title: Sequence-based protein classification: binary Profile Hidden Markov Models and propositionalisation

authors: Mutter, Stefan

subjects: Machine Learning

abstract: Detecting similarity in biological sequences is a key element to understanding the mechanisms of life. Researchers infer potential structural, functional or evolutionary relationships from similarity. However, the concept of similarity is complex in biology. Sequences consist of different molecules with different chemical properties, have short and long distance interactions, form 3D structures and change through evolutionary processes. Amino acids are one of the key molecules of life. Most importantly, a sequence of amino acids constitutes the building block for proteins which play an essential role in cellular processes. This thesis investigates similarity amongst proteins. In this area of research there are two important and closely related classification tasks – the detection of similar proteins and the discrimination amongst them. Hidden Markov Models (HMMs) have been successfully applied to the detection task as they model sequence similarity very well. From a Machine Learning point of view these HMMs are essentially one-class classifiers trained solely on a small number of similar proteins neglecting the vast number of dissimilar ones. Our basic assumption is that integrating this neglected information will be highly beneficial to the classification task. Thus, we transform the problem representation from a one-class to a binary one. Equipped with the necessary sound understanding of Machine Learning, especially concerning problem representation and statistically significant evaluation, our work pursues and combines two different avenues on this aforementioned transformation. First, we introduce a binary HMM that discriminates significantly better than the standard one, even when only a fraction of the negative information is used. Second, we interpret the HMM as a structured graph of information. This information cannot be accessed by highly optimised standard Machine Learning classifiers as they expect a fixed length feature vector representation. Propositionalisation is a technique to transform the former representation into the latter. This thesis introduces new propositionalisation techniques. The change in representation changes the learning problem from a one-class, generative to a propositional, discriminative one. It is a common assumption that discriminative techniques are better suited for classification tasks, and our results validate this assumption. We suggest a new way to significantly improve on discriminative power and runtime by means of terminating the time-intense training of HMMs early, subsequently applying propositionalisation and classifying with a discriminative, binary learner.

text: Sequence-based protein classification: binary Profile Hidden Markov Models and propositionalisation Detecting similarity in biological sequences is a key element to understanding the mechanisms of life. Researchers infer potential structural, functional or evolutionary relationships from similarity. However, the concept of similarity is complex in biology. Sequences consist of different molecules with different chemical properties, have short and long distance interactions, form 3D structures and change through evolutionary processes. Amino acids are one of the key molecules of life. Most importantly, a sequence of amino acids constitutes the building block for proteins which play an essential role in cellular processes. This thesis investigates similarity amongst proteins. In this area of research there are two important and closely related classification tasks – the detection of similar proteins and the discrimination amongst them. Hidden Markov Models (HMMs) have been successfully applied to the detection task as they model sequence similarity very well. From a Machine Learning point of view these HMMs are essentially one-class classifiers trained solely on a small number of similar proteins neglecting the vast number of dissimilar ones. Our basic assumption is that integrating this neglected information will be highly beneficial to the classification task. Thus, we transform the problem representation from a one-class to a binary one. Equipped with the necessary sound understanding of Machine Learning, especially concerning problem representation and statistically significant evaluation, our work pursues and combines two different avenues on this aforementioned transformation. First, we introduce a binary HMM that discriminates significantly better than the standard one, even when only a fraction of the negative information is used. Second, we interpret the HMM as a structured graph of information. This information cannot be accessed by highly optimised standard Machine Learning classifiers as they expect a fixed length feature vector representation. Propositionalisation is a technique to transform the former representation into the latter. This thesis introduces new propositionalisation techniques. The change in representation changes the learning problem from a one-class, generative to a propositional, discriminative one. It is a common assumption that discriminative techniques are better suited for classification tasks, and our results validate this assumption. We suggest a new way to significantly improve on discriminative power and runtime by means of terminating the time-intense training of HMMs early, subsequently applying propositionalisation and classifying with a discriminative, binary learner.

year: 2011

title: A passion for learning Chinese?: Investigating a community-based Chinese cultural education school in Hamilton, New Zealand

authors: Akoorie, Michèle E.M.

subjects: China

abstract: Purpose – Following the Olympic Games of 2008 and the World Expo in 2010, many Westerners have increasingly begun to pay attention to China; a country which combines ancient history with modern economic achievements. As a consequence there has been renewed interest in the West in learning about Chinese language and culture. Confucius education schools have even begun to spring up round the world, with the intention of promoting interest in Chinese language and cultural influences. The purpose of this paper is to focus on a community-based Chinese culture education institution, in a provincial city in New Zealand, to understand the issues and risks of operating a cross-cultural education institution business in a foreign country which is physically distant from China and to identify barriers which need to be overcome in order to run such an institution more effectively. 
Design/methodology/approach – This research used a single site case study research design. Qualitative in-depth interviews were used to develop an understanding of the rich, complex and idiosyncratic nature of human phenomena. In total, ten interviews were conducted with the Principal, Board members, teachers, local students of Institute A, students' parents (both Chinese and New Zealand), and institutional “outsiders”. 
Findings – It was found that Institute's management team preferred the traditional Chinese educational methods which conflicted with ways used in the local (New Zealand) teaching system. It also found that the current management style conflicts with the professional style of organization management. The management team had a chaotic management and operational style, while lacking basic knowledge of the principles of effective administration concepts. 
Practical implications – Identifying the risks and issues associated with the operation of a community-based cultural education institution outside China will assist managers to understand the potential for cross-cultural clashes between their belief in the principles of traditional Chinese education systems and the fit with the local culture. The finding of this study, in identifying the specific issues in relation to operational and professional modes of management, should assist managers to put into place an administrative system which is sufficiently flexible to accommodate both perspectives. 
Originality/value – Although formerly a bi-cultural nation, New Zealand has increasingly become a multicultural society. Interest in Chinese language and culture has also been fuelled by New Zealand's shift in immigration policy from 1974 (to a skills based rather than an ethnicity policy). This study is a first attempt to evaluate the efficacy of a Chinese community-based educational institution in New Zealand.

text: A passion for learning Chinese?: Investigating a community-based Chinese cultural education school in Hamilton, New Zealand Purpose – Following the Olympic Games of 2008 and the World Expo in 2010, many Westerners have increasingly begun to pay attention to China; a country which combines ancient history with modern economic achievements. As a consequence there has been renewed interest in the West in learning about Chinese language and culture. Confucius education schools have even begun to spring up round the world, with the intention of promoting interest in Chinese language and cultural influences. The purpose of this paper is to focus on a community-based Chinese culture education institution, in a provincial city in New Zealand, to understand the issues and risks of operating a cross-cultural education institution business in a foreign country which is physically distant from China and to identify barriers which need to be overcome in order to run such an institution more effectively. 
Design/methodology/approach – This research used a single site case study research design. Qualitative in-depth interviews were used to develop an understanding of the rich, complex and idiosyncratic nature of human phenomena. In total, ten interviews were conducted with the Principal, Board members, teachers, local students of Institute A, students' parents (both Chinese and New Zealand), and institutional “outsiders”. 
Findings – It was found that Institute's management team preferred the traditional Chinese educational methods which conflicted with ways used in the local (New Zealand) teaching system. It also found that the current management style conflicts with the professional style of organization management. The management team had a chaotic management and operational style, while lacking basic knowledge of the principles of effective administration concepts. 
Practical implications – Identifying the risks and issues associated with the operation of a community-based cultural education institution outside China will assist managers to understand the potential for cross-cultural clashes between their belief in the principles of traditional Chinese education systems and the fit with the local culture. The finding of this study, in identifying the specific issues in relation to operational and professional modes of management, should assist managers to put into place an administrative system which is sufficiently flexible to accommodate both perspectives. 
Originality/value – Although formerly a bi-cultural nation, New Zealand has increasingly become a multicultural society. Interest in Chinese language and culture has also been fuelled by New Zealand's shift in immigration policy from 1974 (to a skills based rather than an ethnicity policy). This study is a first attempt to evaluate the efficacy of a Chinese community-based educational institution in New Zealand.

year: 2011

title: Permanent Forum on Indigenous Issues: Report on the thirteenth session (12-23 May 2014)

authors: Toki, Valmaine

abstract: The Permanent Forum on Indigenous Issues recommends to the Economic and Social Council the adoption of the following draft decisions:
Draft decision I
International expert group meeting on the theme “Dialogue on an optional protocol to the United Nations Declaration on the Rights of Indigenous Peoples”
Draft decision II 
Venue and dates of the fourteenth session of the Permanent Forum 
Draft decision III
Report of the Permanent Forum on Indigenous Issues on its thirteenth session and provisional agenda for its fourteenth session 
Draft decision IV
Change of name of the Permanent Forum on Indigenous Issues 
Draft decision V
Additional one-day meeting

text: Permanent Forum on Indigenous Issues: Report on the thirteenth session (12-23 May 2014) The Permanent Forum on Indigenous Issues recommends to the Economic and Social Council the adoption of the following draft decisions:
Draft decision I
International expert group meeting on the theme “Dialogue on an optional protocol to the United Nations Declaration on the Rights of Indigenous Peoples”
Draft decision II 
Venue and dates of the fourteenth session of the Permanent Forum 
Draft decision III
Report of the Permanent Forum on Indigenous Issues on its thirteenth session and provisional agenda for its fourteenth session 
Draft decision IV
Change of name of the Permanent Forum on Indigenous Issues 
Draft decision V
Additional one-day meeting

year: 2014