Pritha Mahata - Academia.edu (original) (raw)

Papers by Pritha Mahata

Lecture Notes in Computer Science, 2006

In this paper, we introduce a novel objective function for the hierarchical clustering of data fr... more In this paper, we introduce a novel objective function for the hierarchical clustering of data from distance matrices, a very relevant task in Bioinformatics. To test the robustness of the method, we test it in two areas: (a) the problem of deriving a phylogeny of languages and (b) subtype cancer classification from microarray data. For comparison purposes, we also consider both the use of ultrametric trees (generated via a two-phase evolutionary approach that creates a large number of hypothesis trees, and then takes a consensus), and the best-known results from the literature. We used a dataset of measured 'separation time' among 84 Indo-European languages. The hierarchy we produce agrees very well with existing data about these languages across a wide range of levels, and it helps to clarify and raise new hypothesis about the evolution of these languages. Our method also generated a classification tree for the different cancers in the NCI60 microarray dataset (comprising gene expression data for 60 cancer cell lines). In this case, the method seems to support the current belief about the heterogeneous nature of the ovarian, breast and non-small-lung cancer, as opposed to the relative homogeneity of other types of cancer. However, our method reveals a close relationship of the melanoma and CNS cell-lines. This is in correspondence with the fact that metastatic melanoma first appears in central nervous system (CNS).

PLoS ONE, 2010

Clustering, particularly hierarchical clustering, is an important method for understanding and an... more Clustering, particularly hierarchical clustering, is an important method for understanding and analysing data across a wide variety of knowledge domains with notable utility in systems where the data can be classified in an evolutionary context. This paper introduces a new hierarchical clustering problem defined by a novel objective function we call the arithmeticharmonic cut. We show that the problem of finding such a cut is NP-hard and APX-hard but is fixed-parameter tractable, which indicates that although the problem is unlikely to have a polynomial time algorithm (even for approximation), exact parameterized and local search based techniques may produce workable algorithms. To this end, we implement a memetic algorithm for the problem and demonstrate the effectiveness of the arithmetic-harmonic cut on a number of datasets including a cancer type dataset and a corona virus dataset. We show favorable performance compared to currently used hierarchical clustering techniques such as k-MEANS, Graclus and NORMALIZED-CUT. The arithmetic-harmonic cut metric overcoming difficulties other hierarchal methods have in representing both intercluster differences and intracluster similarities.

Genome Informatics Series, 2006

Epithelial carcinoma of the ovary is one of the most common gynecological malignancies and the fi... more Epithelial carcinoma of the ovary is one of the most common gynecological malignancies and the fifth most frequent cause of cancer death in women. Currently blood test of advanced epithelial tumors are reflected in a high level of CA 125 antigen. However, it is not a good marker for early stage tumors, and may yield false positives. Clearly, there is a need for better understanding of the molecular pathogenesis of epithelial ovarian cancer, so that new drug targets or biomarkers that facilitate early detection can be identified. This work concentrates on finding genetic markers for three epithelial ovarian tumors, using a simple computational method. We give a small set of genetic markers which are able to distinguish clear cell and mucinous ovarian cancers (13 and 26 genes respectively) from other epithelial ovarian tumors with 100% accuracy. We obtain the genes HNF1-beta (TCF2) and GGT1 as the best markers for the clear cell and CEACAM6 (NCA) as the best marker for mucinous ovaria...

ABSTRACT. We consider Dense-Timed Petri Nets (TPN), an extension of Petri nets in which each toke... more ABSTRACT. We consider Dense-Timed Petri Nets (TPN), an extension of Petri nets in which each token is equipped with a real-valued clock and where the semantics is lazy (i.e., enabled transitions need not fire; time can pass and disable transitions). We consider the following verification problems for TPNs. (i) Zenoness: whether there exists a zeno-computation from a given marking, i.e., an infinite computation which takes only a finite amount of time. We show decidability of zenoness for TPNs, thus solving an open problem from [dFERA00]. Furthermore, the related question if there exist arbitrarily fast computations from a given marking is also decidable. On the other hand, universal zenoness, i.e., the question if all infinite computations from a given marking are zeno, is undecidable. (ii) Token liveness: whether a token is alive in a marking, i.e., whether there is a computation from the marking which eventually consumes the token. We show decidability of the problem by reducing i...

Epithelial carcinoma of the ovary is one of the most common gynecological malignancies and the ft... more Epithelial carcinoma of the ovary is one of the most common gynecological malignancies and the fth most frequent cause of cancer death in women. Currently blood test of advanced epithelial tumors are re ected in a high level of CA 125 antigen. However, it is not a good marker for early stage tumors, and may yield false positives. Clearly, there is a need for better understanding of the molecular pathogenesis of epithelial ovarian cancer, so that new drug targets or biomarkers that facilitate early detection can be identi ed. This work concentrates on nding genetic markers for three epithelial ovarian tumors, using a simple computational method. We give a small set of genetic markers which are able to distinguish clear cell and mucinous ovarian cancers (13 and 26 genes respectively) from other epithelial ovarian tumors with 100% accuracy. We obtain the genes HNF1-beta (TCF2) and GGT1 as the best markers for the clear cell and CEACAM6 (NCA) as the best marker for mucinous ovarian tumo...

Replace this file with prentcsmacro.sty for your meeting,or with entcsmacro.sty for your meeting.... more Replace this file with prentcsmacro.sty for your meeting,or with entcsmacro.sty for your meeting. Both can be found at the ENTCS Macro Home Page.

In this paper, we present an approach for algorithmic verification of infinite-state systems with... more In this paper, we present an approach for algorithmic verification of infinite-state systems with a parameterized tree topology. Our work is a generalization of regular model checking, where we extend the work done with strings toward trees. States are represented by trees over a finite alphabet, and transition relations by regular, structure preserving relations on trees. We use an automata theoretic method to compute the transitive closure of such a transition relation. Although the method is incomplete, we present sufficient conditions to ensure termination.

Abstract. We consider verification of safety properties for parameterized systems of timed proces... more Abstract. We consider verification of safety properties for parameterized systems of timed processes, so called timed networks. A timed network consists of a finite state process, called a controller, and an arbitrary set of identical timed processes. In a previous work, we showed that checking safety properties is decidable in the case where each timed process is equipped with a single real-valued clock. It was left open whether the result could be extended to multi-clock timed networks. We show that the problem becomes undecidable when each timed process has two clocks. On the other hand, we show that the problem is decidable when clocks range over a discrete time domain. This decidability result holds when processes have any finite number of clocks. 1

Software is finding its way into an increasing range of devices (phones, medical equipment, cars.... more Software is finding its way into an increasing range of devices (phones, medical equipment, cars...). A challenge is to design verification methods to ensure correctness of software. We focus on model checking, an approach in which an abstract model of the implementation and a specification of requirements are provided. The task is to answer automatically whether the system conforms with its specification.We concentrate on (i) timed systems, and (ii) parameterized systems. Timed systems can be modeled and verified using the classical model of timed automata. Correctness is translated to language inclusion between two timed automata representing the implementation and the specification. We consider variants of timed automata, and show that the problem is at best highly complex, at worst undecidable. A parameterized system contains a variable number of components. The problem is to verify correctness regardless of the number of components. Regular model checking is a prominent method ...

Abstract: We use downward closed languages for representing sets of states when performing forwar... more Abstract: We use downward closed languages for representing sets of states when performing forward reachability analysis on infinite-state systems. Downward closed languages are often more succinct than exact representations of the set of reachable ...

In recent years, there has been much advancement in the area of verification of infinite-state sy... more In recent years, there has been much advancement in the area of verification of infinite-state systems. A system can have an infinite state-space due to unbounded data structures such as counters, ...

Nord. J. Comput., 2007

We consider verification of safety properties for concurrent real-timed systems modelled as timed... more We consider verification of safety properties for concurrent real-timed systems modelled as timed Petri nets by performing symbolic forward reachability analysis. We introduce a formalism, called region generators, for representing sets of markings of timed Petri nets. Region generators characterize downward closed sets of regions and provide exact abstractions of sets of reachable states with respect to safety properties. We show that the standard operations needed for performing symbolic reachability analysis are computable for region generators. Since forward reachability analysis is necessarily incomplete, we introduce an acceleration technique to make the procedure terminate more often on practical examples. We have implemented a prototype for analyzing timed Petri nets and used it to verify a parameterized version of Fischer's protocol, Lynch and Shavit's mutual exclusion protocol and a producer-consumer protocol. We also used the tool to extract finite-state abstracti...

Upb Scientific Bulletin Series C Electrical Engineering, 2010

Previous works on Parkinson's disease (PD) mainly focused on genes differentially expressed betwe... more Previous works on Parkinson's disease (PD) mainly focused on genes differentially expressed between the anterior and the posterior sections of the brains of a normal mouse and the one with PD. However, no work has been done in finding a hierarchical pattern of gene expression between the different regions of a brain. Such a hierarchy is useful to locate genetic specializations within a normal brain, thus in analyzing how brain infirmities affect these specializations. We use a recently proposed method of robust hierarchical clustering using arithmeticharmonic cut to construct the hierarchical relation between different regions of the brain. Then, we show how similar regions of the normal and PD brain differ in gene expressions, indicating a functional variation due to Parkinson's disease in a few high-level clusters of brain regions.

... NModel provides solutions to the problems of expressing and analysing spec-ifications and des... more ... NModel provides solutions to the problems of expressing and analysing spec-ifications and designs, generating ... B. Using NModel In our experience, NModel is easy to use, since it is well ... of MBT with varied technologies such as UML [16] and the use of SpecExplorer [17] which ...

Genome informatics. International Conference on Genome Informatics, 2006

Formal Techniques, Modelling and Analysis of Timed and Fault-Tolerant Systems, 2004

We consider verification of safety properties for concurrent real-timed systems modelled as timed... more We consider verification of safety properties for concurrent real-timed systems modelled as timed Petri nets, by performing symbolic forward reachability analysis. We introduce a formalism, called region generators for representing sets of markings of timed Petri nets. Region generators characterize downward closed sets of regions, and provide exact abstractions of sets of reachable states with respect to safety properties. We show that the standard operations needed for performing symbolic reachability analysis are computable for region generators. Since forward reachability analysis is necessarily incomplete, we introduce an acceleration technique to make the procedure terminate more often on practical examples. We have implemented a prototype for analyzing timed Petri nets and used it to verify a parameterized version of Fischer's protocol and a producerconsumer protocol. We also used the tool to extract finite-state abstractions of these protocols.

In this paper, we develop a novel feature selection and classification approach using the correla... more In this paper, we develop a novel feature selection and classification approach using the correlation maximization paradigm. This approach is particularly interesting when the number of features is very large in comparison to the number of samples, as in the datasets arising in the bioinformatics applications. We illustrate our method by showing 100 genetic markers which act together in separating ovarian endometroid tumors from other ovarian epithelial tumors. Notice that in the previous works, there was no single marker gene found for this purpose.

Lecture Notes in Computer Science, 2006

PLoS ONE, 2010

Genome Informatics Series, 2006

Nord. J. Comput., 2007

Upb Scientific Bulletin Series C Electrical Engineering, 2010

Genome informatics. International Conference on Genome Informatics, 2006

Formal Techniques, Modelling and Analysis of Timed and Fault-Tolerant Systems, 2004

We consider verification of safety properties for concurrent real-timed systems modelled as timed... more We consider verification of safety properties for concurrent real-timed systems modelled as timed Petri nets, by performing symbolic forward reachability analysis. We introduce a formalism, called region generators for representing sets of markings of timed Petri nets. Region generators characterize downward closed sets of regions, and provide exact abstractions of sets of reachable states with respect to safety properties. We show that the standard operations needed for performing symbolic reachability analysis are computable for region generators. Since forward reachability analysis is necessarily incomplete, we introduce an acceleration technique to make the procedure terminate more often on practical examples. We have implemented a prototype for analyzing timed Petri nets and used it to verify a parameterized version of Fischer's protocol and a producerconsumer protocol. We also used the tool to extract finite-state abstractions of these protocols.