High level synthesis of RDF queries for graph analytics

In this paper we present a set of techniques that enable the synthesis of efficient custom accelerators for memory intensive, irregular applications. To address the challenges of irregular applications (large memory footprint, unpredictable fine-grained data accesses, and high synchronization intensity), and exploit their opportunities (thread level parallelism, memory level parallelism), we propose a novel accelerator design that employs an adaptive and Distributed Controller (DC) architecture, and a Memory Interface Controller (MIC) that supports concurrent and atomic memory operations on a multi-ported/multi-banked shared memory. Among the multitude of algorithms that may benefit from our solution, we focus on the acceleration of graph analytics applications and, in particular, on the synthesis of SPARQL queries on Resource Description Framework (RDF) databases. We achieve this objective by incorporating the synthesis techniques into Bambu, an Open Source high-level synthesis tools, and interfacing it with GEMS, the Graph database Engine for Multithreaded Systems. The GEMS' front-end generates optimized C implementations of the input queries, modeled as graph pattern matching algorithms, which are then automatically synthesized by Bambu. We validate our approach by synthesizing several SPARQL queries from the Lehigh University Benchmark (LUBM)

Exploring Architectural-Aware Affinity Policies in Modern HPC Runtimes

Modern commodity and High-Performance Computing (HPC) systems are evolving with complex CPU architectures. These architectures now feature higher core and NUMA domain counts and implement features such as hyperthreading. When considering significant differences in hardware configurations, library availability, and hardware-tailored system/software stacks, which could substantially vary from one system to another, performance portability is hard to achieve. Throughout the years, this trend resulted in an increasingly high burden on application developers to fine-tune their workloads for each architecture. This work explores how hardware-dependent aspects such as locality/process/thread affinity affect performance in modern CPU architectures. We focus our study on the Global Memory and Threading (GMT) distributed runtime system as a representative of Partitioned Global Address Space (PGAS) software stacks commonly adopted for productivity. In particular, to appreciate performance implications, we evaluate GMT’s thread affinity policies, and, introduce two new ones which exploit architectural awareness. Finally, we explore alternative NUMA configurations via different process bindings and perform a scalability study on three HPC clusters with varying CPU architectures and NUMA layouts. Our analysis indicates that more complex architectures are more affected by affinity and binding policies and highlights the importance of setting proper runtime configurations to achieve superior performance

The ultrasound risk stratification systems for thyroid nodule have been evaluated against papillary carcinoma: a meta-analysis

Thyroid imaging reporting and data systems (TIRADS) are used to stratify the malignancy risk of thyroid nodule by ultrasound (US) examination. We conducted a meta-analysis to evaluate the pooled cancer prevalence and the relative prevalence of papillary, medullary, follicular thyroid cancer (PTC, MTC, and FTC) and other malignancies among nodules included in studies evaluating their performance. Four databases were searched until February 2020. Original articles with at least 1000 nodules, evaluating the performance of at least one TIRADS among AACE/ACE/AME, ACR-TIRADS, ATA, EU-TIRADS, or K-TIRADS, and reporting data on the histological diagnosis of malignant lesions were included. The number of malignant nodules, PTC, FTC, MTC and other malignancies in each study was extracted. For statistical pooling of data, a random-effects model was used. Nine studies were included, evaluating 19,494 thyroid nodules. The overall prevalence of malignancy was 34% (95%CI 21 to 49). Among 6162 histologically proven malignancies, the prevalence of PTC, FTC, MTC and other malignancies was 95%, 2%, 1%, and 1%, respectively. A high heterogeneity was found for all the outcomes. A limited number of studies generally conducted using a retrospective design was found, with possible selection bias. Acknowledging this limitation, TIRADSs should be regarded as accurate tools to diagnose PTC only. Proposed patterns and/or cut-offs should be revised and other strategies considered to improve their performance in the assessment of FTC, MTC and other malignancies

SPARTA: High-Level Synthesis of Parallel Multi-Threaded Accelerators

This paper presents a methodology for the Synthesis of PARallel multi-Threaded Accelerators (SPARTA) from OpenMP annotated C/C++ specifications. SPARTA extends an open-source HLS tool, enabling the generation of accelerators that provide latency tolerance for irregular memory accesses through multithreading, support fine-grained memory-level parallelism through a hot-potato deflection-based network-on-chip (NoC), support synchronization constructs, and can instantiate memory-side caches. Our approach is based on a custom runtime OpenMP library, providing flexibility and extensibility. Experimental results show high scalability when synthesizing irregular graph kernels. The accelerators generated with our approach are, on average, 2.29x faster than state-of-the-art HLS methodologies

Prevalence of the Absence of Cirrhosis in Subjects with NAFLD-Associated Hepatocellular Carcinoma

Background. Hepatocellular carcinoma (HCC) is most commonly considered as a complication of cirrhosis. However, an increasing number of HCC in subjects with non-alcoholic fatty liver disease (NAFLD) without cirrhosis is being reported. We conducted a meta-analysis to assess the prevalence of the absence of cirrhosis in NAFLD-associated HCC. Methods. Four databases were searched until March 2021 (CRD42021242969). The original articles included were those reporting data on the presence or absence of cirrhosis among at least 50 subjects with NAFLD-associated HCC. The number of subjects with absent cirrhosis in each study was extracted. For statistical pooling of data, a random-effects model was used. Subgroup analyses according to the continent, target condition and reference standard for the diagnosis of cirrhosis were conducted. Results. Thirty studies were included, evaluating 13,371 subjects with NAFLD-associated HCC. The overall prevalence of cases without cirrhosis was 37% (95%CI 28 to 46). A higher prevalence was reported in Asia versus Europe, North America and South America (45, 36, 37 and 22%, respectively) as well as in studies adopting histology only as the reference standard for the diagnosis of cirrhosis versus histology and other modalities (e.g., radiology, endoscopy, biochemistry or overt clinical findings) (53 and 27%, respectively). No difference was found between studies including subjects with non-alcoholic steatohepatitis (NASH) only, versus NAFLD with or without NASH (p = 0.385). One in three subjects with NAFLD-associated HCC presented without cirrhosis. This should be reflected in future guidelines and surveillance programs adapted to allow for the early detection of these cancers too

Non Alcoholic Fatty Liver Disease Is Positively Associated with Increased Glycated Haemoglobin Levels in Subjects without Diabetes

Screening for non-alcoholic fatty liver disease (NAFLD) is key step for primary management of fatty liver in the clinical setting. Excess weight subjects carry a greater metabolic risk even before exhibiting pathological patterns, including diabetes. We characterized the cross-sectional relationship between routine circulating biomarkers and NAFLD in a large sample of diabetes-free subjects with overweight or obesity, to elucidate any independent relationship. A population sample of 1232 consecutive subjects with a body mass index of at least 25 kg/m(2), not receiving any drug or supplemental therapy, was studied. Clinical data and routine biochemistry were analyzed. NAFLD was defined using the validated fatty liver index (FLI), classifying subjects with a score >= 60% as at high risk. Due to extreme skewing of variables of interest, resampling matching for age and sex was performed. Our study population was characterized by a majority of females (69.90%) and a prevalence of NAFLD in males (88.90%). As a first step, propensity score matching was explicitly performed to balance the two groups according to the FLI cut-off. Based on the resulting statistical trajectories, corroborated even after data matching, we built two logistic regression models on the matched population (N = 732) to verify any independent association. We found that each unit increase of FT3 implicated a 50% increased risk of NAFLD (OR 1.506, 95%CI 1.064 to 2.131). When including glycated haemoglobin (HbA1c) in the model, free-triiodothyronine (FT3) lost significance (OR 1.557, 95%CI 0.784 to 3.089) while each unit increase in HbA1c (%) indicated a significantly greater NAFLD risk, by almost two-fold (OR 2.32, 95%CI 1.193 to 4.512). Glucose metabolism dominates a key pathway along the hazard trajectories of NAFLD, turned out to be key biomarker in monitoring the risk of fatty liver in diabetes-free overweight subjects. Each unit increase in HbA1c (%) indicated a significantly greater NAFLD risk, by almost two-fold, in our study