title: Efficient compilation of a verification-friendly programming language

authors: Weng, Min-Hsien

subjects: Optimizing Compiler, Program Efficiency, Static Analysis, Formal Verification, Parallel Programming

abstract: This thesis develops a compiler to convert a program written in the verification friendly programming language Whiley into an efficient implementation in C. Our compiler uses a mixture of static analysis, run-time monitoring and a code generator to and faster integer types, eliminate unnecessary array copies and de-allocate unused memory without garbage collection, so that Whiley programs can be translated into C code to run fast and for long periods on general operating systems as well as limited-resource embedded devices. We also present manual and automatic proofs to verify memory safety of our implementations, and benchmark on a variety of test cases for practical use. Our benchmark results show that, in our test suite, our compiler effectively reduces the time complexity to the lowest possible level and stops all memory leaks without causing double-freeing problems. The performance of implementations can be further improved by choosing proper integer types within the ranges and exploiting parallelism in the programs.

text: Efficient compilation of a verification-friendly programming language This thesis develops a compiler to convert a program written in the verification friendly programming language Whiley into an efficient implementation in C. Our compiler uses a mixture of static analysis, run-time monitoring and a code generator to and faster integer types, eliminate unnecessary array copies and de-allocate unused memory without garbage collection, so that Whiley programs can be translated into C code to run fast and for long periods on general operating systems as well as limited-resource embedded devices. We also present manual and automatic proofs to verify memory safety of our implementations, and benchmark on a variety of test cases for practical use. Our benchmark results show that, in our test suite, our compiler effectively reduces the time complexity to the lowest possible level and stops all memory leaks without causing double-freeing problems. The performance of implementations can be further improved by choosing proper integer types within the ranges and exploiting parallelism in the programs.

year: 2019

title: Providing pin-point page-level precision to 1 trillion tokens of text for workset creation

authors: Bainbridge, David

subjects: computer science

abstract: We report on the work undertaken developing a web environment that allows users to search over 1 trillion tokens of text -- down to the page-level -- of the HathiTrust Part-of-Speech Extracted Features Dataset to help produce worksets for scholarly analysis. We present an extended example of the web environment in use, along with details about its implementation.

text: Providing pin-point page-level precision to 1 trillion tokens of text for workset creation We report on the work undertaken developing a web environment that allows users to search over 1 trillion tokens of text -- down to the page-level -- of the HathiTrust Part-of-Speech Extracted Features Dataset to help produce worksets for scholarly analysis. We present an extended example of the web environment in use, along with details about its implementation.

year: 2018

title: eDNA-based detection of New Zealand freshwater mussel (kākahi) populations using digital PCR

authors: Ferris, Kelsey

subjects: eDNA

abstract: Globally, freshwater mussels are one of the most endangered taxa due to pollution, nutrient loading, habitat fragmentation, and species introduction attributable to anthropogenic activities. New Zealand freshwater mussels (kākahi) are ecological engineers and integral species in freshwater ecosystems. However, kākahi populations are expected to decline 70% by 2024 in part due to their unique reproductive cycle involving an obligatory phoretic relationship with declining native fish. Kākahi distribution and abundance throughout New Zealand is poorly understood due to time-consuming surveying techniques of concealed and morphologically cryptic species. A rapid and reliable method is required for the detection and identification of these ‘Threatened’ kākahi populations for conservation and management. Therefore, this study aimed to i) validate an environmental DNA (eDNA) based detection method for New Zealand freshwater mussels using digital PCR (dPCR); ii) determine the most appropriate sampling season for kākahi eDNA; and iii) determine whether eDNA could be used to detect effects of fish barriers on kākahi distribution.
In vivo trials determined that filtration of field samples within 24 hours of collection minimised eDNA degradation and that prefiltration effectively removed inhibitory detritus and glochidia. The lowest concentration of eDNA which could accurately be detected to infer abundance (≥3.2 copies/µL) or presence (0.32-3.19 copies/µL) of kākahi eDNA was determined.  Duplicate field samples were collected from the Waingaro River and Kahuhuru Stream at sites downstream of fish barriers and upstream of low-flow or all-flow barriers in December, May, and August to investigate spatial and temporal variation in eDNA concentrations. As hypothesised, December was the most effective month to sample, yielding the highest eDNA concentrations due to reduced dilution and heightened water temperatures. Based on eDNA, kākahi species distribution did not appear correlated with fish barriers, but all-flow barriers likely impeded fish host movement to significantly reduce the total kākahi eDNA concentrations found upstream. 
eDNA detection can be used by regional councils to effectively infer presence/absence of kākahi populations and direct further conventional surveying efforts to the most impactful locations. This method allows rapid determination of distribution and densities at a national scale to aid conservation management of this taonga (treasured) species.

text: eDNA-based detection of New Zealand freshwater mussel (kākahi) populations using digital PCR Globally, freshwater mussels are one of the most endangered taxa due to pollution, nutrient loading, habitat fragmentation, and species introduction attributable to anthropogenic activities. New Zealand freshwater mussels (kākahi) are ecological engineers and integral species in freshwater ecosystems. However, kākahi populations are expected to decline 70% by 2024 in part due to their unique reproductive cycle involving an obligatory phoretic relationship with declining native fish. Kākahi distribution and abundance throughout New Zealand is poorly understood due to time-consuming surveying techniques of concealed and morphologically cryptic species. A rapid and reliable method is required for the detection and identification of these ‘Threatened’ kākahi populations for conservation and management. Therefore, this study aimed to i) validate an environmental DNA (eDNA) based detection method for New Zealand freshwater mussels using digital PCR (dPCR); ii) determine the most appropriate sampling season for kākahi eDNA; and iii) determine whether eDNA could be used to detect effects of fish barriers on kākahi distribution.
In vivo trials determined that filtration of field samples within 24 hours of collection minimised eDNA degradation and that prefiltration effectively removed inhibitory detritus and glochidia. The lowest concentration of eDNA which could accurately be detected to infer abundance (≥3.2 copies/µL) or presence (0.32-3.19 copies/µL) of kākahi eDNA was determined.  Duplicate field samples were collected from the Waingaro River and Kahuhuru Stream at sites downstream of fish barriers and upstream of low-flow or all-flow barriers in December, May, and August to investigate spatial and temporal variation in eDNA concentrations. As hypothesised, December was the most effective month to sample, yielding the highest eDNA concentrations due to reduced dilution and heightened water temperatures. Based on eDNA, kākahi species distribution did not appear correlated with fish barriers, but all-flow barriers likely impeded fish host movement to significantly reduce the total kākahi eDNA concentrations found upstream. 
eDNA detection can be used by regional councils to effectively infer presence/absence of kākahi populations and direct further conventional surveying efforts to the most impactful locations. This method allows rapid determination of distribution and densities at a national scale to aid conservation management of this taonga (treasured) species.

year: 2020