Publications related to High level synthesis of Smith-Waterman dataflow implementations

Related publications (31)

Strategy to systematically design and deploy the ITER plasma control system: A system engineering and model-based design approach

Richard Pitts, Federico Alberto Alfredo Felici, Federico Pesamosca, Anna Ngoc Minh Trang Vu

The paper details the process of developing the ITER Plasma Control System (PCS), that is, how to design and deploy it systematically, in the most efficient and effective manner. The integrated nature of the ITER PCS, with its multitude of coupled control ...

Elsevier Science Sa2024

Oligolithic Cross-task Optimizations across Isolated Workloads

Anastasia Ailamaki, Panagiotis Sioulas, Eleni Zapridou

Enterprises collect data in large volumes and leverage them to drive numerous concurrent decisions and business processes. Their teams deploy multiple applications that often operate concurrently on the same data and infrastructure but have widely differen ...

2024

Contemporary Logic Synthesis: with an Application to AQFP Circuit Optimization

Siang-Yun Lee

Electronic devices play an irreplaceable role in our lives. With the tightening time to market, exploding demand for computing power, and continuous desire for smaller, faster, less energy-consuming, and lower-cost chips, computer-aided design for electron ...

EPFL2024

Modified capillary number to standardize droplet generation in suction-driven microfluidics

Jatin Panwar

In droplet microfluidic devices with suction-based flow control, the microchannel geometry and suction pressure at the outlet govern the dynamic properties of the two phases that influence the droplet generation. Therefore, it is critical to understand the ...

Springer Heidelberg2024

An aircraft assembly process formalism and verification method based on semantic modeling and MBSE

Dimitrios Kyritsis, Jinzhi Lu, Xiaochen Zheng

The aircraft assembly system is highly complex involving different stakeholders from multiple domains. The design of such a system requires comprehensive consideration of various industrial scenarios aiming to optimize key performance indicators. Tradition ...

Elsevier Sci Ltd2024

A semantic model-based systems engineering approach for assessing the operational performance of metal forming process

Dimitrios Kyritsis, Jinzhi Lu

Metal Forming is a basic and essential industrial process to provide materials for constructing complex products. To design an efficient metal forming process, the functional requirements and operational performance are two important aspects to be consider ...

Pergamon-Elsevier Science Ltd2024

RE:SLAB — a load bearing system for open-ended component reuse in building structures

Corentin Jean Dominique Fivet, Jan Friedrich Georg Brütting, Dario Redaelli, Alex-Manuel Muresan, Edisson Xavier Estrella Arcos

The construction industry plays a major role in the high levels of greenhouse gas emissions, resource consumption, and waste generation observed nowadays. Key to the circular economy, structural component reuse arises as a promising solution to divert cons ...

2024

X-Attack 2.0: The Risk of Power Wasters and Satisfiability Don’t-Care Hardware Trojans to Shared Cloud FPGAs

Mirjana Stojilovic, Dina Gamaleldin Ahmed Shawky Mahmoud, Beatrice Shokry Samir Shokry

Cloud computing environments increasingly provision field-programmable gate arrays (FPGAs) for their programmability and hardware-level parallelism. While FPGAs are typically used by one tenant at a time, multitenant schemes supporting spatial sharing of c ...

2024

Highly Parallel RTL Simulation

Seyedmahyar Emami

Verification and testing of hardware heavily relies on cycle-accurate simulation of RTL. As single-processor performance is growing only slowly, conventional, single-threaded RTL simulation is becoming impractical for increasingly complex chip designs and ...

EPFL2024

Dynamical simulation via quantum machine learning with provable generalization

Zoë Holmes

Much attention has been paid to dynamical simulation and quantum machine learning (QML) independently as applications for quantum advantage, while the possibility of using QML to enhance dynamical simulations has not been thoroughly investigated. Here we d ...

Amer Physical Soc2024

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

Advanced Silicon and SWIR Single-Photon Avalanche Diodes: Design, Simulation, and Characterization

Ekin Kizilkan

Low-level light detection with high spatial and timing accuracy is a growing area of interest by virtue of applications such as light detection and ranging (LiDAR), biomedical imaging, time-resolved Raman spectroscopy, and quantum applications. Single-phot ...

EPFL2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

Molecular hypergraph neural networks

Philippe Schwaller, Junwu Chen

Graph neural networks (GNNs) have demonstrated promising performance across various chemistry-related tasks. However, conventional graphs only model the pairwise connectivity in molecules, failing to adequately represent higher order connections, such as m ...

Aip Publishing2024

Reach For the Arcs: Reconstructing Surfaces from SDFs via Tangent Points

Yingying Ren

We introduce an algorithm to reconstruct a mesh from discrete samples of a shape's Signed Distance Function (SDF). A simple geometric reinterpretation of the SDF lets us formulate the problem through a point cloud, from which a surface can be extracted wit ...

Association for Computing Machinery2024

Generative power of a protein language model trained on multiple sequence alignments

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

eLIFE SCIENCES PUBL LTD2023

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

Automating the Design of Programmable Interconnect for Reconfigurable Architectures

Stefan Nikolic

With Moore's law coming to an end, increasingly more hope is being put in specialized hardware implemented on reconfigurable architectures such as Field-Programmable Gate Arrays (FPGAs). Yet, it is often neglected that these architectures themselves experi ...

EPFL2023

Evaluating, Exploiting, and Hiding Power Side-Channel Leakage of Remote FPGAs

Ognjen Glamocanin

The pervasive adoption of field-programmable gate arrays (FPGAs) in both cyber-physical systems and the cloud has raised many security issues. Being integrated circuits, FPGAs are susceptible to fault and power side-channel attacks, which require physical ...

EPFL2023

IIBLAST: Speeding Up Commercial FPGA Routing by Decoupling and Mitigating the Intra-CLB Bottleneck

Mirjana Stojilovic, Stefan Nikolic, Shashwat Shrivastava

We identified that in modern commercial FPGAs, routing signals from the general interconnect to the configurable logic blocks (CLBs) through a very sparse input interconnect block (IIB) represents a significant runtime bottleneck. This is despite academic ...

IEEE2023