Computational aspects of DNA mixture analysis

Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed locally involving only a few alleles at each step. In addition, we describe a general method for computing the expectation of a product of discrete random variables using auxiliary variables and probability propagation in a Bayesian network, which in combination with the genotype network allows efficient computation of the likelihood function and various other quantities relevant to the inference. Lastly, we introduce a set of diagnostic tools for assessing the adequacy of the model for describing a particular dataset

Matching Natural Language Sentences with Hierarchical Sentence Factorization

Semantic matching of natural language sentences or identifying the relationship between two sentences is a core research problem underlying many natural language tasks. Depending on whether training data is available, prior research has proposed both unsupervised distance-based schemes and supervised deep learning schemes for sentence matching. However, previous approaches either omit or fail to fully utilize the ordered, hierarchical, and flexible structures of language objects, as well as the interactions between them. In this paper, we propose Hierarchical Sentence Factorization---a technique to factorize a sentence into a hierarchical representation, with the components at each different scale reordered into a "predicate-argument" form. The proposed sentence factorization technique leads to the invention of: 1) a new unsupervised distance metric which calculates the semantic distance between a pair of text snippets by solving a penalized optimal transport problem while preserving the logical relationship of words in the reordered sentences, and 2) new multi-scale deep learning models for supervised semantic training, based on factorized sentence hierarchies. We apply our techniques to text-pair similarity estimation and text-pair relationship classification tasks, based on multiple datasets such as STSbenchmark, the Microsoft Research paraphrase identification (MSRP) dataset, the SICK dataset, etc. Extensive experiments show that the proposed hierarchical sentence factorization can be used to significantly improve the performance of existing unsupervised distance-based metrics as well as multiple supervised deep learning models based on the convolutional neural network (CNN) and long short-term memory (LSTM).Comment: Accepted by WWW 2018, 10 page

RRR: Rank-Regret Representative

Selecting the best items in a dataset is a common task in data exploration. However, the concept of "best" lies in the eyes of the beholder: different users may consider different attributes more important, and hence arrive at different rankings. Nevertheless, one can remove "dominated" items and create a "representative" subset of the data set, comprising the "best items" in it. A Pareto-optimal representative is guaranteed to contain the best item of each possible ranking, but it can be almost as big as the full data. Representative can be found if we relax the requirement to include the best item for every possible user, and instead just limit the users' "regret". Existing work defines regret as the loss in score by limiting consideration to the representative instead of the full data set, for any chosen ranking function. However, the score is often not a meaningful number and users may not understand its absolute value. Sometimes small ranges in score can include large fractions of the data set. In contrast, users do understand the notion of rank ordering. Therefore, alternatively, we consider the position of the items in the ranked list for defining the regret and propose the {\em rank-regret representative} as the minimal subset of the data containing at least one of the top-$k$ of any possible ranking function. This problem is NP-complete. We use the geometric interpretation of items to bound their ranks on ranges of functions and to utilize combinatorial geometry notions for developing effective and efficient approximation algorithms for the problem. Experiments on real datasets demonstrate that we can efficiently find small subsets with small rank-regrets

Fastest mixing Markov chain on graphs with symmetries

We show how to exploit symmetries of a graph to efficiently compute the fastest mixing Markov chain on the graph (i.e., find the transition probabilities on the edges to minimize the second-largest eigenvalue modulus of the transition probability matrix). Exploiting symmetry can lead to significant reduction in both the number of variables and the size of matrices in the corresponding semidefinite program, thus enable numerical solution of large-scale instances that are otherwise computationally infeasible. We obtain analytic or semi-analytic results for particular classes of graphs, such as edge-transitive and distance-transitive graphs. We describe two general approaches for symmetry exploitation, based on orbit theory and block-diagonalization, respectively. We also establish the connection between these two approaches.Comment: 39 pages, 15 figure

RDF-TR: Exploiting structural redundancies to boost RDF compression

The number and volume of semantic data have grown impressively over the last decade, promoting compression as an essential tool for RDF preservation, sharing and management. In contrast to universal compressors, RDF compression techniques are able to detect and exploit specific forms of redundancy in RDF data. Thus, state-of-the-art RDF compressors excel at exploiting syntactic and semantic redundancies, i.e., repetitions in the serialization format and information that can be inferred implicitly. However, little attention has been paid to the existence of structural patterns within the RDF dataset; i.e. structural redundancy. In this paper, we analyze structural regularities in real-world datasets, and show three schema-based sources of redundancies that underpin the schema-relaxed nature of RDF. Then, we propose RDF-Tr (RDF Triples Reorganizer), a preprocessing technique that discovers and removes this kind of redundancy before the RDF dataset is effectively compressed. In particular, RDF-Tr groups subjects that are described by the same predicates, and locally re-codes the objects related to these predicates. Finally, we integrate RDF-Tr with two RDF compressors, HDT and k2-triples. Our experiments show that using RDF-Tr with these compressors improves by up to 2.3 times their original effectiveness, outperforming the most prominent state-of-the-art techniques