title: Domain-specific language models for multi-label classification of medical text

authors: Yogarajan, Vithya

subjects: Machine learning

abstract: Recent advancements in machine learning-based medical text multi-label classifications can be used to enhance the understanding of the human body and aid the need for patient care. This research considers predicting medical codes from electronic health records (EHRs) as multi-label problems, where the number of labels ranged from 15 to 923. It is motivated by the advancements in domain-specific language models to better understand and represent electronic health records and improve the predictive accuracy of medical codes.    

The thesis presents an extensive empirical study of language models for binary and multi-label medical text classifications. Domain-specific multi-sourced fastText pre-trained embeddings are introduced. Experimental results show considerable improvements to predictive accuracy when such embeddings are used to represent medical text. It is shown that using domain-specific transformer models outperforms results for multi-label problems with fixed sequence length. If processing time is not an issue for a long medical text, then TransformerXL will be the best model to use. Experimental results show significant improvements over other models, including state-of-the-art results, when TransformerXL is used for down-streaming tasks such as predicting medical codes. 

The thesis considers concatenated language models to handle long medical documents and text data from multiple sources of EHRs. Experimental results show improvements in overall micro and macro F1 scores, and such improvements are achieved with fewer resources. In addition, it is shown that concatenated domain-specific transformers improve F1 scores of infrequent labels across several multi-label problems, especially with long-tail labels.

text: Domain-specific language models for multi-label classification of medical text Recent advancements in machine learning-based medical text multi-label classifications can be used to enhance the understanding of the human body and aid the need for patient care. This research considers predicting medical codes from electronic health records (EHRs) as multi-label problems, where the number of labels ranged from 15 to 923. It is motivated by the advancements in domain-specific language models to better understand and represent electronic health records and improve the predictive accuracy of medical codes.    

The thesis presents an extensive empirical study of language models for binary and multi-label medical text classifications. Domain-specific multi-sourced fastText pre-trained embeddings are introduced. Experimental results show considerable improvements to predictive accuracy when such embeddings are used to represent medical text. It is shown that using domain-specific transformer models outperforms results for multi-label problems with fixed sequence length. If processing time is not an issue for a long medical text, then TransformerXL will be the best model to use. Experimental results show significant improvements over other models, including state-of-the-art results, when TransformerXL is used for down-streaming tasks such as predicting medical codes. 

The thesis considers concatenated language models to handle long medical documents and text data from multiple sources of EHRs. Experimental results show improvements in overall micro and macro F1 scores, and such improvements are achieved with fewer resources. In addition, it is shown that concatenated domain-specific transformers improve F1 scores of infrequent labels across several multi-label problems, especially with long-tail labels.

year: 2022

title: Population genetic structure of New Zealand's endemic corophiid amphipods: evidence for allopatric speciation

authors: Stevens, Mark I.

subjects: allozyme

abstract: Allozyme electrophoresis was used to examine population genetic structure at inter- and intraspecific levels for the New Zealand endemic corophiid amphipods, Paracorophium lucasi and P. excavatum. Individuals were collected from estuarine and freshwater habitats from North, South and Chatham Islands. Analyses of genetic structure among interspecific populations indicated clear allelic differentiation between the two Paracorophium species (Nei's genetic distance, D = 1.62), as well as considerable intraspecific substructuring (D = 0.15–0.65). These levels of divergence are similar to interspecific levels for other amphipods and it is proposed that at least two groups from the P. lucasi complex and three from the P. excavatum complex correspond to sibling species. In most cases allopatry can account for the differentiation among the putative sibling species. For populations that share a common coastline we found low levels of differentiation and little or no correlation with geographical distance, suggesting that gene flow is adequate to maintain homogeneous population genetic structure. By contrast, populations on separate coastlines (i.e. isolated by land) showed moderate levels of geographical differentiation indicating restricted gene flow. The juxtaposition of population genetic and biogeographical data for Paracorophium in conjunction with the geological record infers past histories of glacial extirpation, and possible isolating effects of sea-level and landmass changes that have occurred throughout the Plio-Pleistocene.

text: Population genetic structure of New Zealand's endemic corophiid amphipods: evidence for allopatric speciation Allozyme electrophoresis was used to examine population genetic structure at inter- and intraspecific levels for the New Zealand endemic corophiid amphipods, Paracorophium lucasi and P. excavatum. Individuals were collected from estuarine and freshwater habitats from North, South and Chatham Islands. Analyses of genetic structure among interspecific populations indicated clear allelic differentiation between the two Paracorophium species (Nei's genetic distance, D = 1.62), as well as considerable intraspecific substructuring (D = 0.15–0.65). These levels of divergence are similar to interspecific levels for other amphipods and it is proposed that at least two groups from the P. lucasi complex and three from the P. excavatum complex correspond to sibling species. In most cases allopatry can account for the differentiation among the putative sibling species. For populations that share a common coastline we found low levels of differentiation and little or no correlation with geographical distance, suggesting that gene flow is adequate to maintain homogeneous population genetic structure. By contrast, populations on separate coastlines (i.e. isolated by land) showed moderate levels of geographical differentiation indicating restricted gene flow. The juxtaposition of population genetic and biogeographical data for Paracorophium in conjunction with the geological record infers past histories of glacial extirpation, and possible isolating effects of sea-level and landmass changes that have occurred throughout the Plio-Pleistocene.

year: 2004

title: Lost in translation: western representations of Māori knowledge

authors: Mika, Carl Te Hira

abstract: We recently attended a conference at which a non-Māori presenter, drawing on a particular metaphor already established by Māori writers, related Māori natural world features to a research method. The presentation was useful because it highlighted several issues that call for our concern as Māori philosophers. In this article, we outline these concerns, which are: first, that a blunt response to such a presentation is not undertaken lightly from a Māori viewpoint; and, second, that the presenter’s talk exemplifies a wider problem of warping Māori concepts and labels to fit a Western philosophical approach. We call this latter problem ‘Translation’, because it involves moving the Māori world and its phenomena over into one that is palatable for policy and research. The aim of the article is not to single out the presenter, but rather to refer to his presentation in order to consider the prior issue of Translation. In cases where Translation occurs, a Māori critical philosophical stance is clearly needed, in order to both investigate the warping of Māori thought on which it relies, and review the place of Māori philosophy and philosophical response in the arena of educational research.

text: Lost in translation: western representations of Māori knowledge We recently attended a conference at which a non-Māori presenter, drawing on a particular metaphor already established by Māori writers, related Māori natural world features to a research method. The presentation was useful because it highlighted several issues that call for our concern as Māori philosophers. In this article, we outline these concerns, which are: first, that a blunt response to such a presentation is not undertaken lightly from a Māori viewpoint; and, second, that the presenter’s talk exemplifies a wider problem of warping Māori concepts and labels to fit a Western philosophical approach. We call this latter problem ‘Translation’, because it involves moving the Māori world and its phenomena over into one that is palatable for policy and research. The aim of the article is not to single out the presenter, but rather to refer to his presentation in order to consider the prior issue of Translation. In cases where Translation occurs, a Māori critical philosophical stance is clearly needed, in order to both investigate the warping of Māori thought on which it relies, and review the place of Māori philosophy and philosophical response in the arena of educational research.

year: 2017