A Study of Checkpointing in Large Scale Training of Deep Neural Networks

Deep learning (DL) applications are increasingly being deployed on HPC systems, to leverage the massive parallelism and computing power of those systems for DL model training. While significant effort has been put to facilitate distributed training by DL frameworks, fault tolerance has been largely ignored. In this work, we evaluate checkpoint-restart, a common fault tolerance technique in HPC workloads. We perform experiments with three state-of-the-art DL frameworks common in HPC Chainer, PyTorch, and TensorFlow). We evaluate the computational cost of checkpointing, file formats and file sizes, the impact of scale, and deterministic checkpointing. Our evaluation shows some critical differences in checkpoint mechanisms and exposes several bottlenecks in existing checkpointing implementations. We provide discussion points that can aid users in selecting a fault-tolerant framework to use in HPC. We also provide takeaway points that framework developers can use to facilitate better checkpointing of DL workloads in HPC

Cost of tuberculosis treatment in low- and middle-income countries: systematic review and meta-regression.

BACKGROUND: Despite a scarcity of tuberculosis (TB) cost data, a substantial body of evidence has been accumulating for drug-susceptible TB (DS-TB) treatment. In this study, we review unit costs for DS-TB treatment from a provider´s perspective. We also examine factors driving cost variations and extrapolate unit costs across low- and middle-income countries (LMICs).METHODS: We searched published and grey literature for any empirically collected TB cost estimates. We selected a subgroup of estimates looking at DS-TB treatment. We extracted information on activities and inputs included. We standardised costs into an average per person-month, fitted a multi-level regression model and cross-validated country-level predictions. We then extrapolated estimates for facility-based, directly observed DS-TB treatment across countries.RESULTS: We included 95 cost estimates from 28 studies across 17 countries. Costs predictions were sensitive to characteristics such as delivery mode, whether hospitalisation was included, and inputs accounted for, as well as gross domestic product per capita. Extrapolation results are presented with uncertainty intervals (UIs) for LMICs. Predicted median costs per 6 months of treatment were US$315.30 (95$222.60-US$417.20) for low-income, US$527.10 (95% CI US$395.70-US$743.70) for lower middle-income and US$896.40 (95$654.00-US$1214.40) for upper middle-income countries.CONCLUSIONS: Our study provides country-level DS-TB treatment cost estimates suitable for priority setting. These estimates, while not standing as a substitute for local high-quality primary data, can inform global, regional and national exercises

Nativity Differences in Stress among Asian and Pacific Islander American Women

According to the Stress Process Theory, people who are marginalized in society encounter more stress than those in more advantaged positions. Immigrants are one such marginalized group in the United States (US) who may experience greater psychological stress than their US-born counterparts due to (1) severing of social ties; (2) social disadvantage and marginalization; and (3) adaptation to a new environment. This study examines the disparity in stress by nativity, and how social factors contribute to this disparity for Asian and Pacific Islander (API) women. Data come from the Asian Community Health Initiative, which included a sample of 291 foreign-born and 155 US-born API women in the San Francisco Bay Area. Multivariable linear regression was used to estimate associations between nativity status and stress, measured using the Cohen Perceived Stress Scale, accounting for various social stressors. Foreign-born women had higher levels of stress compared to US-born. Stress was greater among women experiencing fewer socioeconomic resources, more discrimination, more acculturative stress, and low English proficiency. English proficiency accounted for much of the disparity in stress between foreign-born and US-born API women. This study contributes to our understanding of how stress among APIs is influenced by social disadvantage and marginalization in US society. Future research should further study how aspects of the immigrant experience are associated with stress among APIs over time

ECLIM-SEHOP, a new platform to set up and develop international academic clinical trials for childhood cancer and blood disorders in Spain

Introduction: Cancer and blood disorders in children are rare. The progressive improvement in survival over the last decades largely relies on the development of international academic clinical trials that gather the sufcient number of patients globally to elaborate solid conclusions and drive changes in clinical practice. The participation of Spain into large international academic trials has traditionally lagged behind of other European countries, mainly due to the burden of administrative tasks to open new studies, lack of fnancial support and limited research infrastructure in our hospitals. Methods: The objective of ECLIM-SEHOP platform (Ensayos Clínicos Internacionales Multicéntricos-SEHOP) is to overcome these difculties and position Spain among the European countries leading the advances in cancer and blood disorders, facilitate the access of our patients to novel diagnostic and therapeutic approaches and, most importantly, continue to improve survival and reducing long-term sequelae. ECLIM-SEHOP provides to the Spanish clinical investigators with the necessary infrastructural support to open and implement academic clinical trials and registries. Results: In less than 3 years from its inception, the platform has provided support to 20 clinical trials and 8 observational studies, including 8 trials and 4 observational studies where the platform performs all trial-related tasks (integral support: trial setup, monitoring, etc.) with more than 150 patients recruited since 2017 to these studies. In this manuscript, we provide baseline metrics for academic clinical trial performance that permit future comparisons. Conclusions: ECLIM-SEHOP facilitates Spanish children and adolescents diagnosed with cancer and blood disorders to access state-of-the-art diagnostic and therapeutic strategies

In silico Analyses of Immune System Protein Interactome Network, Single-Cell RNA Sequencing of Human Tissues, and Artificial Neural Networks Reveal Potential Therapeutic Targets for Drug Repurposing Against COVID-19

Background: There is pressing urgency to identify therapeutic targets and drugs that allow treating COVID-19 patients effectively.Methods: We performed in silico analyses of immune system protein interactome network, single-cell RNA sequencing of human tissues, and artificial neural networks to reveal potential therapeutic targets for drug repurposing against COVID-19.Results: We screened 1,584 high-confidence immune system proteins in ACE2 and TMPRSS2 co-expressing cells, finding 25 potential therapeutic targets significantly overexpressed in nasal goblet secretory cells, lung type II pneumocytes, and ileal absorptive enterocytes of patients with several immunopathologies. Then, we performed fully connected deep neural networks to find the best multitask classification model to predict the activity of 10,672 drugs, obtaining several approved drugs, compounds under investigation, and experimental compounds with the highest area under the receiver operating characteristics.Conclusion: After being effectively analyzed in clinical trials, these drugs can be considered for treatment of severe COVID-19 patients. Scripts can be downloaded at

Promoción, capacitación y acciones en las enfermedades infecciosas emergentes y reemergentes zoonóticas: el cambio global y el desarrollo sustentable

Las enfermedades infecciosas emergentes y reemergentes zoonóticas (EIEYRZ) bacterianas y virales, pueden ser transmitidas a partir de animales, agua, alimentos, o vectores poniendo en riesgo la salud humana. Muchos factores antropogénicos inciden en el surgimiento de estas enfermedades, tales como eventos sociales, comportamiento humano, cambios ambientales, políticas en salud pública y procedimientos médicos entre otros. Los detonantes de estos eventos infecciosos emergentes o reemergentes, son variados y poco conocidos por lo general en la población a lo que se suman conductas higiénico-sanitarias variables que pueden favorecer la transmisión de este tipo de enfermedades. La instrucción y formación educativa, es una herramienta fundamental para el cambio de actitud de la población. La interacción con grupos referenciales especializados puede favorecer de manera sostenible a la reducción, prevención, control y en algunos casos erradicación de muchas enfermedades. Un mayor conocimiento por parte de la comunidad s puede resultar de gran utilidad en la prevención y control de las mismas. Este proyecto tiene como comunidad de aplicación las áreas programáticas de los Centros de Atención Primaria de la Salud (CAPS) de La Plata y gran La Plata.Facultad de Ciencias Veterinaria

Promoción, capacitación y acciones en las enfermedades infecciosas emergentes y reemergentes zoonóticas: el cambio global y el desarrollo sustentable

Las enfermedades infecciosas emergentes y reemergentes zoonóticas (EIEYRZ) bacterianas y virales, pueden ser transmitidas a partir de animales, agua, alimentos, o vectores poniendo en riesgo la salud humana. Muchos factores antropogénicos inciden en el surgimiento de estas enfermedades, tales como eventos sociales, comportamiento humano, cambios ambientales, políticas en salud pública y procedimientos médicos entre otros. Los detonantes de estos eventos infecciosos emergentes o reemergentes, son variados y poco conocidos por lo general en la población a lo que se suman conductas higiénico-sanitarias variables que pueden favorecer la transmisión de este tipo de enfermedades. La instrucción y formación educativa, es una herramienta fundamental para el cambio de actitud de la población. La interacción con grupos referenciales especializados puede favorecer de manera sostenible a la reducción, prevención, control y en algunos casos erradicación de muchas enfermedades. Un mayor conocimiento por parte de la comunidad s puede resultar de gran utilidad en la prevención y control de las mismas. Este proyecto tiene como comunidad de aplicación las áreas programáticas de los Centros de Atención Primaria de la Salud (CAPS) de La Plata y gran La Plata.Facultad de Ciencias Veterinaria

HLA-Driven Convergence of HIV-1 Viral Subtypes B and F Toward the Adaptation to Immune Responses in Human Populations

BACKGROUND: Cytotoxic T-Lymphocyte (CTL) response drives the evolution of HIV-1 at a host-level by selecting HLA-restricted escape mutations. Dissecting the dynamics of these escape mutations at a population-level would help to understand how HLA-mediated selection drives the evolution of HIV-1. METHODOLOGY/PRINCIPAL FINDINGS: We undertook a study of the dynamics of HIV-1 CTL-escape mutations by analyzing through statistical approaches and phylogenetic methods the viral gene gag sequenced in plasma samples collected between the years 1987 and 2006 from 302 drug-naive HIV-positive patients. By applying logistic regression models and after performing correction for multiple test, we identified 22 potential CTL-escape mutations (p-value<0.05; q-value<0.2); 10 of these associations were confirmed in samples biologically independent by a Bayesian Markov Chain Monte-Carlo method. Analyzing their prevalence back in time we found that escape mutations that are the consensus residue in samples collected after 2003 have actually significantly increased in time in one of either B or F subtype until becoming the most frequent residue, while dominating the other viral subtype. Their estimated prevalence in the viral subtype they did not dominate was lower than 30% for the majority of samples collected at the end of the 80's. In addition, when screening the entire viral region, we found that the 75% of positions significantly changing in time (p<0.05) were located within known CTL epitopes. CONCLUSIONS: Across HIV Gag protein, the rise of polymorphisms from independent origin during the last twenty years of epidemic in our setting was related to an association with an HLA allele. The fact that these mutations accumulated in one of either B or F subtypes have also dominated the other subtype shows how this selection might be causing a convergence of viral subtypes to variants which are more likely to evade the immune response of the population where they circulate