title: A study of hierarchical and flat classification of proteins

authors: Zimek, Arthur

subjects: computer science

abstract: Automatic classification of proteins using machine learning is an important problem that has received significant attention in the literature. One feature of this problem is that expert-defined hierarchies of protein classes exist and can potentially be exploited to improve classification performance. In this article we investigate empirically whether this is the case for two such hierarchies. We compare multi-class classification techniques that exploit the information in those class hierarchies and those that do not, using logistic regression, decision trees, bagged decision trees, and support vector machines as the underlying base learners. In particular, we compare hierarchical and flat variants of ensembles of nested dichotomies. The latter have been shown to deliver strong classification performance in multi-class settings. We present experimental results for synthetic, fold recognition, enzyme classification, and remote homology detection data. Our results show that exploiting the class hierarchy improves performance on the synthetic data, but not in the case of the protein classification problems. Based on this we recommend that strong flat multi-class methods be used as a baseline to establish the benefit of exploiting class hierarchies in this area.

text: A study of hierarchical and flat classification of proteins Automatic classification of proteins using machine learning is an important problem that has received significant attention in the literature. One feature of this problem is that expert-defined hierarchies of protein classes exist and can potentially be exploited to improve classification performance. In this article we investigate empirically whether this is the case for two such hierarchies. We compare multi-class classification techniques that exploit the information in those class hierarchies and those that do not, using logistic regression, decision trees, bagged decision trees, and support vector machines as the underlying base learners. In particular, we compare hierarchical and flat variants of ensembles of nested dichotomies. The latter have been shown to deliver strong classification performance in multi-class settings. We present experimental results for synthetic, fold recognition, enzyme classification, and remote homology detection data. Our results show that exploiting the class hierarchy improves performance on the synthetic data, but not in the case of the protein classification problems. Based on this we recommend that strong flat multi-class methods be used as a baseline to establish the benefit of exploiting class hierarchies in this area.

year: 2008

title: Catania's Concept of the Operant Revisited: Empirical Analysis of Response Variation and Controlling Contingencies

authors: Oliver, Gary Kelson

subjects: Operant

abstract: Six Shaver‐Starcross hens with no prior experimental experience served as participants in two experiments which were designed to empirically test Catania's concept of the operant. The stimulus consisted of a cream coloured rectangle against a black background shown on a standard LCD computer monitor. An infrared touch screen mounted to the front of the LCD monitor recorded the location of all responses made by the participants. Experiment one consisted of autoshaping the rectangle pecking response. This was done using an automated computer program designed to eliminate latencies between responses and reinforcement, as well as positional biases which may have been introduced via manual autoshaping. The program successfully eliminated latencies and positional biases introduced by the experimenter, but took longer than anticipated to autoshape the desired response in the participants. It is suggested that procedural differences account for the unusual length of time taken to autoshape the participants in this experiment. Preliminary inquiry investigating procedural differences shows that it may be possible to model speed of acquisition more accurately than done so at present, without retrospective analysis of the acquisition data itself. In experiment two the active, reinforced zone of the rectangle was reduced. The participants had no visible cue demarcating active and inactive zones of the rectangle, yet in accordance with Catania's operant, responding across all participants came to fall within the active, reinforced zone of the rectangle. The results; shifts in response distributions in relation to the changes in contingencies, offer empirical support for Catania's operant in terms of positive reinforcement across a single parameter of responding. The implications of these findings imply that when variability in responding is important; for example in learning, exploring, creating, and problem solving, Catania's operant may be favourable over Skinner's operant as a vehicle for identifying and controlling variables associated with behavioural outcomes due to its greater topographical inclusivity. Contemporary behavioural analysis favours a behavioural systems approach where the respondent and operant class distinction merges; the environment affects the organism as much as the organism affects the environment. Catania's operant is complementary to behavioural analysis in this vein.

text: Catania's Concept of the Operant Revisited: Empirical Analysis of Response Variation and Controlling Contingencies Six Shaver‐Starcross hens with no prior experimental experience served as participants in two experiments which were designed to empirically test Catania's concept of the operant. The stimulus consisted of a cream coloured rectangle against a black background shown on a standard LCD computer monitor. An infrared touch screen mounted to the front of the LCD monitor recorded the location of all responses made by the participants. Experiment one consisted of autoshaping the rectangle pecking response. This was done using an automated computer program designed to eliminate latencies between responses and reinforcement, as well as positional biases which may have been introduced via manual autoshaping. The program successfully eliminated latencies and positional biases introduced by the experimenter, but took longer than anticipated to autoshape the desired response in the participants. It is suggested that procedural differences account for the unusual length of time taken to autoshape the participants in this experiment. Preliminary inquiry investigating procedural differences shows that it may be possible to model speed of acquisition more accurately than done so at present, without retrospective analysis of the acquisition data itself. In experiment two the active, reinforced zone of the rectangle was reduced. The participants had no visible cue demarcating active and inactive zones of the rectangle, yet in accordance with Catania's operant, responding across all participants came to fall within the active, reinforced zone of the rectangle. The results; shifts in response distributions in relation to the changes in contingencies, offer empirical support for Catania's operant in terms of positive reinforcement across a single parameter of responding. The implications of these findings imply that when variability in responding is important; for example in learning, exploring, creating, and problem solving, Catania's operant may be favourable over Skinner's operant as a vehicle for identifying and controlling variables associated with behavioural outcomes due to its greater topographical inclusivity. Contemporary behavioural analysis favours a behavioural systems approach where the respondent and operant class distinction merges; the environment affects the organism as much as the organism affects the environment. Catania's operant is complementary to behavioural analysis in this vein.

year: 2009

title: Caught in the cross-fire: the realities of being Māori at a bicultural law school

authors: Papuni-Ball, Makere

abstract: This thesis examines the first Waikato Māori Law Graduates’ experiences at law school and our employment choices. It has been written as a result of a research project which was conducted in 1994. The paper begins with establishing the importance of other Māori the guidelines on this project. In this discussion, my role as the researcher is explained together with how the original research project impacted upon this thesis.

Waikato School of Law was established in an era of socio-political changes in our society. Te Matahauariki Report supported its establishment based upon proven demand for law graduates. It also envisaged the School as being a meeting place for all who attended, an institution which might encourage relationships between Māori and Pakeha societies. The Council of Legal Education supported the need to have at least one law school which would not reflect the traditional legal education system and acknowledged the need to incorporate a Māori perspective. Tainui as tangata whenua hoped the school would provide opportunities for Māori students, including Māori in the curriculum and assist in promoting research ensuring the recognition of Māori lore/law.

Amongst this backdrop, the most important reason why we came to law school was because of our whānau expectations. It is the accountability and responsibility we have as Māori to our whānau and the wider Māori community that is a major theme throughout this thesis. As students we were expected to utilise our skills to benefit our wider Māori networks.

We had expected that the School would provide us with a legal education which would be enriched in Māori kaupapa. Our experiences tell another story. Instead of being educated in Māori tikanga and the true discourse of the law as a tool of oppression, we were exposed to continual suppression of our cultural heritage. In class we had become the teachers of the Māori content.

The School, although admiral in its aims, was not prepared in structure, staff or mental processes for biculturalism. The consequences for the Māori students who were exposed to this structure was devastating. Our experiences of being discriminated against and made to justify our Māori perspective against the backdrop of the dominant Pakeha legal culture have affected our perceptions of the law. The myths of one law for all and the neutrality of the justice system have resulted in our choosing to work in jobs that will continue to benefit Māori.

It is suggested that our legal education has influenced our choices to work in areas which focus on benefiting the Māori community. In those monocultural work areas which have few Māori practising, this is because such places repel those of us who know that such work places perpetuate the dominant Pakeha culture. Māori struggle against the oppressive presence of the dominant culture.

This thesis calls upon my own experiences and the experiences of my fellow Māori law graduates. It is a starting point for other Māori to write about their experiences and to reassert Māori rangatiratanga not only in law school, but in the wider community.

text: Caught in the cross-fire: the realities of being Māori at a bicultural law school This thesis examines the first Waikato Māori Law Graduates’ experiences at law school and our employment choices. It has been written as a result of a research project which was conducted in 1994. The paper begins with establishing the importance of other Māori the guidelines on this project. In this discussion, my role as the researcher is explained together with how the original research project impacted upon this thesis.

Waikato School of Law was established in an era of socio-political changes in our society. Te Matahauariki Report supported its establishment based upon proven demand for law graduates. It also envisaged the School as being a meeting place for all who attended, an institution which might encourage relationships between Māori and Pakeha societies. The Council of Legal Education supported the need to have at least one law school which would not reflect the traditional legal education system and acknowledged the need to incorporate a Māori perspective. Tainui as tangata whenua hoped the school would provide opportunities for Māori students, including Māori in the curriculum and assist in promoting research ensuring the recognition of Māori lore/law.

Amongst this backdrop, the most important reason why we came to law school was because of our whānau expectations. It is the accountability and responsibility we have as Māori to our whānau and the wider Māori community that is a major theme throughout this thesis. As students we were expected to utilise our skills to benefit our wider Māori networks.

We had expected that the School would provide us with a legal education which would be enriched in Māori kaupapa. Our experiences tell another story. Instead of being educated in Māori tikanga and the true discourse of the law as a tool of oppression, we were exposed to continual suppression of our cultural heritage. In class we had become the teachers of the Māori content.

The School, although admiral in its aims, was not prepared in structure, staff or mental processes for biculturalism. The consequences for the Māori students who were exposed to this structure was devastating. Our experiences of being discriminated against and made to justify our Māori perspective against the backdrop of the dominant Pakeha legal culture have affected our perceptions of the law. The myths of one law for all and the neutrality of the justice system have resulted in our choosing to work in jobs that will continue to benefit Māori.

It is suggested that our legal education has influenced our choices to work in areas which focus on benefiting the Māori community. In those monocultural work areas which have few Māori practising, this is because such places repel those of us who know that such work places perpetuate the dominant Pakeha culture. Māori struggle against the oppressive presence of the dominant culture.

This thesis calls upon my own experiences and the experiences of my fellow Māori law graduates. It is a starting point for other Māori to write about their experiences and to reassert Māori rangatiratanga not only in law school, but in the wider community.

year: 1996