Identifying the Source of Vulnerability in Explanation Discrepancy: A Case Study in Neural Text Classification

Some recent works observed the instability of post-hoc explanations when input side perturbations are applied to the model. This raises the interest and concern in the stability of post-hoc explanations. However, the remaining question is: is the instability caused by the neural network model or the post-hoc explanation method? This work explores the potential source that leads to unstable post-hoc explanations. To separate the influence from the model, we propose a simple output probability perturbation method. Compared to prior input side perturbation methods, the output probability perturbation method can circumvent the neural model's potential effect on the explanations and allow the analysis on the explanation method. We evaluate the proposed method with three widely-used post-hoc explanation methods (LIME (Ribeiro et al., 2016), Kernel Shapley (Lundberg and Lee, 2017a), and Sample Shapley (Strumbelj and Kononenko, 2010)). The results demonstrate that the post-hoc methods are stable, barely producing discrepant explanations under output probability perturbations. The observation suggests that neural network models may be the primary source of fragile explanations.Comment: EMNLP BlackboxNLP 202

Overexpression of a Water-Forming NADH Oxidase Improves the Metabolism and Stress Tolerance of Saccharomyces cerevisiae in Aerobic Fermentation

Recognising that the world into which students emerge upon graduation is characterised by constant change, we embrace a critical pedagogy that can be implemented in the classroom through the use of freehand drawing. Freehand drawing is a technique that can stimulate a critical stance, as visual representations allow us to comprehend the world differently, while permitting us see how others understand the world. First year students, in their first lecture, were asked to draw their interpretations of Irish politics and to explain in writing what they had drawn. The students were then placed in groups and asked to note what they saw in each other’s drawings, allowing for the identification of general patterns and themes. In this context, freehand drawing facilitates our ability to: ‘see’ how we understand a topic and that there are multiple ways of understanding; test theories, orthodoxies and accepted truths; scrutinise tacit assumptions; and ponder other possibilities. In employing freehand drawing in this manner, our aim is to create a learning environment where students develop their capacity for critical self-reflection

Overexpression of THI4 and HAP4 Improves Glucose Metabolism and Ethanol Production in Saccharomyces cerevisiae

Redox homeostasis is essential to the maintenance of cell metabolism. Changes in the redox state cause global metabolic and transcriptional changes. Our previous study indicated that the overexpression of NADH oxidase in Saccharomyces cerevisiae led to increased glucose consumption and ethanol production. Gene expression related to thiamine synthesis and osmotolerance as well as HAP4 expression was increased in response to redox change caused by the overexpression of NADH oxidase. To identify detailed relationships among cofactor levels, thiamine synthesis, expression of HAP4, and osmotolerance, and to determine whether these changes are interdependent, THI4 and HAP4 were overexpressed in S. cerevisiae BY4741. The glucose consumption rate of THI4-overexpressing strain (thi4-OE) was the highest, followed by HAP4-overexpressing strain (hap4-OE) > NADH oxidase-overexpressing strain (nox-OE) > control strain (con), while strain hap4-OE showed the highest concentration of ethanol after 26 h of fermentation. Reduced glycerol production and increased osmotolerance were observed in thi4-OE and hap4-OE, as well as in nox-OE. HAP4 globally regulated thiamine synthesis, biomass synthesis, respiration, and osmotolerance of cells, which conferred the recombinant strain hap4-OE with faster glucose metabolism and enhanced stress resistance. Moreover, overexpression of HAP4 might extend the life span of cells under caloric restriction by lowering the NADH level. Although overexpression of THI4 and HAP4 induced various similar changes at both the metabolic and the transcriptional level, the regulatory effect of THI4 was more limited than that of HAP4, and was restricted to the growth phase of cells. Our findings are expected to benefit the bio-ethanol industry

FLO Genes Family and Transcription Factor MIG1 Regulate Saccharomyces cerevisiae Biofilm Formation During Immobilized Fermentation

Saccharomyces cerevisiae immobilization is commonly used for efficient ethanol fuel production in industry due to the relatively higher ethanol stress resistance of S. cerevisiae in biofilms relative to planktonic cells. The mechanisms of biofilm formation and stress resistance, however, remain ambiguous. By analyzing biofilm and planktonic cell transcriptomes, this study observed that MIG1 (encoding a transcription factor) expression in cells increases during the biofilm formation process. To identify the role of MIG1 in yeast biofilm formation and the ethanol resistance of these cells, MIG1 was deleted and complemented in S. cerevisiae 1308. Results showed the MIG1 deletion mutant strain demonstrated weaker biofilm formation ability both on fibers and plastic than the wild-type and these could be restored by expressing MIG1 in deletion mutant. To verify the ability of MIG1 to regulate the expression of FLO genes, which encode adhesions responsible for yeast biofilm formation, FLO gene transcription levels were measured via qRT-PCR. Relative to wild-type S. cerevisiae, the adhesion genes FLO1, 5, and 9 which also demonstrate increased expression in the transcriptome of yeast cells during biofilm formation, but not FLO11, were down-regulated in the MIG1 mutant strain. Additionally, the MIG1 mutant lost a majority of its flocculation ability, which depended on cell-cell adhesions and its slightly invasive growth ability, dependent on cell-substrate adhesion. Deleting FLO1, 5, and 9 decreased biofilm formation on plastics, suggesting these FLO genes contribute to the biofilm formation process alongside FLO11. Moreover, the ethanol tolerance of yeast decreased in the MIG1 deletion mutant as well as the FLO11 deletion mutant, resulting in reduced biofilm formation during fermentation. It remains possible that in the later period of fermentation, when ethanol has accumulated, an over-expression of the FLO1, 5, and 9 genes regulated by MIG1 would enhanced cell-cell adhesions and thus protect cells in the outer layer of biofilms from ethanol, a function primarily dependent on cell-cell adhesions. This work offers a possible explanation for how biofilm formation is regulated during the immobilized fermentation process, and can enhance environmental tolerance in industrial production

REV: Information-Theoretic Evaluation of Free-Text Rationales

Generating free-text rationales is a promising step towards explainable NLP, yet evaluating such rationales remains a challenge. Existing metrics have mostly focused on measuring the association between the rationale and a given label. We argue that an ideal metric should focus on the new information uniquely provided in the rationale that is otherwise not provided in the input or the label. We investigate this research problem from an information-theoretic perspective using conditional V-information (Hewitt et al., 2021). More concretely, we propose a metric called REV (Rationale Evaluation with conditional V-information), to quantify the amount of new, label-relevant information in a rationale beyond the information already available in the input or the label. Experiments across four benchmarks with reasoning tasks, including chain-of-thought, demonstrate the effectiveness of REV in evaluating rationale-label pairs, compared to existing metrics. We further demonstrate REV is consistent with human judgments on rationale evaluations and provides more sensitive measurements of new information in free-text rationales. When used alongside traditional performance metrics, REV provides deeper insights into models' reasoning and prediction processes.Comment: ACL 202

Reducing Neuroinflammation in Psychiatric Disorders: Novel Target of Phosphodiesterase 4 (PDE4) and Developing of the PDE4 Inhibitors

Multiple lines of evidence support the pathogenic role of neuroinflammation in psychiatric illness. Cyclic adenosine monophosphate (cAMP) is a critical regulator of microglia homeostasis; as the predominant negative modulator of cyclic AMP signaling within microglia, and phosphodiesterase 4 (PDE4) represents a promising target for modulating immune function. The approach for pharmacological manipulation of cAMP levels using specifc PDE4 inhibitors provokes an ant-iinflammatory response. Specifcally, PDE4 inhibitors have recently emerged as a potential therapeutic strategy for neuroinflammatory, neurodegenerative, and psychiatric diseases. Mechanistically, PDE4 inhibitors produce an anti-inflammatory and neuroprotection effect by increasing the accumulation of cAMP and activating protein kinase A (PKA), the signaling pathway of which is thought to play an important role in the development of psychiatric disorders. This chapter reviews present knowledge of the relationship between neuroinflammation and classical psychiatric disorders (major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia) and demonstrates the signaling pathways that underlie the use of PDE4 inhibitors in neuroinflammation. In addition, among the four subtypes (A-D) of PDE4, it remains unclear which one exerts suppressive effects on neuroinflammation. Understanding how PDE4 and neuroinflammation interact can reveal pathogenic clues and help target new preventive and symptomatic therapies for psychiatric illness