GENESIM : genetic extraction of a single, interpretable model

Models obtained by decision tree induction techniques excel in being interpretable.However, they can be prone to overfitting, which results in a low predictive performance. Ensemble techniques are able to achieve a higher accuracy. However, this comes at a cost of losing interpretability of the resulting model. This makes ensemble techniques impractical in applications where decision support, instead of decision making, is crucial. To bridge this gap, we present the GENESIM algorithm that transforms an ensemble of decision trees to a single decision tree with an enhanced predictive performance by using a genetic algorithm. We compared GENESIM to prevalent decision tree induction and ensemble techniques using twelve publicly available data sets. The results show that GENESIM achieves a better predictive performance on most of these data sets than decision tree induction techniques and a predictive performance in the same order of magnitude as the ensemble techniques. Moreover, the resulting model of GENESIM has a very low complexity, making it very interpretable, in contrast to ensemble techniques.Comment: Presented at NIPS 2016 Workshop on Interpretable Machine Learning in Complex System

Construction and psychometric properties of the Belgian Rheumatoid Arthritis Disability Assessment (BRADA) questionnaire : a new tool for the evaluation of activity limitations in patients with rheumatoid arthritis

Objectives: To describe the construction and psychometric properties of the Belgian Rheumatoid Arthritis Disability Assessment (BRADA) questionnaire, a self-report tool to evaluate chronic activity limitations in patients with rheumatoid arthritis (RA). The BRADA was developed to assess the eligibility of patients with RA for financial and social support measures. Methods: The BRADA questionnaire evaluates functioning in 6 functional domains (mobility, nutrition, self care, household tasks, awareness of danger and communication) over the past week and the past 3 months. To assess the psychometric properties of the BRADA, patients with moderate to severe RA filled out the BRADA, HAQ-DI and SF-36 questionnaires twice, with a four-week interval. At each visit, the total number of swollen and tender joints, and global disease activity were recorded. DAS 28 was measured at the first visit. Internal consistency of items per domain was evaluated with Cronbach's alpha method. Intraclass correlation coefficient (ICC) analysis was used to assess test-retest reliability. BRADA scores were compared to HAQ, SF-36 scores and disease activity parameters with Spearman's Rho correlation coefficients to assess construct validity. Results: Experts considered the content and face validity of BRADA to be adequate. Internal consistency was satisfactory for all functional domains (alpha >0.75), as was the test-retest reliability (ICC 0.78). BRADA scores showed excellent correlation with other validated questionnaires in RA (HAQ-DI, SF-36) and with measures of disease activity (VAS, DAS28) (p<0.001). Conclusions: Its psychometric properties indicate that the BRADA questionnaire is a suitable instrument to evaluate disease-specific activity limitations in patients with RA

Assessment of activity limitations with the Health Assessment Questionnaire predicts the need for support measures in patients with rheumatoid arthritis : a multicenter observational study

Objective: This study investigated whether the Health Assessment Questionnaire (HAQ) can be used as an instrument to assess the need for social support measures that address activity limitations and participation issues in patients with rheumatoid arthritis (RA). Methods: This multicenter observational study included patients with RA and disease duration of at least one year, consulting their rheumatologist for routine evaluation of disease activity. In the single study visit data on demographics, disease history and current treatment were collected. DAS28 values were collected to evaluate current RA disease activity. Patients were asked to fill out the HAQ and SF-36 questionnaires. Receiver Operator Characteristics (ROC) curves were constructed to evaluate the performance of the HAQ, SF-36 and DAS28 in predicting the need for nine supporting measures available for chronically ill patients in the Belgian social security system. The expert opinion of the treating rheumatologist was used as a reference. Results: The study included 316 patients with a mean age of 59.8 +/- 12.6 years, disease duration of 11.4 +/- 9.3 years, mean DAS28 values of 2.83 +/- 1.17. Mean HAQ score was 0.95 +/- 0.73, mean SF-36 score 56.5 +/- 21.3. HAQ scores >1 were observed in 39.4% of patients. The area under the HAQ ROC curve was consistently >0.7 and higher for the HAQ than for SF-36 or DAS28 for all support measures. Rheumatologists on average recommended 3.67 support measures. Conclusion: The HAQ score was found to be a good predictor of the need for social support measures in patients with RA

Health risks associated with the use of automatic milk feeders in calves

The objective of the present article was to summarize available evidence of the economic benefits and health risks associated with the use of automatic milk feeders (AMFs) in calves. Although AMFs are increasingly used in cattle production, clear evidence of their economic benefits (increased average daily gain, gradual weaning and reduced labor time) for the typical Belgian farm size and management is not available. Especially in smaller farms, where labor time is not a limiting factor, a careful economic consideration should be made. Regarding the association of AMFs with calf disease, studies have only been performed for bovine respiratory disease and confirmed an increased risk. However, since the use of AMFs is strongly related with several other risk factors (group housing at young age, large groups, age difference in a group, continuous system versus all-in/all-out), it is difficult to unequivocally identify the risk associated with AMFs alone. A group size of less than ten calves on a single drinking point, an all-in/alloutb grouping system and a minimum age at introduction to the automat of three weeks are recommended for farms with AMFs. To the authors’ knowledge, no scientific evidence supporting the presumed association of diarrhea and tongue ulcers with AMFs is available to date

A generalized matrix profile framework with support for contextual series analysis

The Matrix Profile is a state-of-the-art time series analysis technique that can be used for motif discovery, anomaly detection, segmentation and others, in various domains such as healthcare, robotics, and audio. Where recent techniques use the Matrix Profile as a preprocessing or modeling step, we believe there is unexplored potential in generalizing the approach. We derived a framework that focuses on the implicit distance matrix calculation. We present this framework as the Series Distance Matrix (SDM). In this framework, distance measures (SDM-generators) and distance processors (SDM-consumers) can be freely combined, allowing for more flexibility and easier experimentation. In SDM, the Matrix Profile is but one specific configuration. We also introduce the Contextual Matrix Profile (CMP) as a new SDM-consumer capable of discovering repeating patterns. The CMP provides intuitive visualizations for data analysis and can find anomalies that are not discords. We demonstrate this using two real world cases. The CMP is the first of a wide variety of new techniques for series analysis that fits within SDM and can complement the Matrix Profile

Anticoagulant therapy for nodular regenerative hyperplasia in a HIV-infected patient

<p>Abstract</p> <p>Background</p> <p>Nodular regenerative hyperplasia (NRH) has been recently recognized as an emergent cause of liver disease in HIV-infected patients. NRH may cause non-cirrhotic portal hypertension with potentially severe consequences such as refractory ascites, variceal bleeding and hypersplenism. Obliteration of the small intrahepatic portal veins in association with prothrombotic disorders linked to HIV infection itself or anti-retroviral therapy seem to be the causes of NRH and thus the term HIV-associated obliterative portopathy has been proposed.</p> <p>Case Presentation</p> <p>Here we describe a case of a HIV-infected patient with biopsy-proven NRH and listed for liver transplantation (LT) because of refractory ascites and repeated upper gastrointestinal bleedings. A transjugular intrahepatic portosystemic shunt was placed as a bridge to LT and did not improve liver function. However, anticoagulant therapy with low-molecular-weight heparin (LMWH) was associated with rapid improvement in the liver condition and allowed to avoid LT in this patient.</p> <p>Conclusions</p> <p>Thus, this case underscores the relation between thrombophilia and HIV-associated NRH and emphasizes anticoagulant therapy as possible treatment.</p

The mycotoxin deoxynivalenol predisposes for the development of Clostridium perfringens-induced necrotic enteritis in broiler chickens

Both mycotoxin contamination of feed and Clostridium perfringens-induced necrotic enteritis have an increasing global economic impact on poultry production. Especially the Fusarium mycotoxin deoxynivalenol (DON) is a common feed contaminant. This study aimed at examining the predisposing effect of DON on the development of necrotic enteritis in broiler chickens. An experimental Clostridium perfringens infection study revealed that DON, at a contamination level of 3,000 to 4,000 mg/kg feed, increased the percentage of birds with subclinical necrotic enteritis from 2062.6% to 4763.0% (P<0.001). DON significantly reduced the transepithelial electrical resistance in duodenal segments (P<0.001) and decreased duodenal villus height (P = 0.014) indicating intestinal barrier disruption and intestinal epithelial damage, respectively. This may lead to an increased permeability of the intestinal epithelium and decreased absorption of dietary proteins. Protein analysis of duodenal content indeed showed that DON contamination resulted in a significant increase in total protein concentration (P = 0.023). Furthermore, DON had no effect on in vitro growth, alpha toxin production and netB toxin transcription of Clostridium perfringens. In conclusion, feed contamination with DON at concentrations below the European maximum guidance level of 5,000 mg/kg feed, is a predisposing factor for the development of necrotic enteritis in broilers. These results are associated with a negative effect of DON on the intestinal barrier function and increased intestinal protein availability, which may stimulate growth and toxin production of Clostridium perfringens

Does canine inflammatory bowel disease influence gut microbial profile and host metabolism?

Background: Inflammatory bowel disease (IBD) refers to a diverse group of chronic gastrointestinal diseases, and gut microbial dysbiosis has been proposed as a modulating factor in its pathogenesis. Several studies have investigated the gut microbial ecology of dogs with IBD but it is yet unclear if this microbial profile can alter the nutrient metabolism of the host. The aim of the present study was to characterize the faecal bacterial profile and functionality as well as to determine host metabolic changes in IBD dogs. Twenty-three dogs diagnosed with IBD and ten healthy control dogs were included. Dogs with IBD were given a clinical score using the canine chronic enteropathy clinical activity index (CCECAI). Faecal short-chain fatty acids (SCFA) and ammonia concentrations were measured and quantitative PCR was performed. The concentration of plasma amino acids, acylcarnitines, serum folate, cobalamin, and indoxyl sulfate was determined. Results: No significant differences in the abundance of a selection of bacterial groups and fermentation metabolites were observed between the IBD and control groups. However, significant negative correlations were found between CCECAI and the faecal proportion of Lactobacillus as well as between CCECAI and total SCFA concentration. Serum folate and plasma citrulline were decreased and plasma valine was increased in IBD compared to control dogs. Increased plasma free carnitine and total acylcarnitines were observed in IBD compared with control dogs, whereas short-chain acylcarnitines (butyrylcarnitine + isobutyrylcarnitine and, methylmalonylcarnitine) to free carnitine ratios decreased. Dogs with IBD had a higher 3-hydroxyisovalerylcarnitine + isovalerylcarnitine to leucine ratio compared to control dogs. Conclusions: Canine IBD induced a wide range of changes in metabolic profile, especially for the plasma concentrations of short-chain acylcarnitines and amino acids, which could have evolved from tissue damage and alteration in host metabolism. In addition, dogs with more severe IBD were characterised by a decrease in faecal proportion of Lactobacillus