demonstrate that LCLC outperforms existing methods significantly.

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.

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.

In discriminative machine learning one is interested in training a system to optimize a certain desired measure of performance, or loss. In binary classification one typically tries to minimizes the error rate. But in structured prediction each task often has its own measure of performance such as the BLEU score in machine translation or the intersection-over-union score in PASCAL segmentation. The most common approaches to structured prediction, structural SVMs and CRFs, do not minimize the task loss: the former minimizes a surrogate loss with no guarantees for task loss and the latter minimizes log loss independent of task loss. The main contribution of this paper is a theorem stating that a certain perceptron-like learning rule, involving features vectors derived from loss-adjusted inference, directly corresponds to the gradient of task loss. We give empirical results on phonetic alignment of a standard test set from the TIMIT corpus, which surpasses all previously reported results on this problem.