Network analysis is a growing field across many domains, including computer vision, social media marketing, transportation networks, and intelligence analysis. The growing use of digital communication devices and platforms, as well as persistent surveillance sensors, has resulted in explosion of the quantity of data and stretched the abilities of current technologies to process this data and draw meaningful conclusions. Current tools either require significant levels of manual intervention (e.g., to prepare the data, to define patterns, or to draw conclusions from data) or are unable to generalize to new data sources and analysis needs. In this paper, we present automated solutions to two major problems in network analysis: (a) finding patterns in the network data that contains high levels of noise and irrelevant information; and (b) learning repetitive patterns and dependencies between entities and attributes. Our modeling framework represents network data using multi-attributed graphs that can encode various discrete and continuous features and relationships between network entities. The pattern search and learning model is based on probabilistic multi-attributed graph matching, and implemented using distributed message passing algorithms. Our algorithms achieved high accuracy rates in learning and finding patterns in the data, are flexible to new domains and data types, and scale to large datasets using the Map-Reduce framework.

Images form a significant, yet under-utilized, information source in published biomedical articles. Much current work on biomedical image retrieval and classification uses simple, standard image representation employing features such as edge direction or gray scale histograms. In our earlier work we have used such features as well to classify images, where image-class-tags have been used to represent and classify complete articles. Here we focus on a different literature classification task: identifying articles discussing cis-regulatory elements and modules, motivated by the need to understand complex gene-networks. Curators attempting to identify such articles use as a major cue a certain type of image in which the conserved cis-regulatory region on the DNA is shown. Our experiments show that automatically identifying such images using common image features (such as gray scale) is highly error prone. However, using Optical Character Recognition (OCR) to extract alphabet characters from images, calculating character distribution and using the distribution parameters as image features, forms a novel image representation, which allows us to identify DNA-content in images with high precision and recall (over 0.9). Utilizing the occurrence of DNA-rich images within articles, we train a classifier to identify articles pertaining to cis-regulatory elements with a similarly high precision and recall. Using OCR-based image features has much potential beyond the current task, to identify other types of biomedical sequence-based images showing DNA, RNA and proteins. Moreover, automatically identifying such images is applicable beyond the current use-case, in other important biomedical document classification tasks.

Extracting important relations between biological components and semantic events involving genes or proteins from literature has become a focus for the biomedical text mining community. In this paper, we review a subgraph matching-based approach proposed in our previous work for mining relations and events in the biomedical literature. Our subgraph matching algorithm is formally presented, along with a detailed analysis of its complexity. We present three different relation/event extraction tasks in which our approach has been successfully applied. Our approach is of considerable value in extracting highly precise, binary relations when appropriate training data is available.

This research is a discriminative analysis of conversational dialogs involving individuals suffering from dementia of Alzheimer’s type. Several metric analyses are applied to the transcripts of the Carolina Conversation Corpus (Pope and Davis 2011) in order to determine if there are significant statistical differences between individuals with and without Alzheimer’s disease. Results from the analysis indicate that go-ahead utterances, certain fluency measures, and paraphrasing provide defensible means of differentiating the linguistic characteristics of spontaneous speech between healthy individuals and those with Alzheimer’s disease. Several machine learning algorithms were used to classify the speech of individuals with and without dementia of the Alzheimer’s type.

Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, they face important data quality challenges of noise and incompleteness that adversely affect the results obtained from their analysis. Here, we explore the use of the concept of common neighborhood similarity (CNS), which is a form of local structure in networks, to address these issues. Although several CNS measures have been proposed in the literature, an understanding of their relative efficacies for the analysis of interaction networks has been lacking. We follow the framework of graph transformation to convert the given interaction network into a transformed network corresponding to a variety of CNS measures evaluated. The effectiveness of each measure is then estimated by comparing the quality of protein function predictions obtained from its corresponding transformed network with those from the original network. Using a large set of S. cerevisiae interactions, and a set of 136 GO terms, we find that several of the transformed networks produce more accurate predictions than those obtained from the original network. In particular, the $HC.cont$ measure proposed here performs particularly well for this task. Further investigation reveals that the two major factors contributing to this improvement are the abilities of CNS measures, especially $HC.cont$, to prune out noisy edges and introduce new links between functionally related proteins.

We present CLP(BN), a novel approach that aims at expressing Bayesian networks through the constraint logic programming framework. Arguably, an important limitation of traditional Bayesian networks is that they are propositional, and thus cannot represent relations between multiple similar objects in multiple contexts. Several researchers have thus proposed first-order languages to describe such networks. Namely, one very successful example of this approach are the Probabilistic Relational Models (PRMs), that combine Bayesian networks with relational database technology. The key difficulty that we had to address when designing CLP(cal{BN}) is that logic based representations use ground terms to denote objects. With probabilitic data, we need to be able to uniquely represent an object whose value we are not sure about. We use {sl Skolem functions} as unique new symbols that uniquely represent objects with unknown value. The semantics of CLP(cal{BN}) programs then naturally follow from the general framework of constraint logic programming, as applied to a specific domain where we have probabilistic data. This paper introduces and defines CLP(cal{BN}), and it describes an implementation and initial experiments. The paper also shows how CLP(cal{BN}) relates to Probabilistic Relational Models (PRMs), Ngo and Haddawys Probabilistic Logic Programs, AND Kersting AND De Raedts Bayesian Logic Programs.

Despite its simplicity, the naive Bayes classifier has surprised machine learning researchers by exhibiting good performance on a variety of learning problems. Encouraged by these results, researchers have looked to overcome naive Bayes primary weakness - attribute independence - and improve the performance of the algorithm. This paper presents a locally weighted version of naive Bayes that relaxes the independence assumption by learning local models at prediction time. Experimental results show that locally weighted naive Bayes rarely degrades accuracy compared to standard naive Bayes and, in many cases, improves accuracy dramatically. The main advantage of this method compared to other techniques for enhancing naive Bayes is its conceptual and computational simplicity.

Generative models for graphs have been typically committed to strong prior assumptions concerning the form of the modeled distributions. Moreover, the vast majority of currently available models are either only suitable for characterizing some particular network properties (such as degree distribution or clustering coefficient), or they are aimed at estimating joint probability distributions, which is often intractable in large-scale networks. In this paper, we first propose a novel network statistic, based on the Laplacian spectrum of graphs, which allows to dispense with any parametric assumption concerning the modeled network properties. Second, we use the defined statistic to develop the Fiedler random graph model, switching the focus from the estimation of joint probability distributions to a more tractable conditional estimation setting. After analyzing the dependence structure characterizing Fiedler random graphs, we evaluate them experimentally in edge prediction over several real-world networks, showing that they allow to reach a much higher prediction accuracy than various alternative statistical models.

We introduce a new discrepancy score between two distributions that gives an indication on their similarity. While much research has been done to determine if two samples come from exactly the same distribution, much less research considered the problem of determining if two finite samples come from similar distributions. The new score gives an intuitive interpretation of similarity; it optimally perturbs the distributions so that they best fit each other. The score is defined between distributions, and can be efficiently estimated from samples. We provide convergence bounds of the estimated score, and develop hypothesis testing procedures that test if two data sets come from similar distributions. The statistical power of this procedures is presented in simulations. We also compare the score's capacity to detect similarity with that of other known measures on real data.

Android and Facebook provide third-party applications with access to users' private data and the ability to perform potentially sensitive operations (e.g., post to a user's wall or place phone calls). As a security measure, these platforms restrict applications' privileges with permission systems: users must approve the permissions requested by applications before the applications can make privacy- or security-relevant API calls. However, recent studies have shown that users often do not understand permission requests and lack a notion of typicality of requests. As a first step towards simplifying permission systems, we cluster a corpus of 188,389 Android applications and 27,029 Facebook applications to find patterns in permission requests. Using a method for Boolean matrix factorization for finding overlapping clusters, we find that Facebook permission requests follow a clear structure that exhibits high stability when fitted with only five clusters, whereas Android applications demonstrate more complex permission requests. We also find that low-reputation applications often deviate from the permission request patterns that we identified for high-reputation applications suggesting that permission request patterns are indicative for user satisfaction or application quality.