Efficient Tiled Sparse Matrix Multiplication through Matrix Signatures

International audienceTiling is a key technique to reduce data movement in matrix computations. While tiling is well understood and widely used for dense matrix/tensor computations, effective tiling of sparse matrix computations remains a challenging problem. This paper proposes a novel method to efficiently summarize the impact of the sparsity structure of a matrix on achievable data reuse as a one-dimensional signature, which is then used to build an analytical cost model for tile size optimization for sparse matrix computations. The proposed model-driven approach to sparse tiling is evaluated on two key sparse matrix kernels: Sparse Matrix-Dense Matrix Multiplication (SpMM) and Sampled Dense-Dense Matrix Multiplication (SDDMM). Experimental results demonstrate that model-based tiled SpMM and SDDMM achieve high performance relative to the current state-of-the-art

Register Optimizations for Stencils on GPUs

International audienceThe recent advent of compute-intensive GPU architecture has allowed application developers to explore high-order 3D stencils for better computational accuracy. A common optimization strategy for such stencils is to expose sufficient data reuse by means such as loop unrolling, with the expectation of register-level reuse. However, the resulting code is often highly constrained by register pressure. While current state-of-the-art register allocators are satisfactory for most applications, they are unable to effectively manage register pressure for such complex high-order stencils, resulting in sub-optimal code with a large number of register spills. In this paper, we develop a statement reordering framework that models stencil computations as a DAG of trees with shared leaves, and adapts an optimal scheduling algorithm for minimizing register usage for expression trees. The effectiveness of the approach is demonstrated through experimental results on a range of stencils extracted from application codes

False positive diagnosis of malignancy in a case of cryptogenic organising pneumonia presenting as a pulmonary mass with mediastinal nodes detected on fluorodeoxyglucose-positron emission tomography: a case report

<p>Abstract</p> <p>Introduction</p> <p>We report the case of a patient with positive findings on a lung emission tomography/computed tomography (PET/CT) scan, with possible contra lateral mediastinal involvement, which strongly suggested an inoperable lung carcinoma. The lung mass proved to be a cryptogenic organising pneumonia. While the latter has previously been shown to be PET/CT positive, mediastinal involvement simulating malignant spread has not been previously reported.</p> <p>Case presentation</p> <p>A 50-year-old Caucasian woman presented with a history of unproductive cough and was found to have a mass in the right upper lobe as shown on chest X-ray and a computed tomography scan. A subsequent PET/CT scan showed strong uptake in the right upper lobe (maximum standard uptake values (SUVmax) 9.6) with increased uptake in the adjacent mediastinum and contralateral mediastinal nodes. Surgical resection and mediastinoscopy revealed cryptogenic organising pneumonia, with enlarged reactive mediastinal lymph nodes.</p> <p>Conclusion</p> <p>The case illustrates the limits of PET/CT scanning as a diagnostic tool, and emphasizes the importance of obtaining histological confirmation of malignant diseases whenever possible.</p

Associative Instruction Reordering to Alleviate Register Pressure

International audienceRegister allocation is generally considered a practically solved problem. For most applications, the register allocation strategies in production compilers are very effective in controlling the number of loads/stores and register spills. However, existing register allocation strategies are not effective and result in excessive register spilling for computation patterns with a high degree of many-to-many data reuse, e.g., high-order stencils and tensor contractions. We develop a source-to-source instruction reordering strategy that exploits the flexibility of reordering associative operations to alleviate register pressure. The developed transformation module implements an adaptable strategy that can appropriately control the degree of instruction-level parallelism, while relieving register pressure. The effectiveness of the approach is demonstrated through experimental results using multiple production compilers (GCC, Clang/LLVM) and target platforms (Intel Xeon Phi, and Intel x86 multi-core)

Asthma and COPD as co-morbidities in patients hospitalised with Covid-19 disease: a global systematic review and meta-analysis

Background: Factors predisposing to increased mortality with COVID-19 infection have been identified as male sex, hypertension, obesity, and increasing age. Early studies looking at airway diseases gave some contradictory results. The purpose of our study was to determine global variation in studies in patients hospitalized with COVID-19 in the prevalence of COPD and asthma; and to determine whether the presence of asthma or COPD affected mortality in the same hospital population. Methods: A systematic review and meta-analysis of the published literature of COPD and asthma as co-morbidities in patients hospitalized with COVID-19 was performed, looking firstly at the prevalence of these diseases in patients hospitalized with COVID-19, and secondly at the relative risk of death from any cause for patients with asthma or COPD. Results: Prevalence of both airway diseases varied markedly by region, making meaningful pooled global estimates of prevalence invalid and not of clinical utility. For individual studies, the interquartile range for asthma prevalence was 4.21 to 12.39%, and for COPD, 3.82 to 11.85%. The relative risk of death with COPD for patients hospitalized with COVID-19 was 1.863 (95% CI 1.640–2.115), while the risk with asthma was 0.918 (95% CI 0.767 to 1.098) with no evidence of increased mortality. Conclusions: For asthma and COPD, prevalence in patients hospitalized with COVID-19 varies markedly by region. We found no evidence that asthma predisposed to increased mortality in COVID-19 disease. For COPD, there was clear evidence of an association with increased mortality. Trial registration: The trial was registered with PROSPERO: registration number CRD42021289886

Non-tuberculous mycobacterial pulmonary disease (NTM-PD): Epidemiology, diagnosis and multidisciplinary management

Non-tuberculous mycobacteria (NTM) are ubiquitous environmental organisms that can cause significant disease in both immunocompromised and immunocompetent individuals. The incidence of NTM pulmonary disease (NTM-PD) is rising globally. Diagnostic challenges persist and treatment efficacy is variable. This article provides an overview of NTM-PD for clinicians. We discuss how common it is, who is at risk, how it is diagnosed and the multidisciplinary approach to its clinical management. [Abstract copyright: Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.

Efficient Tiled Sparse Matrix Multiplication through Matrix Signatures

International audienceTiling is a key technique to reduce data movement in matrix computations. While tiling is well understood and widely used for dense matrix/tensor computations, effective tiling of sparse matrix computations remains a challenging problem. This paper proposes a novel method to efficiently summarize the impact of the sparsity structure of a matrix on achievable data reuse as a one-dimensional signature, which is then used to build an analytical cost model for tile size optimization for sparse matrix computations. The proposed model-driven approach to sparse tiling is evaluated on two key sparse matrix kernels: Sparse Matrix-Dense Matrix Multiplication (SpMM) and Sampled Dense-Dense Matrix Multiplication (SDDMM). Experimental results demonstrate that model-based tiled SpMM and SDDMM achieve high performance relative to the current state-of-the-art

Efficacy of antifibrotic drugs, nintedanib and pirfenidone, in treatment of progressive pulmonary fibrosis in both idiopathic pulmonary fibrosis (IPF) and non-IPF: a systematic review and meta-analysis

From Springer Nature via Jisc Publications RouterHistory: received 2021-10-16, collection 2021-12, accepted 2021-12-08, registration 2021-12-09, pub-electronic 2021-12-11, online 2021-12-11Publication status: PublishedAbstract: Background: Research questions To compare the efficacy of nintedanib and pirfenidone in the treatment of progressive pulmonary fibrosis; and to compare the efficacy of anti-fibrotic therapy (grouping nintedanib and pirfenidone together) in patients with IPF versus patients with progressive lung fibrosis not classified as IPF. Study design and methods: A search of databases including MEDLINE, EMBASE, PubMed, and clinicaltrials.gov was conducted. Studies were included if they were randomised controlled trials of pirfenidone or nintedanib in adult patients with IPF or non-IPF patients, and with extractable data on mortality or decline in forced vital capacity (FVC). Random effects meta-analyses were performed on changes in FVC and where possible on mortality in the selected studies. Results: 13 trials of antifibrotic therapy were pooled in a meta-analysis (with pirfenidone and nintedanib considered together as anti-fibrotic therapy). The change in FVC was expressed as a standardised difference to allow pooling of percentage and absolute changes. The mean effect size in the IPF studies was − 0.305 (SE 0.043) (p < 0.001) and in the non-IPF studies the figures were − 0.307 (SE 0.063) (p < 0.001). There was no evidence of any difference between the two groups for standardised rate of FVC decline (p = 0.979). Pooling IPF and non-IPF showed a significant reduction in mortality, with mean risk ratio of 07.01 in favour of antifibrotic therapy (p = 0.008). A separate analysis restricted to non-IPF did not show a significant reduction in mortality (risk ratio 0.908 (0.547 to 1.508), p = 0.71. Interpretation: Anti-fibrotic therapy offers protection against the rate of decline in FVC in progressive lung fibrosis, with similar efficacy shown between the two anti-fibrotic agents currently in clinical use. There was no significant difference in efficacy of antifibrotic therapy whether the underlying condition was IPF or non-IPF with progressive fibrosis, supporting the hypothesis of a common pathogenesis. The data in this analysis was insufficient to be confident about a reduction in mortality in non-IPF with anti-fibrotic therapy. Trial Registration PROSPERO, registration number CRD42021266046