vijay chandru


RESEARCH & IMPACT
 

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Algorithms and Complexity
in Combinatorial Optimization

(1977-1997)

Impact: Academic

Chandru’s doctoral dissertation work was in the computational complexity of combinatorial optimization. Theoretical computer scientists and logicians had developed a hierarchy of computation and the focus in the late 70s was on positioning practical engineering design problems on combinatorial and discrete structures in this hierarchical framework. This approach led to many interesting fundamental problems in “algorithmics” i.e., efficient algorithm design and proofs of intractability of problem classes. The breakthroughs in problems like Karmarkar’s linear programming method and resolution of various graph conjectures kept researchers in this field busy through the 80s and early 90s. Chandru’s work in this area remained strongly academic and intellectual. He became a recognized authority and was invited to write handbook chapters and review papers of the field. A recipient of the Presidents medal of INFORMS (2006) (The Institute for Operations Research and the Management Sciences) and the MC Puri Memorial Award of ORSI (Operations Research Society of India) in 2012, Chandru is the President elect of ORSI for the term 2017-19.

 

·        V. Chandru and  M.R.Rao, Linear Programming, Chapter 31 in  Handbook of Algorithms and Theory of Computing, edited by M.J.Atallah, CRC Press 1999, 31-1 to 31-37.

·        V. Chandru and B.S. Kochar, "Exploring special structures using a variant of Karmarkar's algorithm," Research Memorandum No. 86-10, Purdue University (1986).

·        V.Chandru and M.R.Rao, Combinatorial Optimization: An Integer Programming Perspective,  ACM Computing Surveys, March 1996, pp 55-58

·        V.Chandru, Variable Elimination in Linear Constraints, The Computer Journal No. 5, August 1993, 463-472.

 


Computational Geometry, Manufacturing and 3D-Printing.
(1985-1995)

Impact: Academic and Translational Research

As a young assistant professor at Purdue, Chandru developed a new research area for himself around the computer manipulation of planar and solid geometric objects. The rapid development of computer graphics, solid modelling, robotics and computer-aided design and manufacture were the applications that were driving translational research in this subject. As a professor in industrial engineering at Purdue University, Chandru had exciting opportunities to work on cutting-edge applications in intelligent manufacturing systems.  After returning to India in the 90s, Chandru along with colleagues S. Manohar and B. Gurumoorthy at IISc Bangalore built out the first 3D Printing (Stereolithography on a Stratasys platform) laboratory in the country for rapid prototyping of 3-dimensional designs. This led to the creation of APDAP (advanced product design and prototyping) a joint venture of IISc with Tata Consulting Services that provided design services to industry starting in the mid 90s.

·        V.Chandru and S.Manohar, Volume Modeling for Emerging Manufacturing Technologies, Sadhana, The Engineering Sciences Journal of the Indian Academy of Sciences, April 1997, pp.199-216.

·        V.Chandru, S.Manohar and C.E.Prakash,  Voxel-Based Modeling and Volume Graphics for Rapid Prototyping, IEEE Transactions on the computer Graphics and Applications, pp42-48, November 1995

·        V.Chandru, D.Dutta and C.M.Hoffmann, The Geometry of Dupin Cyclides, {The Visual Computer}, Vol.5, pp. 277-290, 1989.

·        S.S.Abhyankar and S.Chandrasekhar and V.Chandru, Improper Intersection of Algebraic Curves, A.C.M. Transactions on Graphics, 9,  2, pages 147-159, April 1990.


"...the first monograph devoted to a new interesting research area combining logic with optimization methods."

(Mathematical Reviews, Issue 2001j)

 


Foundations of Artificial Intelligence –
Automated Theorem Proving
(1988-1998)

Impact: Academic

Automated Theorem Proving, the cornerstone of “Strong AI”, refers to the ability to create intelligent machines that can implement the formal rules of deductive inference (modus ponens and modus tollens) and derive formal inferences from a set of axioms. In the mid-80s there was a program of research proposed by Professor Robert Jeroslow at Georgia Tech to improve the efficiencies of deductive logic using geometric methods. Jeroslow tragically, passed away soon after and Chandru & Hooker (Prof J N Hooker, Carnegie Mellon University) picked up the baton and through a ten year collaboration were major contributors in building out this research program. In addition to a series of research papers, this work resulted in “Optimization Methods for Logical Inference” a book in computational logic published by Wiley Interscience in 1999. During this period, Chandru was also a visiting academic with the Programming Languages Group at the IBM Watson Research Center at Hawthorne and Yorktown Heights.

 

·        V.Chandru and J.N.Hooker, An Extended Class of Horn Clause Systems, Journal of the Association for Computing Machinery, Vol 38, No. 1, January 1991, pp.  205-221.

·        V.Chandru, C.R.Coullard, P.L.Hammer, M.A.Montanez and X.Sun, On Renamable Horn and Generalized Horn Functions, Annals of Mathematics and Artificial Intelligence, Vol I, pp. 33-47, 1990.

·        Vivek S. Borkar, Vijay Chandru, Sanjoy K. Mitter: Mathematical Programming Embeddings of Logic. J. Autom. Reasoning 29(1): 91-106 (2002)

·        John N. Hooker, G. Rago, V. Chandru, A. Shrivastava: Partial Instantiation Methods for Inference in First-Order Logic. J. Autom. Reasoning 28(5): 371-396 (2002)

 

“The most significant innovation in computer technology in 2001 was not Apple’s gleaming titanium Powerbook G4 or Microsoft’s Windows XP. It was the Simputer, a Net-linked, radically simple portable computer, intended to bring the computer revolution to the third world.”

--- Bruce Sterling, NY Times Magazine, December 9, 2001 “The Year in Ideas”


Bridging the Digital Divide with a People’s Computer
(1998-2005)

Impact: Translational Research, Innovation

 

The Simputer project grew out of a multi-disciplinary dialogue conducted at the National Institute of Advanced Studies by its director Prof R Narasimha, the venerated social anthropologist Prof MN Srinivas and a dynamic young IAS officer Sanjay Biswas who was the IT Secretary of Karnataka in 1998. The topic was information technology and development. The Simputer (Simple Inexpensive Multilingual Peoples compUTER) was about building a people’s computer based on the principle of “radical simplicity for universal access”. A 7-layer mother board designed from scratch, linux operating system ported to minimal hardware, icon driven and touch screen based user interface, smart card integrated for secure financial transactions, Indian languages enabled including text-to-speech in several Indian languages, an open source and viral hardware and software specification, a built in accelerometer (the first handheld to have one) to have motion control – the Simputer was simply a marvel of indigenous technology – perhaps more than a bit ahead of its time.

 

As one of the inventors of the Simputer, Professor Chandru received the Dewang Mehta Award from MCIT, the first time it was awarded in 2001 (the nation’s highest award for innovation in information technology). Chandru also co-founded PicoPeta Simputers, a private limited company that commercialized the novel handheld device technology and brought it to market as the Amida Simputer. He participated actively in its conception and early growth, and continued to serve as an advisor till its successful acquisition by a publicly traded company. PicoPeta was earlier listed among the “seven hottest startups worldwide” by Technology Review magazine in 2002.

 

Over 50,000 Simputers have been manufactured and deployed in India. The product has since been called Geo Amida and was one of the primary devices in conjunction with the Micro ATM application of the national unique ID “Aadhaar” project. Chandru was the recipient of the Hari Om Trust Award for contributions to “Science and Society” given by the University Grants Commission in 2003. The Simputer was not a roaring retail success but is certainly an important “meme” in the technological history of modern India. It was only the second time that a computer had been conceived and built in India (TIFRAC – the TIFR Advanced Calculator was the earlier effort in the late 50s) from scratch.

 

·        V. Chandru, V.L. Deshpande, S. Garg, R. Hariharan, S. Manohar, M. Mathias, V. Vinay (The Simputer Trust),  Radical Simplicity for Universal Access, dyd01 Development by Design, MIT Media Lab, July 2001.

·        Chandru,V and S Manohar, The Global Village: Aspirations and Opportunities for Developing Economies (October 1998), NIAS Report.

·        V. Chandru, The Simputer Meme and Sustainable Development, in Proceedings of the CCC Workshop on Computer Science and Global Development, Berkeley, CA pages 25-26 (2009).

 


Data Science in Biology:
The Avadis Story
(1995-2010)

Impact: Translational Research to Global Innovation

The Human Genome Project had put out the first complete map of a human reference genome. Genomics had arrived. High throughput proteomics, metabolomics, cellomics,... were just around the corner and the first signs of what is now called the "Fourth Paradigm or Data-Intensive Science" was already evident in research biology.

Professor Chandru and his colleagues in computer science at IISc began an interdisciplinary journey at the interface of computation and biology in the mid-90s. In late 2000, Strand Genomics Pvt Ltd had been launched from IISc as India's first example of sanctioned academic entrepreneurship. The promoters were four professors of computer science and the Society for Innovation and Development (SID) - the commercialization arm of IISc.

 Chandru was a key founder of Strand and he has led the company as executive chairman (CMD) from inception. . He was largely responsible for articulating Strand’s vision, recruiting the founding team, helping the venture graduate from IISc through dialog with the university administration, and developing the first version of Strand’s business plan. Subsequently, Prof Chandru helped raise institutional capital, establish business and technology strategy, and build the R&D, production, and sales teams. Strand now employs over 200 scientists and provides bioinformatics solutions to research labs around the globe and services to Indian healthcare establishment using next generation sequencing based diagnostics.

 


Strand was going to build the platform that would enable life scientists to build a quantitative science, much in the same way as MatLab has empowered physicists and electrical engineers in their respective disciplines. The platform was ready by 2004 and was christened AVADIS® (access, visualization, analysis, to discover).


The story of Avadis® over the next ten years has been one of growth of perhaps the only high complexity information technology product conceived and built in India that has achieved large global market share and is a global benchmark even till today  

The Avadis® derived products (distributed globally in partnership with Agilent) have served well over 2000 laboratories around the world and over 20,000 citations in publications.  Strand has undoubtedly been a global trailblazer in bioinformatics.




Strand Life Sciences (Strand), a Bangalore and San Francisco-based bioinformatics and systems biology company has received patent protection for its “method for predicting organ toxicity and a system thereof” in the United States (USPTO patent no. 8,645,075) effective from 4 February 2014. The method is currently employed in the form of a rat-based Virtual Liver model by the pharmaceutical industry to predict and assess hepatotoxicity of novel drug compounds in pre-clinical studies and by the cosmetics industry in the form of a skin and hair model.The human liver model has also been validated.

 

In 2004, Strand embarked on a research project that would be considered audacious. The scientific team set out to build a “Virtual Liver” that would test the hepato-toxicity of  compounds like drug molecules and other synthetic molecules (ingredients in paints, cosmetics, etc.).

In 2016, after the platform had been validated by industrial partners, this business unit of Strand was sold to Syngene International in Bangalore where it now is part of the offering in contract research services to pharmaceutical and chemical industries.
 



Strand Authors - Scientific Publications

·        Gene regulatory network modeling using literature curated and high throughput data. Systems and synthetic biology

·        Construction of a Global Pain Systems Network Highlights Phospholipid Signaling as a Regulator of Heat Nociception, PLoS Genetics

·        Next Generation Sequencing of Human Mitochondrial Reference Genomes Uncovers High Heteroplasmy Frequency. PLoS Computational Biology

·        COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples, PLoS ONE, 7(10): e47812

·        A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica, BMC Genomics, 13: 464

·        Investigation of serum proteome alterations in human glioblastoma multiforme, Proteomics, 12, 2378–2390

·        Proteomic Investigation of Falciparum and Vivax Malaria for Identification of Surrogate Protein Markers, PLoS ONE, Vol 7(8):e41751

·        Transcriptomic profiling of Medial Temporal Lobe Epilepsy, Journal of Proteomics and Bioinformatics, Vol.5(2); 031-039

·        Customisation of the Exome Data Analysis Pipeline Using a Combinatorial Approach, PLoS ONE, 7(1): e30080

·        De novo sequencing and assembly of Azadirachta indica fruit transcriptome, Curr Sci (India), 101(12): 1553

·        Gene Expression Profiling of Tuberculous Meningitis,  J Proteomics Bioinform 4: 098-105

·        A global in vivo Drosophila RNAi screen identifies NOT3 as a conserved regulator of heart function, Cell, 141(1) p142-153

·        Gene Expression Profiling of Gastric Cancer, Journal of Proteomics and Bioinformatics, Vol.4.4; 074-082

·        MultiMCS: A Fast Algorithm for the Maximum Common Substructure Problem on Multiple Molecules, J. Chem. Inf. Model., 51 (4), pp 788–806

·        Phenotype, Function and Gene Expression Profiles of PD-1hi CD8 T cells in Healthy Human Adults, Journal of Immunology, 186:4200-4212

·        A Genome-wide Drosophila Screen for Heat Nociception Identifies α2δ3 as an Evolutionarily Conserved Pain Gene, Cell, 143(4) p628-638

·        A systems biology based integrative framework to enhance the predictivity of in vitro methods for drug-induced liver injury, Expert Opin Drug Saf, Nov;7(6):647-62

·        B. Mishra, V. Chandru, C. Cantor, R. Hariharan, et al. (27 authors).A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes, OMICS: A Journal of Integrative Biology Volume 7, Number 3, 2003.

·        Vijay Chandru, Abhi Dattasharma, V. S. Anil Kumar: The algorithmics of folding proteins on lattices. Discrete Applied Mathematics 127(1): 145-161 (2003)


 

 

 
Strand Ramanujan: Next Generation Genomics to Precision Medicine

(2011-2017)

Impact: Translational Research, Innovation
and Social Impact


In 2012, the founders and management decided to transform Strand into a new generation healthcare company. This bold strategic decision was motivated by the emerging impact of genomics in healthcare and the opportunity for a life sciences company with deep data science capabilities like Strand to push the envelope.

 

Today, Strand is a leader in precision medicine diagnostics, aimed at empowering cancer care and genetic testing for inherited diseases. Strand works with oncologists, pathologists, geneticists, and hospitals to enable faster clinical decision support for accurate molecular diagnosis, prognosis, therapy recommendations, and clinical trials. Strand’s lab in India is a CAP (College of American Pathologists) & NABL (ISO 15189: 2012)  accredited NGS laboratory. Strand has already delivered over 6000 clinical reports in clinical genomics to physicians all over India and is heralding the arrival of precision medicine in India.

 

Over a period of 15 years, Strand has continuously built on and leveraged its proprietary AI platform, christened “Ramanujan” after two great intellectuals of Indian origin: S. Ramanujan (1887-1920) the genius mathematician who greatly contributed to number theory which has regained new significance in the age of computer technology and A.K. Ramanujan (1929-1993), the literature scholar and linguist extraordinaire.

 

Strand Ramanujan is representative of India’s ability to produce world-class AI platforms to aid in disease prevention, diagnostics, and treatment, and capable of competing with the likes of IBM (Watson Health™ and GE (Predix®). At the core of Ramanujan, is Strand’s proprietary natural language processing (NLP) platform Grammatica™ (Avadis Natural Language Processor) that powers Strand’s products, including the market-leading gene expression analysis software GeneSpring® (marketed by Agilent Technologies, Inc.), Strand NGS®, the powerful NGS data analysis and visualization platform, and StrandOmics™, enabling fast and accurate clinical variant interpretation and reporting.

Clinical Publications by Strand:

·        StrandAdvantage test for early-line and advanced-stage treatment decisions in solid tumors, Cancer Medicine, April 2017

·        Genotype-Phenotype Analysis in an Indian Family Affected with Li-Fraumeni Syndrome-Role of Genetic Counselling, International Journal of Human Genetics

·        Incidental Findings in Male Breast Carcinoma: A Genetic Counseling Approach, International Journal of Human Genetics

·        Homozygosity mapping guided next generation sequencing to identify the causative genetic variation in inherited retinal degenerative diseases, Journal of Human Genetics, Nature Press

·        Genetic studies in a patient with X-linked retinoschisis coexisting with developmental delay and sensorineural hearing loss, Ophthalmic Genetics

·        Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort, Molecular Vision

·        Identification of a novel glucokinase mutation in an Indian woman with GCK-MODY, The Lancet Diabetes and Endocrinology

·        Detection of high frequency of mutations in a breast and/or ovarian cancer cohort: implications of embracing a multi-gene panel in molecular diagnosis in India, Journal of Human Genetics

·        Meta-Analyses of Microarray Datasets Identifies ANO1 and FADD as Prognostic Markers of Head and Neck Cancer, PLoS ONE

·        Recurrent and novel GLB1 mutations in India, Gene

·        An integrated transcriptomics and proteomics study of Head and Neck Squamous Cell Carcinoma – methodological and analytical considerations, bioRxiv

·        Release of (and lessons learned from mining) a pioneering large toxicogenomics database, Pharmacogenomics

·        Identification of Novel Mutations in ABCA4 Gene: Clinical and Genetic Analysis of Indian Patients with Stargardt Disease, BioMed Research International

·        Metabolite profiling in posttraumatic stress disorder, Journal of Molecular Psychiatry, 3:2

·        Bioinformatics, Systems Biology and Systems Medicine, in Genomic Medicine: Principles and Practice, Second Edition, Edited by Kumar D and Eng C, Oxford University Press, USA

 

Strand Life Sciences stands out as a unique translational success story in India. It opens up the possibility of innovation driven from the higher educational establishment in India. Eric Schmidt (The Chairman of Google-Alphabet) was asked recently why the US has been such a dominant innovator in the league of nations. His response was that the US higher educational system had figured out how to drive innovation all the way to commercial enterprise. He credited the early insights of post-war leaders like Vannevar Bush and later the Bayh-Dole Act that opened up entrepreneurship for researchers. Strand has shown that this model could work in India and as the success of Strand has come to be known, we have seen an expansion of the faculty driven enterprises spinning off from IISc, JNCASR, etc.