Subhasis Dasgupta

Analytics-driven data ingestion and derivation in the AWESOME polystore

Polystores, i.e., data management systems that use multiple stores for different data models, are gaining popularity. We are developing a polystore-based system called AWESOME to support social data analytics. The AWESOME polystore can support relational, semistructured, graph and text data and houses a Spark computation engine to produce derived data during ingestion. ADIL, the data ingestion language of AWESOME allows a user to flexibly specify the placement of original and derived data into and across component stores and the computation engine. The paper also outlines a number of optimization strategies for managing data placement in AWESOME.

Controlled Access over Documents for Concepts Having Multiple Parents in a Digital Library Ontology

This paper proposes a solution to a problem present in Digital Library ontology for accessing concepts having multiple parents. Instead of considering the underlying structure as a tree, authors consider a DAG structure for concept nodes having multiple parents. A hashing mechanism has been developed to avoid change in document annotations against change in ontological structure. The paper highlights the problem and describes the methodologies avoiding the algorithmic details for paucity of space.

PVT: An Efficient Computational Procedure to Speed up Next-generation Sequence Analysis

BackgroundHigh-throughput Next-Generation Sequencing (NGS) techniques are advancing genomics and molecular biology research. This technology generates substantially large data which puts up a major challenge to the scientists for an efficient, cost and time effective solution to analyse such data. Further, for the different types of NGS data, there are certain common challenging steps involved in analysing those data. Spliced alignment is one such fundamental step in NGS data analysis which is extremely computational intensive as well as time consuming. There exists serious problem even with the most widely used spliced alignment tools. TopHat is one such widely used spliced alignment tools which although supports multithreading, does not efficiently utilize computational resources in terms of CPU utilization and memory. Here we have introduced PVT (Pipelined Version of TopHat) where we take up a modular approach by breaking TopHat’s serial execution into a pipeline of multiple stages, thereby increasing the degree of parallelization and computational resource utilization. Thus we address the discrepancies in TopHat so as to analyze large NGS data efficiently.ResultsWe analysed the SRA dataset (SRX026839 and SRX026838) consisting of single end reads and SRA data SRR1027730 consisting of paired-end reads. We used TopHat v2.0.8 to analyse these datasets and noted the CPU usage, memory footprint and execution time during spliced alignment. With this basic information, we designed PVT, a pipelined version of TopHat that removes the redundant computational steps during ‘spliced alignment’ and breaks the job into a pipeline of multiple stages (each comprising of different step(s)) to improve its resource utilization, thus reducing the execution time.ConclusionsPVT provides an improvement over TopHat for spliced alignment of NGS data analysis. PVT thus resulted in the reduction of the execution time to ~23% for the single end read dataset. Further, PVT designed for paired end reads showed an improved performance of ~41% over TopHat (for the chosen data) with respect to execution time. Moreover we propose PVT-Cloud which implements PVT pipeline in cloud computing system.

A graph-based formalism for controlling access to a digital library ontology

This paper presents a graph-based formalism for an Ontology Based Access Control (OBAC) system applied to Digital Library (DL) ontology. It uses graph transformations, a graphical specification technique based on a generalization of classical string grammars to nonlinear structures. The proposed formalism provides an executable specification that exploits existing tools of graph grammar to verify the properties of a graph-based access control mechanism applicable to a digital library ontology description. It also provides a uniform specification for controlling access not only at the concept level but also at the level of the documents covered by the concepts including node obfuscation, if required.

Resolving authorization conflicts by ontology views for controlled access to a digital library

– This paper provides a new Digital Library architecture that supports polyhierarchic ontology structure where a child concept representing an interdisciplinary subject area can have multiple parent concepts. The paper further proposes an access control mechanism for controlled access to different concepts by different users depending on the authorizations available to each such user. The proposed model thus provides a better knowledge representation and faster searching possibility of documents for modern Digital Libraries with controlled access to the system. , – Since the proposed Digital Library Architecture considers polyhierarchy, the underlying hierarchical structure becomes a Directed Acyclic Graph instead of a tree. A new access control model has been developed for such a polyhierarchic ontology structure. It has been shown that such model may give rise to undecidability problem. A client specific view generation mechanism has been developed to solve the problem. , – The paper has three major contributions. First, it provides better knowledge representation for present-day digital libraries, as new interdisciplinary subject areas are getting introduced. Concepts representing interdisciplinary subject areas will have multiple parents, and consequently, the library ontology introduces a new set of nodes representing document classes. This concept also provides faster search mechanism. Secondly, a new access control model has been introduced for the ontology structure where a user gets authorizations to access a concept node only if its credential supports it. Lastly, a client-based view generation algorithm has been developed so that a client’s access remains limited to its view and avoids any possibility of undecidability in authorization specification. , – The proposed model, in its present form, supports only read and browse facilities. It would later be extended for addition and update of documents. Moreover, the paper explains the model in a single user environment. It will be augmented later to consider simultaneous access from multiple users. , – The paper emphasizes the need for changing the present digital library ontology to a polyhierarchic structure to provide proper representation of knowledge related to the concepts covering interdisciplinary subject areas. Possible implementation strategies have also been mentioned. This design method can also be extended for other semantic web applications. , – This paper offers a new knowledge management strategy to cover the gradual proliferation of interdisciplinary subject areas along with a suitable access control model for a digital library ontology. This methodology can also be extended for other semantic web applications.

Resolving conflicts between role-hierarchy and concept-hierarchy in a Digital Library ontology

Permitting a child concept to have multiple parent concepts in a Digital Library ontology, this paper ventures to propose solutions to conflicts between role hierarchy of the users and concept hierarchy of the ontology.

PROFORMA: Proactive Forensics with Message Analytics

Proactive forensics uses the investigative principles of digital forensics to develop automated techniques that prevent cybercrime. One such prevention-minded methodology is PROFORMA, a prototype system that continuously evaluates the trustworthiness and risk of social communications.