Flexible user-guided network layout for biomedical applications. This project will develop techniques for automatic layout of biological network diagrams, allowing users to guide the layout while satisfying any required placement constraints and drawing conventions. As part of the project, these methods will be integrated into several real-world systems biology applications for network browsing and authoring.
Deep correction of DNA sequencing errors by data mining algorithms. This project aims to investigate the many layers of error correction problems in the terabytes of genomic sequence data, and aims to solve these problems by novel data mining algorithms. High-throughput sequencing platforms have generated massive amounts of useful raw data, but also made widespread errors. The new algorithms are capable of correcting errors at deeper layers to further enhance data quality. Expected outcome inclu ....Deep correction of DNA sequencing errors by data mining algorithms. This project aims to investigate the many layers of error correction problems in the terabytes of genomic sequence data, and aims to solve these problems by novel data mining algorithms. High-throughput sequencing platforms have generated massive amounts of useful raw data, but also made widespread errors. The new algorithms are capable of correcting errors at deeper layers to further enhance data quality. Expected outcome includes the knowledge advancement of genomic data industry and interdisciplinary collaboration between biotechnology and data mining. This also provides significant benefit for genomic decisions in forensics and personalised medicine which demand accurate genomic information.Read moreRead less
Efficient data mining methods for evidence-based decision making. This project aims to develop efficient data mining methods for causal predictions. Evidence-based decision making (EBD), such as evidence-based medicine and policy, is always preferable. To support EBD, causal predictions forecast how outcomes change when conditions are manipulated. Progress has been made in theoretical research on causal inference based on observational data, but few methods can automatically mine causal signals ....Efficient data mining methods for evidence-based decision making. This project aims to develop efficient data mining methods for causal predictions. Evidence-based decision making (EBD), such as evidence-based medicine and policy, is always preferable. To support EBD, causal predictions forecast how outcomes change when conditions are manipulated. Progress has been made in theoretical research on causal inference based on observational data, but few methods can automatically mine causal signals from the data and methods for efficient causal predictions based on data are even fewer. This project will apply its methods to biomedical problems. The outcomes could support smart and data-driven evidence based decision making in many areas, such as therapeutics and government policy making.Read moreRead less
Searching for near-exact protein models. This project aims to develop novel and efficient heuristic-based algorithms leading to near accurate protein tertiary structure models. Knowledge about protein structures is fundamental to our understanding of living systems. The progress on experimental determination of these structures has been extremely limited and remains an open challenge in molecular biology. Computational prediction of protein structures from sequences is emerging as a promising ap ....Searching for near-exact protein models. This project aims to develop novel and efficient heuristic-based algorithms leading to near accurate protein tertiary structure models. Knowledge about protein structures is fundamental to our understanding of living systems. The progress on experimental determination of these structures has been extremely limited and remains an open challenge in molecular biology. Computational prediction of protein structures from sequences is emerging as a promising approach, but its accuracy is far from satisfactory. The software systems developed in this project will be used in structural identification of target proteins in drug design. This will make drug design process more efficient, saving time and cost, potentially saving lives.Read moreRead less
Reconstructing proteins to explain and engineer biological diversity. The aim of this project is to develop computational methods to construct entirely new proteins. Computational reconstruction of enzymes that have been extinct for over 400 million years has revealed remarkable opportunities for biotechnological innovation. The intended outcomes are to develop bioinformatics methods to broaden the scope of ancestral protein reconstruction to include protein super-families, to establish what spe ....Reconstructing proteins to explain and engineer biological diversity. The aim of this project is to develop computational methods to construct entirely new proteins. Computational reconstruction of enzymes that have been extinct for over 400 million years has revealed remarkable opportunities for biotechnological innovation. The intended outcomes are to develop bioinformatics methods to broaden the scope of ancestral protein reconstruction to include protein super-families, to establish what specific changes led to the evolutionary success of a protein, and to re-run evolution to generate proteins that perform in conditions suitable for industrial and agricultural applications, in particular the production of hydroxylated fatty acids for bioplastics. By examining proteins from many life forms, the project plans to develop a novel bioinformatics strategy to understand their evolution and engineer new proteins for use in production of chemical commodities.Read moreRead less
RNA structure prediction by deep learning and evolution-derived restraints. This project addresses the long-standing structure-folding problem of Ribonucleic acids (RNA) whose solution is essential for elucidating the roles of noncoding RNAs in living organisms. The proposed approach will detect hidden homologous sequences and enhance evolutionary covariation signals by developing new algorithms for search and smarter neural networks for deep learning. The project expects to generate new tools ....RNA structure prediction by deep learning and evolution-derived restraints. This project addresses the long-standing structure-folding problem of Ribonucleic acids (RNA) whose solution is essential for elucidating the roles of noncoding RNAs in living organisms. The proposed approach will detect hidden homologous sequences and enhance evolutionary covariation signals by developing new algorithms for search and smarter neural networks for deep learning. The project expects to generate new tools for structure-based probing of RNA evolutional and functional mechanisms. The outcomes should provide significant benefits by high-accuracy computational modelling of RNA structures that are difficult and costly to solve by current structural biology techniques but important for enabling biotech and clinical applications.Read moreRead less
Domain-specific visual languages for big data analytics applications. This project aims to invent domain-specific visual languages and support model-driven engineering based infrastructure so domain experts can specify, generate and apply complex data analytics and visualisation techniques. Many domains, including intelligent transport, business intelligence, and population health, need more effective “big data” analytics and visualisation. A challenge is to combine detailed domain knowledge – w ....Domain-specific visual languages for big data analytics applications. This project aims to invent domain-specific visual languages and support model-driven engineering based infrastructure so domain experts can specify, generate and apply complex data analytics and visualisation techniques. Many domains, including intelligent transport, business intelligence, and population health, need more effective “big data” analytics and visualisation. A challenge is to combine detailed domain knowledge – what the data means and what it can be used for – with sophisticated, scalable computational techniques to mine and present information from the huge volumes of raw data. This project is expected to improve productivity and quality of big data analytics and visualisation in critical domains.Read moreRead less
Metamorphic slices and their applications in fault localization. The main purpose of this project is to enhance the quality of software. The expected outcomes include the delivery of new cost-effective methods to debug software, and the extension of current debugging methods to be applicable in wider contexts.
Cost-effective use of assertions in the verification and validation of distributed and real-time systems. The project will reinforce Australia as a world leader in empirical software engineering and software verification and validation research, thus building on Australia's strengths in ICT research and innovation. Through the involvement of a local software verification and validation company and through industrial case studies, this project will also improve the software verification and valid ....Cost-effective use of assertions in the verification and validation of distributed and real-time systems. The project will reinforce Australia as a world leader in empirical software engineering and software verification and validation research, thus building on Australia's strengths in ICT research and innovation. Through the involvement of a local software verification and validation company and through industrial case studies, this project will also improve the software verification and validation capabilities of local industry, allow them to save software development costs, and improve the quality of the software produced.Read moreRead less
Mapping the Effectiveness of Automated Software Testing. This project aims to help software engineers build complex software systems in far more reliable and cost-effective ways. It takes an interdisciplinary approach by applying machine learning techniques to automatically test complex software systems. Expected outcomes include a novel methodology for assessing the strengths and weaknesses of test suites generated by automated software testing techniques and the approaches required for generat ....Mapping the Effectiveness of Automated Software Testing. This project aims to help software engineers build complex software systems in far more reliable and cost-effective ways. It takes an interdisciplinary approach by applying machine learning techniques to automatically test complex software systems. Expected outcomes include a novel methodology for assessing the strengths and weaknesses of test suites generated by automated software testing techniques and the approaches required for generating high-quality test cases. Such advances are urgently needed to avoid disasters when deploying software systems in the real world.Read moreRead less