Right for the Right Reason: Training Agnostic Networks

We consider the problem of a neural network being requested to classify images (or other inputs) without making implicit use of a "protected concept", that is a concept that should not play any role in the decision of the network. Typically these concepts include information such as gender or race, or other contextual information such as image backgrounds that might be implicitly reflected in unknown correlations with other variables, making it insufficient to simply remove them from the input features. In other words, making accurate predictions is not good enough if those predictions rely on information that should not be used: predictive performance is not the only important metric for learning systems. We apply a method developed in the context of domain adaptation to address this problem of "being right for the right reason", where we request a classifier to make a decision in a way that is entirely 'agnostic' to a given protected concept (e.g. gender, race, background etc.), even if this could be implicitly reflected in other attributes via unknown correlations. After defining the concept of an 'agnostic model', we demonstrate how the Domain-Adversarial Neural Network can remove unwanted information from a model using a gradient reversal layer.Comment: Author's original versio

Consumer protection in Turkey: law, informality and the role of the media. Monash University, Workplace and Corporate Law Research Group, Working Paper No. 21

This report is part of a University of Oxford John Fell funded collaborative project: Informality and the Media in Consumer Protection in Emerging Economies. This pilot project seeks to shed light upon consumer complaint behaviour through social media in emerging economies

Programmed –1 frameshifting by kinetic partitioning during impeded translocation.

Programmed –1 ribosomal frameshifting (−1PRF) is an mRNA recoding event utilized by cells to enhance the information content of the genome and to regulate gene expression. The mechanism of –1PRF and its timing during translation elongation are unclear. Here, we identified the steps that govern –1PRF by following the stepwise movement of the ribosome through the frameshifting site of a model mRNA derived from the IBV 1a/1b gene in a reconstituted in vitro translation system from Escherichia coli. Frameshifting occurs at a late stage of translocation when the two tRNAs are bound to adjacent slippery sequence codons of the mRNA. The downstream pseudoknot in the mRNA impairs the closing movement of the 30S subunit head, the dissociation of EF-G, and the release of tRNA from the ribosome. The slippage of the ribosome into the –1 frame accelerates the completion of translocation, thereby further favoring translation in the new reading frame

Mitigating Gender Bias in Machine Learning Data Sets

Artificial Intelligence has the capacity to amplify and perpetuate societal biases and presents profound ethical implications for society. Gender bias has been identified in the context of employment advertising and recruitment tools, due to their reliance on underlying language processing and recommendation algorithms. Attempts to address such issues have involved testing learned associations, integrating concepts of fairness to machine learning and performing more rigorous analysis of training data. Mitigating bias when algorithms are trained on textual data is particularly challenging given the complex way gender ideology is embedded in language. This paper proposes a framework for the identification of gender bias in training data for machine learning.The work draws upon gender theory and sociolinguistics to systematically indicate levels of bias in textual training data and associated neural word embedding models, thus highlighting pathways for both removing bias from training data and critically assessing its impact.Comment: 10 pages, 5 figures, 5 Tables, Presented as Bias2020 workshop (as part of the ECIR Conference) - http://bias.disim.univaq.i

Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins

Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of electrostatic fluctuations, expressed in terms of the reorganization energy of changing the redox state of the protein, is related to the formation of the hydrophobic protein/water interface allowing large-amplitude collective fluctuations of the water density in the protein's first solvation shell. On the top of the monotonic increase of the reorganization energy with increasing temperature, we have observed a spike at 220 K also accompanied by a significant slowing of the exponential collective Stokes shift dynamics. In contrast to the local density fluctuations of the hydration-shell waters, these spikes might be related to the global property of the water solvent crossing the Widom line.Comment: 9 pages, 8 figure

Physiological, Biochemical, and Transcriptional Responses to Single and Combined Abiotic Stress in Stress-Tolerant and Stress-Sensitive Potato Genotypes

Potato production is often constrained by abiotic stresses such as drought and high temperatures which are often present in combination. In the present work, we aimed to identify key mechanisms and processes underlying single and combined abiotic stress tolerance by comparative analysis of tolerant and susceptible cultivars. Physiological data indicated that the cultivars Desiree and Unica were stress tolerant while Agria and Russett Burbank were stress susceptible. Abiotic stress caused a greater reduction of photosynthetic carbon assimilation in the susceptible cultivars which was associated with a lower leaf transpiration rate. Oxidative stress, as estimated by the accumulation of malondialdehyde was not induced by stress treatments in any of the genotypes with the exception of drought stress in Russett Burbank. Stress treatment resulted in increases in ascorbate peroxidase activity in all cultivars except Agria which increased catalase activity in response to stress. Transcript profiling highlighted a decrease in the abundance of transcripts encoding proteins associated with PSII light harvesting complex in stress tolerant cultivars. Furthermore, stress tolerant cultivars accumulated fewer transcripts encoding a type-1 metacaspase implicated in programmed cell death. Stress tolerant cultivars exhibited stronger expression of genes associated with plant growth and development, hormone metabolism and primary and secondary metabolism than stress susceptible cultivars. Metabolite profiling revealed accumulation of proline in all genotypes following drought stress that was partially suppressed in combined heat and drought. On the contrary, the sugar alcohols inositol and mannitol were strongly accumulated under heat and combined heat and drought stress while galactinol was most strongly accumulated under drought. Combined heat and drought also resulted in the accumulation of Valine, isoleucine, and lysine in all genotypes. These data indicate that single and multiple abiotic stress tolerance in potato is associated with a maintenance of CO2 assimilation and protection of PSII by a reduction of light harvesting capacity. The data further suggests that stress tolerant cultivars suppress cell death and maintain growth and development via fine tuning of hormone signaling, and primary and secondary metabolism. This study highlights potential targets for the development of stress tolerant potato cultivars

The role of long-term mechanical circulatory support in patients with advanced heart failure

In patients with end-stage heart failure, advanced therapies such as heart transplantation and long-term mechanical circulatory support (MCS) with a left ventricular assist device (LVAD) have to be considered. LVADs can be implanted as a bridge to transplantation or as an alternative to heart transplantation: destination therapy. In the Netherlands, long-term LVAD therapy is gaining importance as a result of increased prevalence of heart failure together with a low number of heart transplantations due to shortage of donor hearts. As a result, the difference between bridge to transplantation and destination therapy is becoming more artificial since, at present, most patients initially implanted as bridge to transplantation end up receiving extended LVAD therapy. Following LVAD implantation, survival after 1, 2 and 3 years is 83%, 76% and 70%, respectively. Quality of life improves substantially despite important adverse events such as device-related infection, stroke, major bleeding and right heart failure. Early referral of potential candidates for long-term MCS is of utmost importance and positively influences outcome. In this review, an overview of the indications, contraindications, patient selection, clinical outcome and optimal time of referral for long-term MCS is given

Theory of biopolymer stretching at high forces

We provide a unified theory for the high force elasticity of biopolymers solely in terms of the persistence length, $\xi_p$, and the monomer spacing, $a$. When the force f>\fh \sim k_BT\xi_p/a^2 the biopolymers behave as Freely Jointed Chains (FJCs) while in the range \fl \sim k_BT/\xi_p < f < \fh the Worm-like Chain (WLC) is a better model. We show that $\xi_p$ can be estimated from the force extension curve (FEC) at the extension $x\approx 1/2$ (normalized by the contour length of the biopolymer). After validating the theory using simulations, we provide a quantitative analysis of the FECs for a diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and unstructured PEVK domain of titin) for $x \ge 1/2$. The success of a specific polymer model (FJC or WLC) to describe the FEC of a given biopolymer is naturally explained by the theory. Only by probing the response of biopolymers over a wide range of forces can the $f$-dependent elasticity be fully described.Comment: 20 pages, 4 figure