ORCID Profile
0000-0002-6666-514X
Current Organisation
Monash University
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Artificial Intelligence and Image Processing | Artificial Intelligence and Image Processing not elsewhere classified | Biochemistry And Cell Biology Not Elsewhere Classified | Biochemistry and Cell Biology | Computer Software | Programming Languages | Information Storage, Retrieval And Management | Computer Software Not Elsewhere Classified | Applied Mathematics | Processor Architectures | Pattern Recognition and Data Mining | Programming Languages | Programming Techniques | Software Engineering | Optimisation | Biological Sciences Not Elsewhere Classified | Operations Research | Stochastic Analysis and Modelling | Other Biological Sciences |
ANZSRC Socio-Economic Objective (SEO)
Computer Software and Services not elsewhere classified | Biological sciences | Computer software and services not elsewhere classified | Application Software Packages (excl. Computer Games) | Application tools and system utilities | Infectious diseases | Energy Services and Utilities | Urban and Industrial Water Management | Industrial Energy Conservation and Efficiency | Expanding Knowledge in the Information and Computing Sciences | Expanding Knowledge in the Biological Sciences | Other
Related Links
Publications
A CLP heap solver for test case generation
Publisher: Cambridge University Press (CUP)
Date: 07-2013
DOI: 10.1017/S1471068413000458
Abstract: One of the main challenges to software testing today is to efficiently handle heap-manipulating programs. These programs often build complex, dynamically allocated data structures during execution and, to ensure reliability, the testing process needs to consider all possible shapes these data structures can take. This creates scalability issues since high (often exponential) numbers of shapes may be built due to the aliasing of references. This paper presents a novel CLP heap solver for the test case generation of heap-manipulating programs that is more scalable than previous proposals, thanks to the treatment of reference aliasing by means of disjunction , and to the use of advanced back-propagation of heap related constraints. In addition, the heap solver supports the use of heap assumptions to avoid aliasing of data that, though legal, should not be provided as input.
Symmetries, almost symmetries, and lazy clause generation
Publisher: Springer Science and Business Media LLC
Date: 16-03-2014
Solver-Independent Large Neighbourhood Search
Publisher: Springer International Publishing
Date: 2018
The Design of the Zinc Modelling Language
Publisher: Springer Science and Business Media LLC
Date: 14-05-2008
Optimal dynamic partial order reduction with context-sensitive independence and observers
Publisher: Elsevier BV
Date: 08-2023
Checking modes of HAL programs
Publisher: Cambridge University Press (CUP)
Date: 31-10-2005
DOI: 10.1017/S1471068404002327
Abstract: Recent constraint logic programming (CLP) languages, such as HAL and Mercury, require type, mode and determinism declarations for predicates. This information allows the generation of efficient target code and the detection of many errors at compile-time. Unfortunately, mode checking in such languages is difficult. One of the main reasons is that, for each predicate mode declaration, the compiler is required to appropriately re-order literals in the predicate's definition. The task is further complicated by the need to handle complex instantiations (which interact with type declarations and higher-order predicates) and automatic initialization of solver variables. Here we define mode checking for strongly typed CLP languages which require reordering of clause body literals. In addition, we show how to handle a simple case of polymorphic modes by using the corresponding polymorphic types.
Towards semi-automatic learning-based model transformation
Publisher: Springer International Publishing
Date: 2018
Redundant Sudoku rules
Publisher: Cambridge University Press (CUP)
Date: 30-10-2014
DOI: 10.1017/S1471068412000361
Abstract: The rules of Sudoku are often specified using 27 all_different constraints, referred to as the big constraints. Using graphical proofs and exploratory logic programming, the following main and new result is obtained: Many subsets of six of these big constraints are redundant (i.e., they are entailed by the remaining 21 constraints), and six is maximal (i.e., removing more than six constraints is not possible while maintaining equivalence). The corresponding result for binary inequality constraints, referred to as the small constraints, is stated as a conjecture.
Optimizing compilation of constraint handling rules in HAL
Publisher: Cambridge University Press (CUP)
Date: 07-2005
DOI: 10.1017/S1471068405002413
Abstract: In this paper we discuss the optimizing compilation of Constraint Handling Rules (CHRs). CHRs are a multi-headed committed choice constraint language, commonly applied for writing incremental constraint solvers. CHRs are usually implemented as a language extension that compiles to the underlying language. In this paper we show how we can use different kinds of information in the compilation of CHRs to obtain access efficiency, and a better translation of the CHR rules into the underlying language, which in this case is HAL. The kinds of information used include the types, modes, determinism, functional dependencies and symmetries of the CHR constraints. We also show how to analyze CHR programs to determine this information about functional dependencies, symmetries and other kinds of information supporting optimizations.
Visual search tree profiling
Publisher: Springer Science and Business Media LLC
Date: 16-08-2016
What do Constraint Programming Users Want to See? Exploring the Role of Visualisation in Profiling of Models and Search
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 2017
Improving PARMA trailing
Publisher: Cambridge University Press (CUP)
Date: 16-10-2006
On implementing symmetry detection
Publisher: Springer Science and Business Media LLC
Date: 23-07-2008
RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins
Publisher: Cold Spring Harbor Laboratory
Date: 13-06-2007
DOI: 10.1101/GR.6255407
Abstract: Over 3% of human proteins contain single amino acid repeats (repeat-containing proteins, RCPs). Many repeats (homopeptides) localize to important proteins involved in transcription, and the expansion of certain repeats, in particular poly-Q and poly-A tracts, can also lead to the development of neurological diseases. Previous studies have suggested that the homopeptide makeup is a result of the presence of G+C-rich tracts in the encoding genes and that expansion occurs via replication slippage. Here, we have performed a large-scale genomic analysis of the variation of the genes encoding RCPs in 13 species and present these data in an online database ( repeats.med.monash.edu.au/genetic_analysis/ ). This resource allows rapid comparison and analysis of RCPs, homopeptides, and their underlying genetic tracts across the eukaryotic species considered. We report three major findings. First, there is a bias for a small subset of codons being reiterated within homopeptides, and there is no G+C or A+T bias relative to the organism’s transcriptome. Second, single base pair transversions from the homocodon are unusually common and may represent a mechanism of reducing the rate of homopeptide mutations. Third, homopeptides that are conserved across different species lie within regions that are under stronger purifying selection in contrast to nonconserved homopeptides.
Adding Search to Zinc
Publisher: Springer Berlin Heidelberg
Date: 2008
Functional insights from the distribution and role of homopeptide repeat-containing proteins
Publisher: Cold Spring Harbor Laboratory
Date: 04-2021
DOI: 10.1101/GR.3096505
Abstract: Expansion of “low complex” repeats of amino acids such as glutamine (Poly-Q) is associated with protein misfolding and the development of degenerative diseases such as Huntington's disease. The mechanism by which such regions promote misfolding remains controversial, the function of many repeat-containing proteins (RCPs) remains obscure, and the role (if any) of repeat regions remains to be determined. Here, a Web-accessible database of RCPs is presented. The distribution and evolution of RCPs that contain homopeptide repeats tracts are considered, and the existence of functional patterns investigated. Generally, it is found that while polyamino acid repeats are extremely rare in prokaryotes, several eukaryote putative homologs of prokaryote RCP—involved in important housekeeping processes—retain the repetitive region, suggesting an ancient origin for certain repeats. Within eukarya, the most common uninterrupted amino acid repeats are glutamine, asparagines, and alanine. Interestingly, while poly-Q repeats are found in vertebrates and nonvertebrates, poly-N repeats are only common in more primitive nonvertebrate organisms, such as insects and nematodes. We have assigned function to eukaryote RCPs using Online Mendelian Inheritance in Man (OMIM), the Human Reference Protein Database (HRPD), FlyBase, and Wormpep. Prokaryote RCPs were annotated using BLASTp searches and Gene Ontology. These data reveal that the majority of RCPs are involved in processes that require the assembly of large, multiprotein complexes, such as transcription and signaling.
Globalizing constraint models
Publisher: Springer Berlin Heidelberg
Date: 2013
Lock-free parallel dynamic programming
Publisher: Elsevier BV
Date: 08-2010
Process Plant Layout Optimization: Equipment Allocation
Publisher: Springer International Publishing
Date: 2018
Introduction to the 24th international conference on logic programming special issue
Publisher: Cambridge University Press (CUP)
Date: 22-02-2011
DOI: 10.1017/S1471068411000020
Abstract: The ICLP series of conferences provides a technical forum for presenting and disseminating innovative research in the field of logic programming. The 24th International Conference on Logic Programming took place from December 9–13, 2008 in the city of Udine, Italy. The conference attracted 177 submissions and featured a high-quality program focused on the foundations, developments, and applications of logic programming. Of particular significance was the special session celebrating the 20th anniversary of the seminal paper on the stable model semantics.
Lightweight dynamic symmetry breaking
Publisher: Springer Science and Business Media LLC
Date: 13-12-2013
On representing protein folding patterns using non-linear parametric curves
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 11-2014
Information-Theoretic Inference of an Optimal Dictionary of Protein Supersecondary Structures
Publisher: Springer New York
Date: 2019
The G12 Project: Mapping Solver Independent Models to Efficient Solutions
Publisher: Springer Berlin Heidelberg
Date: 2005
DOI: 10.1007/11564751_4
Adding Constraint Solving to Mercury
Publisher: Springer Berlin Heidelberg
Date: 2005
DOI: 10.1007/11603023_9
Exploiting subproblem dominance in constraint programming
Publisher: Springer Science and Business Media LLC
Date: 16-11-2012
The future of optimization technology
Publisher: Springer Science and Business Media LLC
Date: 07-09-2013
Cooperative effects in the substrate specificity of the complement protease C1s
Publisher: Walter de Gruyter GmbH
Date: 10-04-2009
DOI: 10.1515/BC.2009.064
Abstract: Complement is a key component of the immune system, but can contribute to inflammatory diseases. The substrate specificity of C1s protease has been successfully investigated using a combinatorial approach, while a positional scanning method failed. The lack of success of the latter approach is possibly due to cooperativity in the active site, which could confound such analyses. With a panel of peptides devised using factorial design, we show pronounced cooperativity between the S 4 and S 1 ′ subsites in the active site of the enzyme, and weaker cooperativity between the S 1 ′ and S 3 ′ subsites. The use of factorial design has promise as a methodology for determining cooperativity in protease active sites.
Solving talent scheduling with dynamic programming
Publisher: Institute for Operations Research and the Management Sciences (INFORMS)
Date: 02-2011
Abstract: We give a dynamic programming solution to the problem of scheduling scenes to minimize the cost of the talent. Starting from a basic dynamic program, we show a number of ways to improve the dynamic programming solution by preprocessing and restricting the search. We show how by considering a bounded version of the problem, and determining lower and upper bounds, we can improve the search. We then show how ordering the scenes from both ends can drastically reduce the search space. The final dynamic programming solution is orders of magnitude faster than competing approaches and finds optimal solutions to larger problems than were considered previously.
Independence in dynamically scheduled logic languages
Publisher: Springer Berlin Heidelberg
Date: 1996
Functional and Logic Programming
Publisher: Springer Berlin Heidelberg
Date: 2002
A new statistical framework to assess structural alignment quality using information compression
Publisher: Oxford University Press (OUP)
Date: 22-08-2014
DOI: 10.1093/BIOINFORMATICS/BTU460
Abstract: Motivation: Progress in protein biology depends on the reliability of results from a handful of computational techniques, structural alignments being one. Recent reviews have highlighted substantial inconsistencies and differences between alignment results generated by the ever-growing stock of structural alignment programs. The lack of consensus on how the quality of structural alignments must be assessed has been identified as the main cause for the observed differences. Current methods assess structural alignment quality by constructing a scoring function that attempts to balance conflicting criteria, mainly alignment coverage and fidelity of structures under superposition. This traditional approach to measuring alignment quality, the subject of considerable literature, has failed to solve the problem. Further development along the same lines is unlikely to rectify the current deficiencies in the field. Results: This paper proposes a new statistical framework to assess structural alignment quality and significance based on lossless information compression. This is a radical departure from the traditional approach of formulating scoring functions. It links the structural alignment problem to the general class of statistical inductive inference problems, solved using the information-theoretic criterion of minimum message length. Based on this, we developed an efficient and reliable measure of structural alignment quality, I-value. The performance of I-value is demonstrated in comparison with a number of popular scoring functions, on a large collection of competing alignments. Our analysis shows that I-value provides a rigorous and reliable quantification of structural alignment quality, addressing a major gap in the field. Availability: lcb.infotech.monash.edu.au/I-value Contact: arun.konagurthu@monash.edu Supplementary information: Online supplementary data are available at lcb.infotech.monash.edu.au/I-value/suppl.html
Optimal context-sensitive dynamic partial order reduction with observers
Publisher: ACM
Date: 10-07-2019
Globalizing constraint models
Publisher: Elsevier BV
Date: 2022
Improving Abstract Interpretations by Combining Domains
Publisher: Association for Computing Machinery (ACM)
Date: 1995
Abstract: This article considers static analysis based on abstract interpretation of logic programs over combined domains. It is known that analyses over combined domains provide more information potentially than obtained by the independent analyses. However, the construction of a combined analysis often requires redefining the basic operations for the combined domain. A practical approach to maintain precision in combined analyses of logic programs which reuses the in idual analyses and does not redefine the basic operations is illustrated. The advantages of the approach are that (1) proofs of correctness for the new domains are not required and (2) implementations can be reused. The approach is demonstrated by showing that a combined sharing analysis—constructed from “old” proposals—compares well with other “new” proposals suggested in recent literature both from the point of view of efficiency and accuracy.
Towards independent and-parallelism in CLP
Publisher: Springer Berlin Heidelberg
Date: 1996
Learning from learning solvers
Publisher: Springer International Publishing
Date: 2016
Piloting a Shared Source Water Treatment Intervention among Elementary Schools in Bangladesh
Publisher: American Society of Tropical Medicine and Hygiene
Date: 06-11-2019
Redundant disequalities in the Latin Square problem
Publisher: Springer Science and Business Media LLC
Date: 06-08-2013
Human-centred feasibility restoration in practice
Publisher: Springer Science and Business Media LLC
Date: 06-2023
DOI: 10.1007/S10601-023-09344-5
Abstract: Decision systems for solving real-world combinatorial problems must be able to report infeasibility in such a way that users can understand the reasons behind it, and determine how to modify the problem to restore feasibility. Current methods mainly focus on reporting one or more subsets of the problem constraints that cause infeasibility. Methods that also show users how to restore feasibility tend to be less flexible and/or problem-dependent. We describe a problem-independent approach to feasibility restoration that combines existing techniques from the literature in novel ways to yield meaningful, useful, practical, and flexible user support. We evaluated the resulting framework on three real-world applications and conducted a qualitative expert user study with participants from different application domains.
A Novel Approach For Detecting Symmetries in CSP Models
Publisher: Springer Berlin Heidelberg
Date: 2008
An Optimization Model for 3D Pipe Routing with Flexibility Constraints
Publisher: Springer International Publishing
Date: 2017
Automatically exploiting subproblem equivalence in constraint programming
Publisher: Springer Berlin Heidelberg
Date: 2010
Massacres and Morality
Publisher: Oxford University Press
Date: 27-09-2012
Aggregation and Garbage Collection for Online Optimization
Publisher: Springer International Publishing
Date: 2020
Statistical inference of protein structural alignments using information and compression
Publisher: Oxford University Press (OUP)
Date: 04-01-2017
DOI: 10.1093/BIOINFORMATICS/BTW757
Abstract: Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML). The quality of any alignment is measured by its explanatory power—the amount of lossless compression achieved to explain the protein coordinates using that alignment. We have implemented this approach in MMLigner, the first program able to infer statistically significant structural alignments. We also demonstrate the reliability of MMLigner’s alignment results when compared with the state of the art. Importantly, MMLigner can also discover different structural alignments of comparable quality, a challenging problem for oligomers and protein complexes. Source code, binaries and an interactive web version are available at lcb.infotech.monash.edu.au/mmligner. Supplementary data are available at Bioinformatics online.
Using relaxations in maximum density still life
Publisher: Springer Berlin Heidelberg
Date: 2009
POPS: A COMPUTATIONAL TOOL FOR MODELING AND PREDICTING PROTEASE SPECIFICITY
Publisher: World Scientific Pub Co Pte Lt
Date: 06-2005
DOI: 10.1142/S021972000500117X
Abstract: Proteases play a fundamental role in the control of intra- and extra-cellular processes by binding and cleaving specific amino acid sequences. Identifying these targets is extremely challenging. Current computational attempts to predict cleavage sites are limited, representing these amino acid sequences as patterns or frequency matrices. Here we present PoPS, a publicly accessible bioinformatics tool () that provides a novel method for building computational models of protease specificity, which while still being based on these amino acid sequences, can be built from any experimental data or expert knowledge available to the user. PoPS specificity models can be used to predict and rank likely cleavages within a single substrate, and within entire proteomes. Other factors, such as the secondary or tertiary structure of the substrate, can be used to screen unlikely sites. Furthermore, the tool also provides facilities to infer, compare and test models, and to store them in a publicly accessible database.
Structural determinants of GAD antigenicity
Publisher: Elsevier BV
Date: 12-2009
DOI: 10.1016/J.MOLIMM.2009.08.022
Abstract: Our aim was to ascertain structural determinants of autoantigenicity based on the model of the diabetes autoantigen glutamic acid decarboxylase 65 kDa isoform (GAD65) in comparison with that of the non-autoantigenic isoform GAD67. This difference exists despite the two isoforms having the same fold and high sequence identity. Autoantibodies to GAD65 precede the development of type 1 diabetes and are clinical markers of this and certain neural autoimmune diseases. To date, epitope mapping has been based on particular amino acid differences between the two isoforms, and there is no explanation as to why autoantibodies that react with GAD65 only infrequently cross-react with GAD67. To characterize each isoform of the enzyme and gain insights into their contrasting autoantigenic properties, we have used the recently determined crystal structures of GAD65 and GAD67 to compare their structure, hydrophobicity, electrostatics, flexibility and physiochemical properties. The results revealed striking differences which appear almost exclusively at the C-terminal domain of the isoforms. Whereas GAD65 displayed a highly charged and flexible C-terminal domain containing numerous patches of high electrostatic and solvation energies, these characteristics were absent in the GAD67 molecule. Additionally, analysis indicated potential N-terminal and PLP domain binding sites surrounding the C-terminal domain of GAD65, a major region of autoantigenic activity, but not of GAD67. These features agree with good accuracy with published epitope-mapping data. Our analysis suggests that the high flexibility and charge of GAD65 in the C-terminal domain is coupled with the mobility of its catalytic loop, a property that is absolutely required for its enzymatic function. Thus, the structural features that distinguish GAD65 from GAD67 as a B cell autoantigen are related to functional requirements for its enzymatic mechanism. This could well apply to the various other enzyme autoantigens and, if so, these features could be used as the basis of future predictive strategies.
Introduction to the special issue on Prolog systems
Publisher: Cambridge University Press (CUP)
Date: 12-09-2012
DOI: 10.1017/S1471068411000524
Abstract: It has now been 40 years since the birth of the Prolog language and of its first implementation by A. Colmerauer and P. Roussel. Since then, a large number of Prolog systems have been implemented. While the core of the Prolog language has not changed much in these 40 years, Prolog systems have undergone an extraordinary evolution that stems from two main sources. One is the trend to extend Prolog to incorporate ideas from other language paradigms that have proved useful in real-world applications. This includes concurrency, parallelism, higher order predicates, object-oriented programming, Web interfaces, processing of large amounts of data, and flexible developer tools that enhance reliability and robustness through assertions. A second source of change is the exploration of ideas for which Prolog systems are uniquely suitable and that have led to the creation of new programming paradigms. This includes tabling, constraint logic programming, answer set programming, and probabilistic logic programming.
A method for detecting symmetries in constraint models and its generalisation
Publisher: Springer Science and Business Media LLC
Date: 15-11-2014
An overview of HAL
Publisher: Springer Berlin Heidelberg
Date: 1999
Super: A web server to rapidly screen superposable oligopeptide fragments from the protein data bank
Publisher: Oxford University Press (OUP)
Date: 24-05-2012
DOI: 10.1093/NAR/GKS436
Core-Guided Model Reformulation
Publisher: Springer International Publishing
Date: 2020
Elucidation of the Substrate Specificity of the C1s Protease of the Classical Complement Pathway
Publisher: Elsevier BV
Date: 11-2005
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