CleanML: A Study for Evaluating the Impact of Data Cleaning on ML Classification Tasks

Data quality affects machine learning (ML) model performances, and data scientists spend considerable amount of time on data cleaning before model training. However, to date, there does not exist a rigorous study on how exactly cleaning affects ML -- ML community usually focuses on developing ML algorithms that are robust to some particular noise types of certain distributions, while database (DB) community has been mostly studying the problem of data cleaning alone without considering how data is consumed by downstream ML analytics. We propose a CleanML study that systematically investigates the impact of data cleaning on ML classification tasks. The open-source and extensible CleanML study currently includes 14 real-world datasets with real errors, five common error types, seven different ML models, and multiple cleaning algorithms for each error type (including both commonly used algorithms in practice as well as state-of-the-art solutions in academic literature). We control the randomness in ML experiments using statistical hypothesis testing, and we also control false discovery rate in our experiments using the Benjamini-Yekutieli (BY) procedure. We analyze the results in a systematic way to derive many interesting and nontrivial observations. We also put forward multiple research directions for researchers.Comment: published in ICDE 202

Mice with genetic deletion of group VIA phospholipase A2β exhibit impaired macrophage function and increased parasite load in Trypanosoma cruzi-induced myocarditis

Trypanosoma cruzi infection, which is the etiological agent of Chagas disease, is associated with intense inflammation during the acute and chronic phases. The pathological progression of Chagas disease is influenced by the infiltration and transmigration of inflammatory cells across the endothelium to infected tissues, which are carefully regulated processes involving several molecular mediators, including adhesion molecules and platelet-activating factor (PAF). We have shown that PAF production is dependent upon calcium-independent group VIA phospholipase A(2)β (iPLA(2)β) following infection of human coronary artery endothelial cells (HCAECs) with T. cruzi, suggesting that the absence of iPLA(2)β may decrease the recruitment of inflammatory cells to the heart to manage parasite accumulation. Cardiac endothelial cells isolated from iPLA(2)β-knockout (iPLA(2)β-KO) mice infected with T. cruzi demonstrated decreased PAF production compared to that by cells isolated from wild-type (WT) mice but demonstrated increases in adhesion molecule expression similar to those seen in WT mice. Myocardial inflammation in iPLA(2)β-KO mice infected with T. cruzi was similar in severity to that in WT mice, but the iPLA(2)β-KO mouse myocardium contained more parasite pseudocysts. Upon activation, macrophages from iPLA(2)β-KO mice produced significantly less nitric oxide (NO) and caused less T. cruzi inhibition than macrophages from wild-type mice. Thus, the absence of iPLA(2)β activity does not influence myocardial inflammation, but iPLA(2)β is essential for T. cruzi clearance

Charting the future of cancer health disparities research: A position statement from the American Association for Cancer Research, the American Cancer Society, the American Society of Clinical Oncology, and the National Cancer Institute

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/138314/1/caac21404_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/138314/2/caac21404.pd

Th17 cells are more protective than Th1 cells against the intracellular parasite Trypanosoma cruzi

Th17 cells are a subset of CD4+ T cells known to play a central role in the pathogenesis of many autoimmune diseases, as well as in the defense against some extracellular bacteria and fungi. However, Th17 cells are not believed to have a significant function against intracellular infections. In contrast to this paradigm, we have discovered that Th17 cells provide robust protection against Trypanosoma cruzi, the intracellular protozoan parasite that causes Chagas disease. Th17 cells confer significantly stronger protection against T. cruzi-related mortality than even Th1 cells, traditionally thought to be the CD4+ T cell subset most important for immunity to T. cruzi and other intracellular microorganisms. Mechanistically, Th17 cells can directly protect infected cells through the IL-17A-dependent induction of NADPH oxidase, involved in the phagocyte respiratory burst response, and provide indirect help through IL-21-dependent activation of CD8+ T cells. The discovery of these novel Th17 cell-mediated direct protective and indirect helper effects important for intracellular immunity highlights the diversity of Th17 cell roles, and increases understanding of protective T. cruzi immunity, aiding the development of therapeutics and vaccines for Chagas disease

World News

The UN Food and Agricultural Organization (“FAO”) announced that there is an increased risk of the bird flu spread- ing to North Africa and East Africa. The FAO warns that East Africa in particular will have difficulties containing the flu. The close proximity between humans and animals in East Africa creates an ideal situation for spreading the flu to people. A number of African countries have already responded to predictions of avian flu. For instance, Congo-Brazzaville banned poultry imports. South Africa’s Department of Health placed an urgent request for the flu medicine Tamiflu to be approved for use in the country. Kenya has established a surveillance network of the health ministry, veterinarians, and the livestock ministry to monitor incidences of bird flu

CleanML: A Study for Evaluating the Impact of Data Cleaning on ML Classification Tasks

Data quality affects machine learning (ML) model performances, and data scientists spend considerable amount of time on data cleaning before model training. However, to date, there does not exist a rigorous study on how exactly cleaning affects ML — ML community usually focuses on developing ML algorithms that are robust to some particular noise types of certain distributions, while database (DB) community has been mostly studying the problem of data cleaning alone without considering how data is consumed by downstream ML analytics. We propose a CleanML study that systematically investigates the impact of data cleaning on ML classification tasks. The opensource and extensible CleanML study currently includes 14 realworld datasets with real errors, five common error types, seven different ML models, and multiple cleaning algorithms for each error type (including both commonly used algorithms in practice as well as state-of-the-art solutions in academic literature). We control the randomness in ML experiments using statistical hypothesis testing, and we also control false discovery rate in our experiments using the Benjamini-Yekutieli (BY) procedure. We analyze the results in a systematic way to derive many interesting and nontrivial observations. We also put forward multiple research directions for researchers

IL-17A alone is not responsible for the Th17-mediated enhanced protective effects.

<p>(A-B) <i>T</i>. <i>cruzi</i>-specific Th17 cells were co-transferred with CD8⁺ T cells into RAG KO mice (5/group) prior to <i>T</i>. <i>cruzi</i> challenge. Neutralizing anti-IL-17A or control IgG1 antibodies were injected intraperitoneally every 48 hours. IL-17A neutralization did not reduce protection as measured by both parasitemia (A) and survival (B). *p<0.001 by two-tailed Student t test, **p<0.01 by log-rank test compared with negative controls. (C-D) Polyclonal CD8⁺ T cells were transferred intravenously (i.v.) into RAG KO mice prior to <i>T</i>. <i>cruzi</i> infection. Either control AdV or IL-17 AdV was injected 1 day prior to infection and 7 days post-infection at 5x10⁹ PFU i.v. Protection was measured by parasitemia 18 days post-infection (C) and survival (D).</p

Enhanced protection by Th17 cells involves more potent qualitative and quantitative helper effects for the development of <i>T</i>. <i>cruzi</i>-specific CD8⁺ T cells.

<p>RAG KO mice were adoptively transferred with polyclonal CD8⁺ T cells and Th1 or Th17 cells and then infected systemically with <i>T</i>. <i>cruzi</i>. (A) Greater absolute numbers of CD8⁺ T cells were recovered from mice co-adoptively transferred with Th17 cells at 7 days post-infection. (B) The mean fluorescence intensity (MFI) of T-bet expression in these same CD8⁺ T cells was increased over mice receiving CD8⁺ T cells alone or CD8⁺ T cells with Th1 cells, as measured by ICS. (C) Co-culture of sub-optimally stimulated CD8⁺ T cells with activated Th17 cell SN <i>in vitro</i> also induced higher T-bet expression than co-culture with Th1 cell SN. (D-E) Antigen-specific total and CD8⁺ T cell responses were studied 7 days post-challenge by IFN-γ ELISPOT (D) and intracellular cytokine staining (E), respectively. Similar results were detected in multiple experiments.</p