Search Marsden awards 2008–2017
Search awarded Marsden Fund grants 2008–2017
Fund Type: Marsden Fund
Category: Fast-Start
Year Awarded: 2016
Title: Large-scale Evolutionary Feature Selection for Classification
Recipient(s): Dr B Xue | PI | Victoria University of Wellington
Professor X Yao | AI | University of Birmingham
Professor M Zhang | AI | Victoria University of Wellington
Public Summary: Classification is a fundamental task in real-world problems. The quality of classification often suffers when the feature set is large, not only because of the “curse of dimensionality”, but also because of the irrelevant features, redundant features and complex feature interactions. Large feature sets often lead to low accuracy, overly complex classifiers/models, and slow processing.
Feature selection can address these issues by identifying a small set of effective features, but it is a challenging task because of the exponentially increasing search space, complex interactions between features, difficult search spaces containing many local optima, and conflicting objectives with unpredictable trade-offs.
This project aims to propose a novel evolutionary feature selection approach to classification tasks with a large number of features by developing novel representations to incorporate information about feature interactions, new fitness measures to capture redundancy, complementarity or other feature interaction information, new search mechanisms to efficiently explore the huge complex search space, and new large-scale multi-objective methods to handle multiple conflicting criteria of feature sets. We expect this approach to significantly improve classification accuracy, reduce the number of features by at least an order of magnitude, significantly enhance the understandability of the learned classifiers, and substantially shorten the computational time.
Total Awarded: $300,000
Duration: 3
Host: Victoria University of Wellington
Contact Person: Dr B Xue
Panel: MIS
Project ID: 16-VUW-111
Fund Type: Marsden Fund
Category: Standard
Year Awarded: 2017
Title: Lattice polytope samplers: theory, methods and applications
Recipient(s): Professor ML Hazelton | PI | Massey University
Professor AJ Lee | AI | The University of Auckland
Dr K Parry | AI | Massey University Manawatu
Dr MR Schofield | AI | University of Otago
Public Summary: Statistical inverse problems occur when we wish to learn about some random process that is observed only indirectly. Inference in such situations typically involves sampling possible values for the latent variables of interest conditional on the indirect observations. This project is concerned with inverse problems for count data, for which the latent variables are constrained to lie on the integer lattice within a convex polytope (a bounded multidimensional polyhedron). An illustrative example arises in transport engineering where we observe vehicle counts entering or leaving each zone of the network, then want to sample possible interzonal patterns of traffic flow consistent with those entry/exit counts.
In principle such sampling can be conducted using Markov chain Monte Carlo methods through a random walk on the lattice polytope, but it is challenging to design algorithms for doing so that are both computationally efficient and have guaranteed theoretical properties. The overall aim of this project is to combine techniques from algebraic statistics with recent geometric insights in order to develop and study new polytope samplers that address these issues. These methods will be applied to confidentialisation of cross-tabulated official statistics, to capture-recapture modelling in ecology, and to inference for traffic flows in transport engineering.
Total Awarded: $535,000
Duration: 3
Host: Massey University
Contact Person: Professor ML Hazelton
Panel: MIS
Project ID: 17-MAU-037
Fund Type: Marsden Fund
Category: Standard
Year Awarded: 2008
Title: Learning to tell life's tales: the development of narrative identity and well-being in adolescence
Recipient(s): Assoc Prof E Reese | PI | University of Otago
Dr Q Wang | AI | Cornell University
Public Summary: Life stories are a vital means of understanding and expressing identity for adults. Adults who tell more coherent life stories also enjoy greater well-being. Our aim is to explore how young people in three NZ cultures (Maori, European, and recently immigrated Chinese) learn to tell the stories of their lives. Our aim is to identify the pathways by which young people in each culture come to develop a narrative identity. We will also explore the health implications of a narrative identity for well-being in adolescence.
Total Awarded: $729,778
Duration: 3
Host: University of Otago
Contact Person: Assoc Prof E Reese
Panel: SOC
Project ID: 08-UOO-042
Fund Type: Marsden Fund
Category: Standard
Year Awarded: 2008
Title: Life at the extreme: resolving the genetic basis of microbial endemism in the super-heated soils of Mt Erebus, Antarctica
Recipient(s): Prof C Cary | PI | University of Waikato
Prof JA Eisen | AI | University of California, Davis
Dr IR McDonald | AI | University of Waikato
Public Summary: Globally distributed geothermal environments are thought to provide a natural portal to the deep-subsurface biosphere and possible access to the genetics of archaic lineages. Tramway Ridge, Mt. Erebus, Antarctica is probably the most geographically and physico-chemically isolated geothermal site on Earth providing an excellent system for studies of microbial speciation, diversification and biogeography. A preliminary genetic survey of the Tramway microflora has revealed extensive novel deep-branching lineages. Employing a combination of community-level metagenomic and culture dependent approaches we will undertake a gene-centric analysis of the Tramway Ridge microflora to address questions and test hypotheses on endemism, evolution, and adaptation.
Total Awarded: $709,333
Duration: 3
Host: University of Waikato
Contact Person: Prof C Cary
Panel: EEB
Project ID: 08-UOW-042
Fund Type: Marsden Fund
Category: Standard
Year Awarded: 2011
Title: Life in and beyond maars: a revolution in understanding New Zealand Miocene terrestrial biodiversity and ecosystems
Recipient(s): Assoc Prof DE Lee | PI | University of Otago
Dr DC Mildenhall | PI | GNS Science
Dr JG Conran | AI | The University of Adelaide
Prof DM Crayn | AI | James Cook University
Dr JK Lindqvist | AI | University of Otago
Dr AR Schmidt | AI | University of Goettingen
Public Summary: The origins and history of the New Zealand terrestrial biota are complex, controversial and poorly understood. During the Miocene (23-10 Ma) large environmental and biotic changes shaped the ancestors of plants and animals we have today, but little is known about what occurred and its impact on the flora and fauna. We propose to investigate globally significant maar lake, oil shale lake, swamp and river deposits that hold a cornucopia of exquisitely well-preserved Miocene fossils. Flowers with in situ pollen, fruits, seeds, mummified leaves with cuticle, amber inclusions of soft-bodied organisms, insects, spiders, fish and microscopic algae will be identified and analysed to determine phylogenetic and biogeographic relations. Data from sediment and leaf features will enable us to determine environments and climate. These fossils provide a remarkably comprehensive window into the world from which the distinctive modern day biota originated. We will be able to reconstruct entire Miocene ecosystems and integrate fossil evidence with phylogenetic analysis of the modern flora and fauna. This research will settle controversial issues around local evolution versus immigration (by long-distance dispersal), and the part played by extinction to provide a new understanding of how Miocene events created the modern biota of New Zealand.
Total Awarded: $666,957
Duration: 3
Host: University of Otago
Contact Person: Assoc Prof DE Lee
Panel: ESA
Project ID: 11-UOO-043
Fund Type: Marsden Fund
Category: Fast-Start
Year Awarded: 2010
Title: Life Partners: How do symbiotic fungi tell plants they want a relationship?
Recipient(s): Dr DJ Fleetwood | PI | AgResearch
Prof RC Gardner | AI | The University of Auckland
Public Summary: Few, if any, plants live alone. From forest trees to pasture grasses plants harbour fungi called endophytes in their leaves in a mutually beneficial “symbiotic” relationship where the plant provides nutrition to the fungi, which in return produce chemicals that protect the plant from an array of stresses. We know why plants harbour endophytes, but little is known about how these relationships are formed. Plants have sophisticated defence mechanisms to ward off pathogens and somehow symbiotic fungi must evade these defences and signal that they are not pathogens.
We propose to use the latest molecular approaches to dissect why a genetically-altered endophyte we have identified no longer forms a symbiotic relationship with its host plant. Results from this research will elucidate how endophytes avoid host defences and will advance our fundamental knowledge about how these important relationships between plants and fungi really work.
Total Awarded: $260,870
Duration: 3
Host: AgResearch
Contact Person: Dr DJ Fleetwood
Panel: CMP
Project ID: 10-AGR-036
Fund Type: Marsden Fund
Category: Standard
Year Awarded: 2014
Title: Light switchable functional metal-organic cages
Recipient(s): Professor PE Kruger | PI | University of Canterbury
Dr ND McClenaghan | AI | CNRS / University of Bordeaux
Dr R Clérac | AI | CNRS / University of Bordeaux
Public Summary: Molecular cages with geometrically predefined internal voids are capable of binding guest molecules. This host-guest behaviour allows these nano-capsules to catalyse reactions, protect otherwise unstable molecules and selectively bind guests. Certain applications call for dynamic control over the host-guest interaction. For example, systems designed for the uptake, delivery, and release of cargo requires temporal and spatial control over the localisation of the guest. A desirable outcome would be if the cage itself governed the presence or absence of guests inside its interior, most preferably controlled by non-invasive external stimuli (light or heat), that also trigger modulation of its properties following stimulation.
We will develop functional, responsive and adaptive molecular cages and related complexes able to change their properties under the influence of external stimuli by using photoswitching ligands and spin-switching Fe(II) centres in their synthesis. Photoswitching will toggle the cages between open and closed forms to control guest exchange; and spin-switching will reversibly modulate their magnetic and other allied properties. We will study the interplay between external stimuli, photo-isomerisation and spin-switching behaviour in molecular cages for the first time. Potential applications for such species lie in molecule delivery, temperature or light activated switches, sensors and magnetic resonance contrast agents.
Total Awarded: $750,000
Duration: 3
Host: University of Canterbury
Contact Person: Professor PE Kruger
Panel: PCB
Project ID: 14-UOC-007
Fund Type: Marsden Fund
Category: Standard
Year Awarded: 2015
Title: Lighting up sugars: fluorescent probes for saccharides
Recipient(s): Professor PJ Brothers | PI | The University of Auckland
Dr BL Stocker | AI | Victoria University of Wellington
Dr DC Ware | AI | The University of Auckland
Dr MSM Timmer | AI | Victoria University of Wellington
Professor MAK Williams | AI | Massey University
Public Summary: Although sugars in their myriad forms, collectively known as saccharides, are essential to life, the emerging fields of glycobiology and glycomics presently suffer from a lack of distinct functional probes and enabling tools for the analysis, structure determination and visualisation of saccharides. We have developed an unprecedented attachment of a fluorescent BODIPY label directly to glucose through boron-oxygen-sugar links, an alternative to the less sensitive and more expensive remote tethering through the BODIPY backbone. Our O-BODIPY probe contains a boronic acid sugar binding site in which the boron atom is also part of the extremely well-defined BODIPY fluorophore. Our O-BODIPY-sugar conjugates are strongly fluorescent and hydrolytically stable. We will develop a tool for highly targeted, sensitive, fluorescent labelling of sugars. This could be applied to challenges ranging from the detection of specific sugar disease markers on cell surfaces to the determination of polysaccharide fine structure in biology and materials science. We must first explore the specificity, scope, reactivity and fluorescence behaviour of these unique, new O-BODIPY-saccharide conjugates. We will draw on the depth of knowledge in BODIPY biosensor chemistry and boronic acid sugar binding to create for the first time a new tool in which these two technologies are combined.
Total Awarded: $675,000
Duration: 3
Host: The University of Auckland
Contact Person: Professor PJ Brothers
Panel: PCB
Project ID: 15-UOA-180
Fund Type: Marsden Fund
Category: Standard
Year Awarded: 2014
Title: Lineage selection and the evolution of cancer
Recipient(s): Professor PB Rainey | PI | Massey University
Dr C Gokhale | AI | Massey University
Public Summary: The evolution of multicellular life was underpinned by cooperation, but driven by conflict. From the earliest stages of emergence, conflict between the short-term interests of cells and the long-term interests of individuals fuelled the evolution of cancer: it also lead to mechanisms of cancer suppression essential for the maintenance of multicellularity. In previous work we witnessed the de novo evolution of simple multicellular organisms replete with a soma-germ distinction. Using these primitive organisms we will perform a combined experimental and theoretical analysis of the earliest events underpinning the evolution of cancer and the mechanisms that suppress it.
Total Awarded: $808,000
Duration: 3
Host: Massey University
Contact Person: Professor PB Rainey
Panel: EEB
Project ID: 14-MAU-050
Fund Type: Marsden Fund
Category: Standard
Year Awarded: 2011
Title: Linking cell division with differentiation: is stem cell fate sealed by cohesin?
Recipient(s): Dr J Horsfield | PI | University of Otago
Dr S Young | AI | University of Otago
Public Summary: A newly fertilised embryo contains rapidly dividing stem cells with the capacity of developing into all tissues of the body. One of life's biggest mysteries is the process by which these cells decide their fate. It has recently been noted that Cohesin proteins, well known for roles in chromosome stability and in controlling developmental gene expression, also regulate genes that maintain stem cell identity. Therefore, we hypothesise that Cohesin forms a key link between stem cell identity and differentiation.
This project aims to uncover novel Cohesin-dependent mechanisms of cell fate using zebrafish embryos, an ideal model for embryology. Cohesin directly binds genes to control their expression, so we will first identify genes that are cohesin-bound before and after cell fate commitment. Next, we will determine if Cohesin controls expression of fate determination genes, by measuring their levels during cell differentiation, and by examining whether altering Cohesin changes their expression. Finally, as a model for interpreting findings made above, we will investigate how Cohesin controls tissue-specific expression of Runx1, a key developmental gene important for blood stem cell development. Together, these goals will greatly enhance our understanding of how cells of the embryo determine their fate.
Total Awarded: $860,870
Duration: 3
Host: University of Otago
Contact Person: Dr J Horsfield
Panel: CMP
Project ID: 11-UOO-027