Code Smells for Machine Learning Applications

The popularity of machine learning has wildly expanded in recent years. Machine learning techniques have been heatedly studied in academia and applied in the industry to create business value. However, there is a lack of guidelines for code quality in machine learning applications. In particular, code smells have rarely been studied in this domain. Although machine learning code is usually integrated as a small part of an overarching system, it usually plays an important role in its core functionality. Hence ensuring code quality is quintessential to avoid issues in the long run. This paper proposes and identifies a list of 22 machine learning-specific code smells collected from various sources, including papers, grey literature, GitHub commits, and Stack Overflow posts. We pinpoint each smell with a description of its context, potential issues in the long run, and proposed solutions. In addition, we link them to their respective pipeline stage and the evidence from both academic and grey literature. The code smell catalog helps data scientists and developers produce and maintain high-quality machine learning application code.Comment: Accepted at CAI

A Study on the Individualized Training Mode of the Professional Degree Graduate Students of the Army

From the learning motivation, training process, professional direction of the diversified characteristics, this paper analyzes the realistic requirements of personalized training of military professional degree students, analyzes the problem of current personalized training of military professional degree students that training courses teaching lack of humanity, courses research lack of pertinence, and the training standard is not clear, put forward the suggests that graduate student selection protruding flexibility strategy, subject based on the problem oriented, study research subject to the forces demand, and cooperative establish the graduate training standards to improve the personalized professional degree graduate training ability

Genome Sequencing Reveals Unique Mutations in Characteristic Metabolic Pathways and the Transfer of Virulence Genes between V. mimicus and V. cholerae

Vibrio mimicus, the species most similar to V. cholerae, is a microbe present in the natural environmental and sometimes causes diarrhea and internal infections in humans. It shows similar phenotypes to V. cholerae but differs in some biochemical characteristics. The molecular mechanisms underlying the differences in biochemical metabolism between V. mimicus and V. cholerae are currently unclear. Several V. mimicus isolates have been found that carry cholera toxin genes (ctxAB) and cause cholera-like diarrhea in humans. Here, the genome of the V. mimicus isolate SX-4, which carries an intact CTX element, was sequenced and annotated. Analysis of its genome, together with those of other Vibrio species, revealed extensive differences within the Vibrionaceae. Common mutations in gene clusters involved in three biochemical metabolism pathways that are used for discrimination between V. mimicus and V. cholerae were found in V. mimicus strains. We also constructed detailed genomic structures and evolution maps for the general types of genomic drift associated with pathogenic characters in polysaccharides, CTX elements and toxin co-regulated pilus (TCP) gene clusters. Overall, the whole-genome sequencing of the V. mimicus strain carrying the cholera toxin gene provides detailed information for understanding genomic differences among Vibrio spp. V. mimicus has a large number of diverse gene and nucleotide differences from its nearest neighbor, V. cholerae. The observed mutations in the characteristic metabolism pathways may indicate different adaptations to different niches for these species and may be caused by ancient events in evolution before the divergence of V. cholerae and V. mimicus. Horizontal transfers of virulence-related genes from an uncommon clone of V. cholerae, rather than the seventh pandemic strains, have generated the pathogenic V. mimicus strain carrying cholera toxin genes

AMELIORATIVE POTENTIAL OF ARTEMISIA CAPILLARIS FORMULA ON NONALCOHOLIC FATTY LIVER DISEASE IN RATS THROUGH REGULATION OF FAT METABOLISM

Background: Artemisia Capillaris Formula (ACF), a traditional Chinese medicinal therapy, has been used clinically in China to treat Nonalcoholic Fatty Liver Disease (NAFLD) for many years. However, the mechanism of action of this treatment on NAFLD is still unknown. The goal of the present study is to test whether Artemisia Capillaris Formula protects against NAFLD through regulation of lipid metabolism. Methods: Rat models of NAFLD were established through consumption of a high-fat diet (HFD) for 8 weeks. 60 rats were randomly divided into 6 groups (10 rats per group): the control (standard diet) group, the model (HFD) group, the polyene phosphatidylcholine treated HFD group, and the ACF-treated HFD groups (high-, medium- and low-dose). During weeks 5−8 of the HFD regimen, drugs were intra-gastrically administrated to selected groups for a total of 4 weeks. Hepatic changes were observed through pathological examination of Hematoxylin and eosin-stained tissues, quantification of lipid metabolites from sera (ALT, AST, ALP activity and TG, TC, HDL-C, LDL-C), and quantification of related gene and protein expression levels by RT-PCR and Western blotting. Results: A high-fat diet promoted obesity and the development of hepatomegaly, hepatosteatosis and dyslipidemia in rats after 8 weeks. Treatment with ACF alleviated hepatosteatosis and also protected against high fat diet-induced dyslipidemia. We found that ACF reduced ALT, AST, ALP, TG, TC, and LDL-C and increased HDL-C levels in sera from treated NAFLD rats. In addition, gene and protein expression levels of FAS and ACC were down-regulated following ACF treatment, whereas expression levels of CPT were up-regulated. Conclusion: ACF ameliorates high-fat diet-induced hepatosteatosis and dyslipidemia in rats by altering lipid metabolism-related gene expression, specifically of FAS, ACC, and CPT

Evaluating the Individualized Treatment of Traditional Chinese Medicine: A Pilot Study of N-of-1 Trials

Purpose. To compare the efficacy of individualized herbal decoction with controlled decoction for individual patients with stable bronchiectasis. Methods. We conducted N-of-1 RCTs (single-patient, double-blind, randomized, multiple crossover design) in 3 patients with stable bronchiectasis. The primary outcome was patient self-rated symptom scores on visual analogue scales. Secondary outcome was 24-hour sputum volume. A clinical efficacy criterion which combined symptoms score and medication preference was also formulated. Results. All three patients showed various degrees of improvement on their symptoms and one patient’s (Case 3) 24 h sputum volume decreased from 70 mL to 30 mL. However, no significant differences were found between individualized herbal decoction and control decoction on symptoms score, or on 24-hour sputum volume. One patient (Case 2) had clear preference for the individualized herbal decoction over the standard one with the confirmation after unblinding. We therefore considered this case as clinically important. Discussion. N-of-1 trials comply with individualized philosophy of TCM clinical practice and had good compliance. It is necessary to set up clinical efficacy criteria and to consider the interference of acute exacerbation

Skin Gene Expression Is Prognostic for the Trajectory of Skin Disease in Patients With Diffuse Cutaneous Systemic Sclerosis

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Psychometric Properties of the Chinese Version of the Perceived Stress Scale in Policewomen

BACKGROUND: The 10-item Perceived Stress Scale (PSS-10) is one of most widely used instruments to measure a global level of perceived stress in a range of clinical and research settings. This study was conducted to examine the psychometric properties of the Simplified Chinese version of the PSS-10 in policewomen. METHODOLOGY: A total of 240 policewomen were recruited in this study. The Simplified Chinese versions of the PSS-10, the Beck Depression Inventory Revised (BDI-II), and the Beck Anxiety Inventory (BAI) were administered to all participants, and 36 of the participants were re-tested two weeks after the initial testing. PRINCIPAL FINDINGS: The overall Cronbach's alpha was 0.86, and the test-retest reliability coefficient was 0.68. Exploratory Factor Analysis (EFA) yielded 2 factors with eigenvalues of 4.76 and 1.48, accounting for 62.41% of variance. Factor 1 consisted of 6 items representing "negative feelings"; whereas Factor 2 consisted of 4 items representing "positive feelings". The item loadings ranged from 0.72 to 0.83. The Confirmatory factor analysis (CFA) indicated a very good fit of this two-factor model to this sample. The PSS-10 significantly correlated with both BDI-II and BAI, indicating an acceptable concurrent validity. CONCLUSIONS: The Simplified Chinese version of the PSS-10 demonstrated adequate psychometric properties for evaluating stress levels. The results support its use among the Chinese population

De Novo Peroxisome Biogenesis in Penicillium Chrysogenum Is Not Dependent on the Pex11 Family Members or Pex16

We have analyzed the role of the three members of the Pex11 protein family in peroxisome formation in the filamentous fungus Penicillium chrysogenum. Two of these, Pex11 and Pex11C, are components of the peroxisomal membrane, while Pex11B is present at the endoplasmic reticulum. We show that Pex11 is a major factor involved in peroxisome proliferation. We also demonstrate that P. chrysogenum cells deleted for known peroxisome fission factors (all Pex11 family proteins and Vps1) still contain peroxisomes. Interestingly, we find that, unlike in mammals, Pex16 is not essential for peroxisome biogenesis in P. chrysogenum, as partially functional peroxisomes are present in a pex16 deletion strain. We also show that Pex16 is not involved in de novo biogenesis of peroxisomes, as peroxisomes were still present in quadruple Δpex11 Δpex11B Δpex11C Δpex16 mutant cells. By contrast, pex3 deletion in P. chrysogenum led to cells devoid of peroxisomes, suggesting that Pex3 may function independently of Pex16. Finally, we demonstrate that the presence of intact peroxisomes is important for the efficiency of ß-lactam antibiotics production by P. chrysogenum. Remarkably, distinct from earlier results with low penicillin producing laboratory strains, upregulation of peroxisome numbers in a high producing P. chrysogenum strain had no significant effect on penicillin production