Vinay Jethava

The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination

Plasmids are important members of the bacterial mobile gene pool, and are among the most important contributors to horizontal gene transfer between bacteria. They typically harbour a wide spectrum of host beneficial traits, such as antibiotic resistance, inserted into their backbones. Although these inserted elements have drawn considerable interest, evolutionary information about the plasmid backbones, which encode plasmid related traits, is sparse. Here we analyse 25 complete backbone genomes from the broad-host-range IncP-1 plasmid family. Phylogenetic analysis reveals seven clades, in which two plasmids that we isolated from a marine biofilm represent a novel clade. We also found that homologous recombination is a prominent feature of the plasmid backbone evolution. Analysis of genomic signatures indicates that the plasmids have adapted to different host bacterial species. Globally circulating IncP-1 plasmids hence contain mosaic structures of segments derived from several parental plasmids that have evolved in, and adapted to, different, phylogenetically very distant host bacterial species.

Entity disambiguation in anonymized graphs using graph kernels

This paper presents a novel method for entity disambiguation in anonymized graphs using local neighborhood structure. Most existing approaches leverage node information, which might not be available in several contexts due to privacy concerns, or information about the sources of the data. We consider this problem in the supervised setting where we are provided only with a base graph and a set of nodes labelled as ambiguous or unambiguous. We characterize the similarity between two nodes based on their local neighborhood structure using graph kernels; and solve the resulting classification task using SVMs. We give empirical evidence on two real-world datasets, comparing our approach to a state-of-the-art method, highlighting the advantages of our approach. We show that using less information, our method is significantly better in terms of either speed or accuracy or both. We also present extensions of two existing graphs kernels, namely, the direct product kernel and the shortest-path kernel, with significant improvements in accuracy. For the direct product kernel, our extension also provides significant computational benefits. Moreover, we design and implement the algorithms of our method to work in a distributed fashion using the GraphLab framework, ensuring high scalability.

Scalable multi-dimensional user intent identification using tree structured distributions

The problem of identifying user intent has received considerable attention in recent years, particularly in the context of improving the search experience via query contextualization. Intent can be characterized by multiple dimensions, which are often not observed from query words alone. Accurate identification of Intent from query words remains a challenging problem primarily because it is extremely difficult to discover these dimensions. The problem is often significantly compounded due to lack of representative training sample. We present a generic, extensible framework for learning the multi-dimensional representation of user intent from the query words. The approach models the latent relationships between facets using tree structured distribution which leads to an efficient and convergent algorithm, FastQ, for identifying the multi-faceted intent of users based on just the query words. We also incorporated WordNet to extend the system capabilities to queries which contain words that do not appear in the training data. Empirical results show that FastQ yields accurate identification of intent when compared to a gold standard.

NETGEM: Network Embedded Temporal GEnerative Model for gene expression data

BackgroundTemporal analysis of gene expression data has been limited to identifying genes whose expression varies with time and/or correlation between genes that have similar temporal profiles. Often, the methods do not consider the underlying network constraints that connect the genes. It is becoming increasingly evident that interactions change substantially with time. Thus far, there is no systematic method to relate the temporal changes in gene expression to the dynamics of interactions between them. Information on interaction dynamics would open up possibilities for discovering new mechanisms of regulation by providing valuable insight into identifying time-sensitive interactions as well as permit studies on the effect of a genetic perturbation.ResultsWe present NETGEM, a tractable model rooted in Markov dynamics, for analyzing the dynamics of the interactions between proteins based on the dynamics of the expression changes of the genes that encode them. The model treats the interaction strengths as random variables which are modulated by suitable priors. This approach is necessitated by the extremely small sample size of the datasets, relative to the number of interactions. The model is amenable to a linear time algorithm for efficient inference. Using temporal gene expression data, NETGEM was successful in identifying (i) temporal interactions and determining their strength, (ii) functional categories of the actively interacting partners and (iii) dynamics of interactions in perturbed networks.ConclusionsNETGEM represents an optimal trade-off between model complexity and data requirement. It was able to deduce actively interacting genes and functional categories from temporal gene expression data. It permits inference by incorporating the information available in perturbed networks. Given that the inputs to NETGEM are only the network and the temporal variation of the nodes, this algorithm promises to have widespread applications, beyond biological systems.The source code for NETGEM is available from https://github.com/vjethava/NETGEM

Intent-aware temporal query modeling for keyword suggestion

This paper presents a data-driven approach for capturing the temporal variations in user search behaviour by modeling the dynamic query relationships using query-log data. The dependence between different queries (in terms of the query words and latent user intent) is represented using hypergraphs which allows us to explore more complex relationships compared to graph-based approaches. This time-varying dependence is modeled using the framework of probabilistic graphical models. The inferred interactions are used for query keyword suggestion - a key task in web information retrieval. Preliminary experiments using query logs collected from internal search engine of a large health care organization yield promising results. In particular, our model is able to capture temporal variations between queries relationships that reflect known trends in disease occurrence. Further, hypergraph-based modeling captures relationships significantly better compared to graph-based approaches.

DLOREAN: Dynamic Location-Aware Reconstruction of Multiway Networks

This paper presents a method for learning time-varying higher-order interactions based on node observations, with application to short-term traffic forecasting based on traffic flow sensor measurements. We incorporate domain knowledge into the design of a new damped periodic kernel which leverages traffic flow patterns towards better structure learning. We introduce location-based regularization for learning models with desirable geographical properties (short-range or long-range interactions). We show using experiments on synthetic and real data, that our approach performs better than static methods for reconstruction of multiway interactions, as well as time-varying methods which recover only pair-wise interactions. Further, we show on real traffic data that our model is useful for short-term traffic forecasting, improving over state-of-the-art.

Lovasz ϑ, SVMs and applications

Lovász introduced the theta function in his seminal paper [23] giving his celebrated solution to the problem of computing the Shannon capacity of the pentagon. Since then, the Lovász theta function has come to play a central role in information theory, graph theory and combinatorial optimization [11, 10], indeed Goemans [10] was led to remark: “it seems all paths lead to ϑ!”. The definition of the theta function also gives an elegant geometrical representation of the graph via an embedding in a spherical cap on the unit sphere which has many applications in graph theory and machine learning, some of them perhaps not yet fully appreciated. It is one of the goals of this paper to highlight how the Lovász embedding is a powerful and unifying tool in diverse graph theory and data mining applications.

Computational Approaches for Reconstruction of Time-Varying Biological Networks from Omics Data

This chapter presents a survey of recent methods for reconstruction of time-varying biological networks such as gene interaction networks based on time series node observations (e.g. gene expressions) from a modeling perspective. Time series gene expression data has been extensively used for analysis of gene interaction networks, and studying the influence of regulatory relationships on different phenotypes. Traditional correlation and regression based methods have focussed on identifying a single interaction network based on time series data. However, interaction networks vary over time and in response to environmental and genetic stress during the course of the experiment. Identifying such time-varying networks promises new insight into transient interactions and their role in the biological process. A key challenge in inferring such networks is the problem of high-dimensional data i.e. the number of unknowns p is much larger than the number of observations n. We discuss the computational aspects of this problem and examine recent methods that have addressed this problem. These methods have modeled the relationship between the latent regulatory network and the observed time series data using the framework of probabilistic graphical models. A key advantage of this approach is natural interpretability of network reconstruction results; and easy incorporation of domain knowledge into the model. We also discuss methods that have addressed the problem of inferring such time-varying regulatory networks by integrating multiple sources or experiments including time series data from multiple perturbed networks. Finally, we mention software tools that implement some of the methods discussed in this chapter. With next generation sequencing promising yet further growth in publicly available -omics data, the potential of such methods is significant.