Request, Coalesce, Serve, and Forget: Miss-Optimized Memory Systems for Bandwidth-Bound Cache-Unfriendly Applications on FPGAs

Applications such as large-scale sparse linear algebra and graph analytics are challenging to accelerate on FPGAs due to the short irregular memory accesses, resulting in low cache hit rates. Nonblocking caches reduce the bandwidth required by misses by requesting each cache line only once, even when there are multiple misses corresponding to it. However, such reuse mechanism is traditionally implemented using an associative lookup. This limits the number of misses that are considered for reuse to a few tens, at most. In this article, we present an efficient pipeline that can process and store thousands of outstanding misses in cuckoo hash tables in on-chip SRAM with minimal stalls. This brings the same bandwidth advantage as a larger cache for a fraction of the area budget, because outstanding misses do not need a data array, which can significantly speed up irregular memory-bound latency-insensitive applications. In addition, we extend nonblocking caches to generate variable-length bursts to memory, which increases the bandwidth delivered by DRAMs and their controllers. The resulting miss-optimized memory system provides up to 25% speedup with 24× area reduction on 15 large sparse matrix-vector multiplication benchmarks evaluated on an embedded and a datacenter FPGA system.

Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination

Background LINCS, "Library of Integrated Network-based Cellular Signatures", and IDG, "Illuminating the Druggable Genome", are both NIH projects and consortia that have generated rich datasets for the study of the molecular basis of human health and disease. LINCS L1000 expression signatures provide unbiased systems/omics experimental evidence. IDG provides compiled and curated knowledge for illumination and prioritization of novel drug target hypotheses. Together, these resources can support a powerful new approach to identifying novel drug targets for complex diseases, such as Parkinson's disease (PD), which continues to inflict severe harm on human health, and resist traditional research approaches. Results Integrating LINCS and IDG, we built the Knowledge Graph Analytics Platform (KGAP) to support an important use case: identification and prioritization of drug target hypotheses for associated diseases. The KGAP approach includes strong semantics interpretable by domain scientists and a robust, high performance implementation of a graph database and related analytical methods. Illustrating the value of our approach, we investigated results from queries relevant to PD. Approved PD drug indications from IDG’s resource DrugCentral were used as starting points for evidence paths exploring chemogenomic space via LINCS expression signatures for associated genes, evaluated as target hypotheses by integration with IDG. The KG-analytic scoring function was validated against a gold standard dataset of genes associated with PD as elucidated, published mechanism-of-action drug targets, also from DrugCentral. IDG's resource TIN-X was used to rank and filter KGAP results for novel PD targets, and one, SYNGR3 (Synaptogyrin-3), was manually investigated further as a case study and plausible new drug target for PD. Conclusions The synergy of LINCS and IDG, via KG methods, empowers graph analytics methods for the investigation of the molecular basis of complex diseases, and specifically for identification and prioritization of novel drug targets. The KGAP approach enables downstream applications via integration with resources similarly aligned with modern KG methodology. The generality of the approach indicates that KGAP is applicable to many disease areas, in addition to PD, the focus of this paper.

Understanding Horizon 2020 Data: A Knowledge Graph-Based Approach

This paper aims to meaningfully analyse the Horizon 2020 data existing in the CORDIS repository of EU, and accordingly offer evidence and insights to aid organizations in the formulation of consortia that will prepare and submit winning research proposals to forthcoming calls. The analysis is performed on aggregated data concerning 32,090 funded projects, 34,295 organizations participated in them, and 87,067 public deliverables produced. The modelling of data is performed through a knowledge graph-based approach, aiming to semantically capture existing relationships and reveal hidden information. The main contribution of this work lies in the proper utilization and orchestration of keyphrase extraction and named entity recognition models, together with meaningful graph analytics on top of an efficient graph database. The proposed approach enables users to ask complex questions about the interconnection of various entities related to previously funded research projects. A set of representative queries demonstrating our data representation and analysis approach are given at the end of the paper.

Graph analytics and visualization for cyber situational understanding

This paper describes the Cyber Situational Understanding (Cyber SU) Proof of Concept (CySUP) software system for exploring advanced Cyber SU capabilities. CySUP distills complex interrelationships among cyberspace entities to provide the “so what” of cyber events for tactical operations. It combines a variety of software components to build an end-to-end pipeline for live data ingest that populates a graph knowledge base, with query-driven exploratory analysis and interactive visualizations. CySUP integrates with the core infrastructure environment supporting command posts to provide a cyber overlay onto a common operating picture oriented to tactical commanders. It also supports detailed analysis of cyberspace entities and relationships driven by ad hoc graph queries, including the conversion of natural language inquiries to formal query language. To help assess its Cyber SU capabilities, CySUP leverages automated cyber adversary emulation to carry out controlled cyberattack campaigns that impact elements of tactical missions.