title: Annotate-Sample-Average (ASA): A New Distant Supervision Approach for Twitter Sentiment Analysis

authors: Bravo-Marquez, Felipe

subjects: Science & Technology

abstract: The classification of tweets into polarity classes is a popular task in sentiment analysis. State-of-the-art solutions to this problem are based on supervised machine learning models trained from manually annotated examples. A drawback of these approaches is the high cost involved in data annotation. Two freely available resources that can be exploited to solve the problem are: 1) large amounts of unlabelled tweets obtained from the Twitter API and 2) prior lexical knowledge in the form of opinion lexicons. In this paper, we propose Annotate-Sample-Average (ASA), a distant supervision method that uses these two resources to generate synthetic training data for Twitter polarity classification. Positive and negative training instances are generated by sampling and averaging unlabelled tweets containing words with the corresponding polarity. Polarity of words is determined from a given polarity lexicon. Our experimental results show that the training data generated by ASA (after tuning its parameters) produces a classifier that performs significantly better than a classifier trained from tweets annotated with emoticons and a classifier trained, without any sampling and averaging, from tweets annotated according to the polarity of their words.

text: Annotate-Sample-Average (ASA): A New Distant Supervision Approach for Twitter Sentiment Analysis The classification of tweets into polarity classes is a popular task in sentiment analysis. State-of-the-art solutions to this problem are based on supervised machine learning models trained from manually annotated examples. A drawback of these approaches is the high cost involved in data annotation. Two freely available resources that can be exploited to solve the problem are: 1) large amounts of unlabelled tweets obtained from the Twitter API and 2) prior lexical knowledge in the form of opinion lexicons. In this paper, we propose Annotate-Sample-Average (ASA), a distant supervision method that uses these two resources to generate synthetic training data for Twitter polarity classification. Positive and negative training instances are generated by sampling and averaging unlabelled tweets containing words with the corresponding polarity. Polarity of words is determined from a given polarity lexicon. Our experimental results show that the training data generated by ASA (after tuning its parameters) produces a classifier that performs significantly better than a classifier trained from tweets annotated with emoticons and a classifier trained, without any sampling and averaging, from tweets annotated according to the polarity of their words.

year: 2016-01-01

title: Understanding enzymatic mechanism and allostery using macromolecular rate theory

authors: Grout, Emily Katherine

subjects: Biochemistry

abstract: Intricate systems of regulation at many levels act to control enzyme rates to tune metabolism across biosynthetic pathways. Allostery is a ubiquitous regulatory mechanism for feedback and regulation of enzymes in biosynthetic pathways. ATP-phosphoribosyltransferase from Mycobacterium tuberculosis (mtuATP-PRT) catalyses the first committed step in de novo histidine biosynthesis, and allosteric product inhibition of ATP-PRT by L-His is key to regulating metabolic flux in this pathway. mtuATP-PRT also exhibits allosteric activation by a histidine analogue 3 (2-Thienyl)-L-alanine (TIH). This compound binds in the same allosteric site as L-His and appears to elicit a structurally identical “tensed” conformation, apparently contradicting previous suggestions that the tensed conformation drives inhibitory regulation in mtuATP-PRT. 

Through mutations adjacent to the allosteric binding site, we have interrupted allosteric inhibition by L-His while retaining allosteric activation by TIH. Kinetic assays of wild type ATP-PRT and mutants across a large temperature range with various allosteric effects, has identified dynamic changes between allosterically modulated states of the enzyme, and suggests an enthalpy-entropy (∆H‡-∆S‡) trade off occurring in allosteric states. 

Complementing our kinetic data, crystallographic analysis and molecular dynamics (MD) simulations of wild type and mutant ATP-PRT have identified two residues that differ upon the binding of TIH (in comparison to L-His binding). Glu-18 and Arg-27 rotate between ligand bound states and form interacting bonds in L-His bound structures that may serve to stabilise and reduce the overall flexibility of the hexameric conformation. This Glu-18 and Arg-27 interaction varies between L-His-bound, APO-mtuATP-PRT and TIH-bound structures, suggesting this interaction may demarcate allosteric activation and inhibition.

An evolutionary analysis of ATP-PRT was undertaken and has identified the long form of ATP-PRT as the ancestral form, and the short form ATP-PRT has subsequently co-opted a histidyl-tRNA synthetase (HisRS) gene product (HisZ) as its regulatory domain. Aminoacyl-tRNA synthetases are known to be prone to horizontal gene transfer, therefore the co-option of HisRS and the loss of the C-terminal domain in ATP-PRTs provides an evolutionary trajectory for diverse ATP-PRT isoforms.

text: Understanding enzymatic mechanism and allostery using macromolecular rate theory Intricate systems of regulation at many levels act to control enzyme rates to tune metabolism across biosynthetic pathways. Allostery is a ubiquitous regulatory mechanism for feedback and regulation of enzymes in biosynthetic pathways. ATP-phosphoribosyltransferase from Mycobacterium tuberculosis (mtuATP-PRT) catalyses the first committed step in de novo histidine biosynthesis, and allosteric product inhibition of ATP-PRT by L-His is key to regulating metabolic flux in this pathway. mtuATP-PRT also exhibits allosteric activation by a histidine analogue 3 (2-Thienyl)-L-alanine (TIH). This compound binds in the same allosteric site as L-His and appears to elicit a structurally identical “tensed” conformation, apparently contradicting previous suggestions that the tensed conformation drives inhibitory regulation in mtuATP-PRT. 

Through mutations adjacent to the allosteric binding site, we have interrupted allosteric inhibition by L-His while retaining allosteric activation by TIH. Kinetic assays of wild type ATP-PRT and mutants across a large temperature range with various allosteric effects, has identified dynamic changes between allosterically modulated states of the enzyme, and suggests an enthalpy-entropy (∆H‡-∆S‡) trade off occurring in allosteric states. 

Complementing our kinetic data, crystallographic analysis and molecular dynamics (MD) simulations of wild type and mutant ATP-PRT have identified two residues that differ upon the binding of TIH (in comparison to L-His binding). Glu-18 and Arg-27 rotate between ligand bound states and form interacting bonds in L-His bound structures that may serve to stabilise and reduce the overall flexibility of the hexameric conformation. This Glu-18 and Arg-27 interaction varies between L-His-bound, APO-mtuATP-PRT and TIH-bound structures, suggesting this interaction may demarcate allosteric activation and inhibition.

An evolutionary analysis of ATP-PRT was undertaken and has identified the long form of ATP-PRT as the ancestral form, and the short form ATP-PRT has subsequently co-opted a histidyl-tRNA synthetase (HisRS) gene product (HisZ) as its regulatory domain. Aminoacyl-tRNA synthetases are known to be prone to horizontal gene transfer, therefore the co-option of HisRS and the loss of the C-terminal domain in ATP-PRTs provides an evolutionary trajectory for diverse ATP-PRT isoforms.

year: 2022

title: Supervision and culture: Meetings at thresholds

authors: Crocket, Kathie

subjects: supervision

abstract: Counsellors are required to engage in supervision in order to reflect on, reflexively review, and extend their practice. Supervision, then, might be understood as a partnership in which the focus of practitioners and supervisors is on ethical and effective practice with all clients. In Aotearoa/New Zealand, there has recently been interest in the implications for supervision of cultural difference, particularly in terms of the Treaty of Waitangi as a practice metaphor, and when non-Māori practitioners counsel Māori clients. This article offers an account of a qualitative investigation by a group of counsellors/supervisors into their experiences of supervision as cultural partnership. Based on interviews and then using writing-as-research, the article explores the playing out of supervision’s contribution to practitioners’ effective and ethical practice in the context of Aotearoa/New Zealand, showing a range of possible accounts and strategies and discussing their effects. Employing the metaphor of threshold, the article includes a series of reflections and considerations for supervision practice when attention is drawn to difference.

text: Supervision and culture: Meetings at thresholds Counsellors are required to engage in supervision in order to reflect on, reflexively review, and extend their practice. Supervision, then, might be understood as a partnership in which the focus of practitioners and supervisors is on ethical and effective practice with all clients. In Aotearoa/New Zealand, there has recently been interest in the implications for supervision of cultural difference, particularly in terms of the Treaty of Waitangi as a practice metaphor, and when non-Māori practitioners counsel Māori clients. This article offers an account of a qualitative investigation by a group of counsellors/supervisors into their experiences of supervision as cultural partnership. Based on interviews and then using writing-as-research, the article explores the playing out of supervision’s contribution to practitioners’ effective and ethical practice in the context of Aotearoa/New Zealand, showing a range of possible accounts and strategies and discussing their effects. Employing the metaphor of threshold, the article includes a series of reflections and considerations for supervision practice when attention is drawn to difference.

year: 2013