arXiv subjects

Vipin Kumar

Publications and source records attributed to Vipin Kumar.

85 records · Page 5Linked to original sources

arXiv2018

Mining Sub-Interval Relationships In Time Series Data

Time-series data is being increasingly collected and stud- ied in several areas such as neuroscience, climate science, transportation, and social media. Discovery of complex patterns of relationships between individual time-series, using data-driven approaches can improve our understanding of real-world systems. While traditional approaches typically study relationships between two entire time series, many interesting relationships in real-world applications exist in small sub-intervals of time while remaining absent or feeble during other sub-intervals. In this paper, we define the notion of a sub-interval relationship (SIR) to capture inter- actions between two time series that are prominent only in certain sub-intervals of time. We propose a novel and efficient approach to find most interesting SIR in a pair of time series. We evaluate our proposed approach on two real-world datasets from climate science and neuroscience domain and demonstrated the scalability and computational efficiency of our proposed approach. We further evaluated our discovered SIRs based on a randomization based procedure. Our results indicated the existence of several such relationships that are statistically significant, some of which were also found to have physical interpretation.

stat.ML↗

arXiv2018

Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.

cs.CE↗

arXiv2017

Discovery of Shifting Patterns in Sequence Classification

In this paper, we investigate the multi-variate sequence classification problem from a multi-instance learning perspective. Real-world sequential data commonly show discriminative patterns only at specific time periods. For instance, we can identify a cropland during its growing season, but it looks similar to a barren land after harvest or before planting. Besides, even within the same class, the discriminative patterns can appear in different periods of sequential data. Due to such property, these discriminative patterns are also referred to as shifting patterns. The shifting patterns in sequential data severely degrade the performance of traditional classification methods without sufficient training data. We propose a novel sequence classification method by automatically mining shifting patterns from multi-variate sequence. The method employs a multi-instance learning approach to detect shifting patterns while also modeling temporal relationships within each multi-instance bag by an LSTM model to further improve the classification performance. We extensively evaluate our method on two real-world applications - cropland mapping and affective state recognition. The experiments demonstrate the superiority of our proposed method in sequence classification performance and in detecting discriminative shifting patterns.

cs.LG↗

arXiv2017

Spatio-Temporal Data Mining: A Survey of Problems and Methods

Large volumes of spatio-temporal data are increasingly collected and studied in diverse domains including, climate science, social sciences, neuroscience, epidemiology, transportation, mobile health, and Earth sciences. Spatio-temporal data differs from relational data for which computational approaches are developed in the data mining community for multiple decades, in that both spatial and temporal attributes are available in addition to the actual measurements/attributes. The presence of these attributes introduces additional challenges that needs to be dealt with. Approaches for mining spatio-temporal data have been studied for over a decade in the data mining community. In this article we present a broad survey of this relatively young field of spatio-temporal data mining. We discuss different types of spatio-temporal data and the relevant data mining questions that arise in the context of analyzing each of these datasets. Based on the nature of the data mining problem studied, we classify literature on spatio-temporal data mining into six major categories: clustering, predictive learning, change detection, frequent pattern mining, anomaly detection, and relationship mining. We discuss the various forms of spatio-temporal data mining problems in each of these categories.

cs.LG↗

arXiv2017

ORBIT: Ordering Based Information Transfer Across Space and Time for Global Surface Water Monitoring

Many earth science applications require data at both high spatial and temporal resolution for effective monitoring of various ecosystem resources. Due to practical limitations in sensor design, there is often a trade-off in different resolutions of spatio-temporal datasets and hence a single sensor alone cannot provide the required information. Various data fusion methods have been proposed in the literature that mainly rely on individual timesteps when both datasets are available to learn a mapping between features values at different resolutions using local relationships between pixels. Earth observation data is often plagued with spatially and temporally correlated noise, outliers and missing data due to atmospheric disturbances which pose a challenge in learning the mapping from a local neighborhood at individual timesteps. In this paper, we aim to exploit time-independent global relationships between pixels for robust transfer of information across different scales. Specifically, we propose a new framework, ORBIT (Ordering Based Information Transfer) that uses relative ordering constraint among pixels to transfer information across both time and scales. The effectiveness of the framework is demonstrated for global surface water monitoring using both synthetic and real-world datasets.

cs.LG↗

arXiv2017

Machine Learning for the Geosciences: Challenges and Opportunities

Geosciences is a field of great societal relevance that requires solutions to several urgent problems facing our humanity and the planet. As geosciences enters the era of big data, machine learning (ML) -- that has been widely successful in commercial domains -- offers immense potential to contribute to problems in geosciences. However, problems in geosciences have several unique challenges that are seldom found in traditional applications, requiring novel problem formulations and methodologies in machine learning. This article introduces researchers in the machine learning (ML) community to these challenges offered by geoscience problems and the opportunities that exist for advancing both machine learning and geosciences. We first highlight typical sources of geoscience data and describe their properties that make it challenging to use traditional machine learning techniques. We then describe some of the common categories of geoscience problems where machine learning can play a role, and discuss some of the existing efforts and promising directions for methodological development in machine learning. We conclude by discussing some of the emerging research themes in machine learning that are applicable across all problems in the geosciences, and the importance of a deep collaboration between machine learning and geosciences for synergistic advancements in both disciplines.

cs.LG↗

arXiv2017

Theory-guided Data Science: A New Paradigm for Scientific Discovery from Data

Data science models, although successful in a number of commercial domains, have had limited applicability in scientific problems involving complex physical phenomena. Theory-guided data science (TGDS) is an emerging paradigm that aims to leverage the wealth of scientific knowledge for improving the effectiveness of data science models in enabling scientific discovery. The overarching vision of TGDS is to introduce scientific consistency as an essential component for learning generalizable models. Further, by producing scientifically interpretable models, TGDS aims to advance our scientific understanding by discovering novel domain insights. Indeed, the paradigm of TGDS has started to gain prominence in a number of scientific disciplines such as turbulence modeling, material discovery, quantum chemistry, bio-medical science, bio-marker discovery, climate science, and hydrology. In this paper, we formally conceptualize the paradigm of TGDS and present a taxonomy of research themes in TGDS. We describe several approaches for integrating domain knowledge in different research themes using illustrative examples from different disciplines. We also highlight some of the promising avenues of novel research for realizing the full potential of theory-guided data science.

cs.LG↗

arXiv2017

Mining Electronic Health Records: A Survey

The continuously increasing cost of the US healthcare system has received significant attention. Central to the ideas aimed at curbing this trend is the use of technology, in the form of the mandate to implement electronic health records (EHRs). EHRs consist of patient information such as demographics, medications, laboratory test results, diagnosis codes and procedures. Mining EHRs could lead to improvement in patient health management as EHRs contain detailed information related to disease prognosis for large patient populations. In this manuscript, we provide a structured and comprehensive overview of data mining techniques for modeling EHR data. We first provide a detailed understanding of the major application areas to which EHR mining has been applied and then discuss the nature of EHR data and its accompanying challenges. Next, we describe major approaches used for EHR mining, the metrics associated with EHRs, and the various study designs. With this foundation, we then provide a systematic and methodological organization of existing data mining techniques used to model EHRs and discuss ideas for future research. We conclude this survey with a comprehensive summary of clinical data mining applications of EHR data, as illustrated in the online supplement.

cs.IR↗

arXiv2016

Causal Inference in Observational Data

Our aging population increasingly suffers from multiple chronic diseases simultaneously, necessitating the comprehensive treatment of these conditions. Finding the optimal set of drugs for a combinatorial set of diseases is a combinatorial pattern exploration problem. Association rule mining is a popular tool for such problems, but the requirement of health care for finding causal, rather than associative, patterns renders association rule mining unsuitable. To address this issue, we propose a novel framework based on the Rubin-Neyman causal model for extracting causal rules from observational data, correcting for a number of common biases. Specifically, given a set of interventions and a set of items that define subpopulations (e.g., diseases), we wish to find all subpopulations in which effective intervention combinations exist and in each such subpopulation, we wish to find all intervention combinations such that dropping any intervention from this combination will reduce the efficacy of the treatment. A key aspect of our framework is the concept of closed intervention sets which extend the concept of quantifying the effect of a single intervention to a set of concurrent interventions. We also evaluated our causal rule mining framework on the Electronic Health Records (EHR) data of a large cohort of patients from Mayo Clinic and showed that the patterns we extracted are sufficiently rich to explain the controversial findings in the medical literature regarding the effect of a class of cholesterol drugs on Type-II Diabetes Mellitus (T2DM).

cs.AI↗

arXiv2012

Enhancing the functional content of protein interaction networks

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.

q-bio.MN↗

arXiv2011

Characterizing Discriminative Patterns

Discriminative patterns are association patterns that occur with disproportionate frequency in some classes versus others, and have been studied under names such as emerging patterns and contrast sets. Such patterns have demonstrated considerable value for classification and subgroup discovery, but a detailed understanding of the types of interactions among items in a discriminative pattern is lacking. To address this issue, we propose to categorize discriminative patterns according to four types of item interaction: (i) driver-passenger, (ii) coherent, (iii) independent additive and (iv) synergistic beyond independent additive. Either of the last three is of practical importance, with the latter two representing a gain in the discriminative power of a pattern over its subsets. Synergistic patterns are most restrictive, but perhaps the most interesting since they capture a cooperative effect. For domains such as genetic research, differentiating among these types of patterns is critical since each yields very different biological interpretations. For general domains, the characterization provides a novel view of the nature of the discriminative patterns in a dataset, which yields insights beyond those provided by current approaches that focus mostly on pattern-based classification and subgroup discovery. This paper presents a comprehensive discussion that defines these four pattern types and investigates their properties and their relationship to one another. In addition, these ideas are explored for a variety of datasets (ten UCI datasets, one gene expression dataset and two genetic-variation datasets). The results demonstrate the existence, characteristics and statistical significance of the different types of patterns. They also illustrate how pattern characterization can provide novel insights into discriminative pattern mining and the discriminative structure of different datasets.

cs.DB↗

arXiv2011

Integration of Differential Gene-combination Search and Gene Set Enrichment Analysis: A General Approach

Gene Set Enrichment Analysis (GSEA) and its variations aim to discover collections of genes that show moderate but coordinated differences in expression. However, such techniques may be ineffective if many individual genes in a phenotype-related gene set have weak discriminative power. A potential solution is to search for combinations of genes that are highly differentiating even when individual genes are not. Although such techniques have been developed, these approaches have not been used with GSEA to any significant degree because of the large number of potential gene combinations and the heterogeneity of measures that assess the differentiation provided by gene groups of different sizes. To integrate the search for differentiating gene combinations and GSEA, we propose a general framework with two key components: (A) a procedure that reduces the number of scores to be handled by GSEA to the number of genes by summarizing the scores of the gene combinations involving a particular gene in a single score, and (B) a procedure to integrate the heterogeneous scores from combinations of different sizes and from different gene combination measures by mapping the scores to p-values. Experiments on four gene expression data sets demonstrate that the integration of GSEA and gene combination search can enhance the power of traditional GSEA by discovering gene sets that include genes with weak individual differentiation but strong joint discriminative power. Also, gene sets discovered by the integrative framework share several common biological processes and improve the consistency of the results among three lung cancer data sets.

q-bio.GN↗

arXiv2011

Construction and Functional Analysis of Human Genetic Interaction Networks with Genome-wide Association Data

Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic interactions has revealed genetic interaction networks that provide novel insights either when analyzed by themselves or when integrated with other functional genomic datasets. For higher eukaryotes such as human, the above reverse-genetics approaches are not straightforward since the phenotypes of interest for higher eukaryotes are difficult to study in a cell based assay. We propose a general framework for constructing and analyzing human genetic interaction networks from genome-wide single nucleotide polymorphism (SNP) data used for case-control studies on complex diseases. Specifically, the approach contains three major steps: (1) estimating SNP-SNP genetic interactions, (2) identifying linkage disequilibrium (LD) blocks and mapping SNP-SNP interactions to block-block interactions, and (3) functional mapping for LD blocks. We performed two sets of functional analyses for each of the six datasets used in the paper, and demonstrated that (i) the constructed genetic interaction networks are supported by functional evidence from independent biological databases, and (ii) the network can be used to discover pairs of compensatory gene modules (between-pathway models) in their joint association with a disease phenotype. The proposed framework should provide novel insights beyond existing approaches that either ignore interactions between SNPs or model different SNP-SNP pairs with genetic interactions separately. Furthermore, our study provides evidence that some of the core properties of genetic interaction networks based on reverse genetics in model organisms like yeast are also present in genetic interactions revealed by natural variation in human populations.

q-bio.MN↗