Nikolaos Alachiotis

64 papers A* 1A 5B 9C 4Misc 2Journal 14Unranked 28

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Physical Analog Kolmogorov-Arnold Networks based on Reconfigurable Nonlinear-Processing Units. CoRR Manuel Escudero, Mohamadreza Zolfagharinejad, Sjoerd van den Belt, Nikolaos Alachiotis, Wilfred G. van der Wiel
2025	—	`conf`	Accelerated CNN-based Scans for Traces of Positive Selection. PASC Sjoerd van den Belt, Nikolaos Alachiotis
2025	J	`jnl`	Accelerated Phylogenetics on the AMD Versal Adaptive SoC. ACM Trans. Reconfigurable Technol. Syst. Geert Roks, Mario Ruiz Noguera, Nikolaos Alachiotis
2025	C	`conf`	Accelerating Multiple Sequence Alignment Via Maximal Exact Match Identification. BIBE Tim Wehning, Nikolaos Alachiotis
2025	—	`conf`	Exploring the AMD IPDPS (Workshops) Nikolaos Alachiotis, Matthijs Leon Souilljee
2025	J	`jnl`	FPGA Innovation Research in the Netherlands: Present Landscape and Future Outlook. CoRR Nikolaos Alachiotis, Sjoerd van den Belt, Steven van der Vlugt, Reinier van der Walle, Mohsen Safari, Bruno Endres Forlin, Tiziano De Matteis, Zaid Al-Ars, Roel Jordans, António J. Sousa de Almeida, Federico Corradi, Christiaan Baaij, Ana Lucia Varbanescu
2024	—	`conf`	Accelerated Spiking Convolutional Neural Networks for Scalable Population Genomics. HEART Federico Corradi, Zhanbo Shen, Hanqing Zhao, Nikolaos Alachiotis
2024	B	`conf`	Exploring the Versal AI Engines for Signal Processing in Radio Astronomy. FPL Victor Van Wijhe, Vincent Sprave, Daniele Passaretti, Nikolaos Alachiotis, Gerrit Grutzeck, Thilo Pionteck, Steven van der Vlugt
2024	A	`conf`	Lightweight Instrumentation for Accurate Performance Monitoring in RTOSes. DATE Bruno Endres Forlin, Kuan-Hsun Chen, Nikolaos Alachiotis, Luca Cassano, Marco Ottavi
2024	J	`jnl`	Scalable CNN-based classification of selective sweeps using derived allele frequencies. Bioinform. Sjoerd van den Belt, Hanqing Zhao, Nikolaos Alachiotis
2024	—	`conf`	SoftCache: A Software Cache for PCIe-Attached Hardware Accelerators. PASC Steven Wijnja, Nikolaos Alachiotis
2023	J	`jnl`	A Survey of Processing Systems for Phylogenetics and Population Genetics. ACM Trans. Reconfigurable Technol. Syst. Reinout Corts, Nikolaos Alachiotis
2023	—	`conf`	Accelerated Real-Time Classification of Evolving Data Streams using Adaptive Random Forests. ICFPT Frank Ridder, Kuan-Hsun Chen, Nikolaos Alachiotis
2023	B	`conf`	An unprotected RISC-V Soft-core processor on an SRAM FPGA: Is it as bad as it sounds? ETS Bruno E. Forlin, Wouter van Huffelen, Carlo Cazzaniga, Paolo Rech, Nikolaos Alachiotis, Marco Ottavi
2023	—	`conf`	Effective Data Preprocessing Techniques for CNN-based Selective Sweep Detection. BIBM Hanqing Zhao, Nikolaos Alachiotis
2023	—	`conf`	Exploring Genomic Sequence Alignment for Improving Side-Channel Analysis. ESORICS (3) Heitor Uchoa, Vipul Arora, Dennis Vermoen, Marco Ottavi, Nikolaos Alachiotis
2023	—	`conf`	FPGA-accelerated Quantum Transport Measurements. ICFPT Timo Haarman, António J. Sousa de Almeida, Amber Heskes, Floris Zwanenburg, Nikolaos Alachiotis
2023	J	`jnl`	Genome-wide scans for selective sweeps using convolutional neural networks. Bioinform. Hanqing Zhao, Matthijs Leon Souilljee, Pavlos Pavlidis, Nikolaos Alachiotis
2023	—	`conf`	Neutron Radiation Tests of the NEORV32 RISC-V SoC on Flash-Based FPGAs. DFT Kevin Böhmer, Bruno Endres Forlin, Carlo Cazzaniga, Paolo Rech, Gianluca Furano, Nikolaos Alachiotis, Marco Ottavi
2023	—	`conf`	SweepNet: A Lightweight CNN Architecture for the Classification of Adaptive Genomic Regions. PASC Hanqing Zhao, Pavlos Pavlidis, Nikolaos Alachiotis
2022	—	`conf`	A novel approximation scheme for floating-point square root and inverse square root for FPGAs. MOCAST Pietro Pennestrì, Yanqiu Huang, Nikolaos Alachiotis
2022	—	`conf`	Accelerated LD-based selective sweep detection using GPUs and FPGAs. IPDPS Workshops Reinout Corts, Niek Sterenborg, Nikolaos Alachiotis
2022	—	`conf`	An Event-driven Recurrent Spiking Neural Network Architecture for Efficient Inference on FPGA. ICONS Anand Sankaran, Paul Detterer, Kalpana Kannan, Nikolaos Alachiotis, Federico Corradi
2022	J	`jnl`	Scalable Phylogeny Reconstruction with Disaggregated Near-memory Processing. ACM Trans. Reconfigurable Technol. Syst. Nikolaos Alachiotis, Panagiotis Skrimponis, Manolis Pissadakis, Dionisios N. Pnevmatikatos
2021	J	`jnl`	Accelerating Phylogenetics Using FPGAs in the Cloud. IEEE Micro Nikolaos Alachiotis, Andreas Brokalakis, Vasilis Amourgianos, Sotiris Ioannidis, Pavlos Malakonakis, Tasos Bokalidis
2021	—	`conf`	An Energy-Efficient FPGA-based Convolutional Neural Network Implementation. SIU Hasan Irmak, Nikolaos Alachiotis, Daniel Ziener
2021	—	`conf`	EDRA: A Hardware-Assisted Decoupled Access/Execute Framework on the Digital Market - Invited Paper. SAMOS Dimitris Theodoropoulos, Andreas Brokalakis, Nikolaos Alachiotis, Dionisios N. Pnevmatikatos
2021	B	`conf`	Increasing Flexibility of FPGA-based CNN Accelerators with Dynamic Partial Reconfiguration. FPL Hasan Irmak, Daniel Ziener, Nikolaos Alachiotis
2021	—	`conf`	Integrative hierarchical ensemble clustering for improved disease subtype discovery. BIBM Bastian Pfeifer, Andrei Voicu-Spineanu, Michael G. Schimek, Nikolaos Alachiotis
2020	C	`conf`	Exploring Modern FPGA Platforms for Faster Phylogeny Reconstruction with RAxML. BIBE Pavlos Malakonakis, Andreas Brokalakis, Nikolaos Alachiotis, Euripides Sotiriades, Apostolos Dollas
2020	A	`conf`	Near-memory Acceleration for Scalable Phylogenetic Inference. FPGA Nikolaos Alachiotis, Panagiotis Skrimponis, Emmanouil Pissadakis, Sundeep Rangan, Dionisios N. Pnevmatikatos
2020	J	`jnl`	RAiSD-X: A Fast and Accurate FPGA System for the Detection of Positive Selection in Thousands of Genomes. ACM Trans. Reconfigurable Technol. Syst. Nikolaos Alachiotis, Charalampos Vatsolakis, Grigorios Chrysos, Dionisios N. Pnevmatikatos
2020	C	`conf`	qLD: High-performance Computation of Linkage Disequilibrium on CPU and GPU. BIBE Charalampos Theodoris, Nikolaos Alachiotis, Tze Meng Low, Pavlos Pavlidis
2019	—	`conf`	Accelerating Binarized Convolutional Neural Networks with Dynamic Partial Reconfiguration on Disaggregated FPGAs. PARCO Panagiotis Skrimponis, Emmanouil Pissadakis, Nikolaos Alachiotis, Dionisios N. Pnevmatikatos
2018	B	`conf`	Accelerated Inference of Positive Selection on Whole Genomes. FPL Nikolaos Alachiotis, Charalampos Vatsolakis, Grigorios Chrysos, Dionisios N. Pnevmatikatos
2018	—	`conf`	REMAP: Remote mEmory Manager for disAggregated Platforms. ASAP Dimitris Theodoropoulos, Andrea Reale, Dimitris Syrivelis, Maciej Bielski, Nikolaos Alachiotis, Dionisios N. Pnevmatikatos
2018	—	`conf`	ReFiRe: Efficient Deployment of Remote Fine-Grained Reconfigurable Accelerators. FPT Emmanouil Pissadakis, Nikolaos Alachiotis, Panagiotis Skrimponis, Dimitris Theodoropoulos, Thanasis Korakis, Dionisios N. Pnevmatikatos
2018	A	`conf`	dReDBox: Materializing a full-stack rack-scale system prototype of a next-generation disaggregated datacenter. DATE Maciej Bielski, Ilias Syrigos, Kostas Katrinis, Dimitris Syrivelis, Andrea Reale, Dimitris Theodoropoulos, Nikolaos Alachiotis, Dionisis N. Pnevmatikatos, E. H. Pap, George Zervas, Vaibhawa Mishra, Arsalan Saljoghei, Alvise Rigo, Jose Fernando Zazo, Sergio López-Buedo, Martí Torrents, Ferad Zyulkyarov, Michael Enrico, Óscar González de Dios
2017	B	`conf`	Deploying FPGAs to future-proof genome-wide analyses based on linkage disequilibrium. FPL Dimitrios Bozikas, Nikolaos Alachiotis, Pavlos Pavlidis, Euripides Sotiriades, Apostolos Dollas
2017	—	`conf`	FPGA-based evaluation platform for disaggregated computing. SAMOS Dimitris Theodoropoulos, Nikolaos Alachiotis, Dionisios N. Pnevmatikatos
2017	Misc	`conf`	Multi-FPGA Evaluation Platform for Disaggregated Computing. FCCM Dimitris Theodoropoulos, Nikolaos Alachiotis, Dionisios N. Pnevmatikatos
2017	B	`conf`	Versatile deployment of FPGA accelerators in disaggregated data centers: A bioinformatics case study. FPL Nikolaos Alachiotis, Dimitris Theodoropoulos, Dionisios N. Pnevmatikatos
2016	—	`conf`	Efficient Computation of Linkage Disequilibria as Dense Linear Algebra Operations. IPDPS Workshops Nikolaos Alachiotis, Doru-Thom Popovici, Tze Meng Low
2016	A	`conf`	High Performance Linkage Disequilibrium: FPGAs Hold the Key. FPGA Nikolaos Alachiotis, Gabriel Weisz
2015	A*	`conf`	Enabling portable energy efficiency with memory accelerated library. MICRO Qi Guo, Tze Meng Low, Nikolaos Alachiotis, Berkin Akin, Larry T. Pileggi, James C. Hoe, Franz Franchetti
2015	B	`conf`	Generating FPGA accelerators for chemical similarity assessment. FPL Nikolaos Alachiotis
2013	—	`conf`	A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library. IPDPS Workshops Fernando Izquierdo-Carrasco, Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis
2013	J	`jnl`	libgapmis: extending short-read alignments. BMC Bioinform. Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis
2012	—	`conf`	A versatile UDP/IP based PC ↔ FPGA communication platform. ReConFig Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis
2012	—	`—`	Algorithms and Computer Architectures for Evolutionary Bioinformatics. Nikolaos Alachiotis
2012	—	`conf`	An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data. IPDPS Workshops Simon A. Berger, Nikolaos Alachiotis, Alexandros Stamatakis
2012	J	`jnl`	Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel. BMC Bioinform. Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis
2012	—	`conf`	Exploiting Multi-grain Parallelism for Efficient Selective Sweep Detection. ICA3PP (1) Nikolaos Alachiotis, Pavlos Pavlidis, Alexandros Stamatakis
2012	—	`conf`	Libgapmis: An ultrafast library for short-read single-gap alignment. BIBM Workshops Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis
2012	J	`jnl`	OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets. Bioinform. Nikolaos Alachiotis, Alexandros Stamatakis, Pavlos Pavlidis
2011	J	`jnl`	A Vector-Like Reconfigurable Floating-Point Unit for the Logarithm. Int. J. Reconfigurable Comput. Nikolaos Alachiotis, Alexandros Stamatakis
2011	Misc	`conf`	Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs. FCCM Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis
2011	B	`conf`	FPGA Acceleration of the Phylogenetic Parsimony Kernel? FPL Nikolaos Alachiotis, Alexandros Stamatakis
2011	—	`conf`	FPGA Optimizations for a Pipelined Floating-Point Exponential Unit. ARC Nikolaos Alachiotis, Alexandros Stamatakis
2010	C	`conf`	Efficient PC-FPGA Communication over Gigabit Ethernet. CIT Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis
2010	—	`conf`	Efficient floating-point logarithm unit for FPGAs. IPDPS Workshops Nikolaos Alachiotis, Alexandros Stamatakis
2010	J	`jnl`	Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data. Bioinform. Alexandros Stamatakis, Nikolaos Alachiotis
2009	B	`conf`	A reconfigurable architecture for the Phylogenetic Likelihood Function. FPL Nikolaos Alachiotis, Alexandros Stamatakis, Euripides Sotiriades, Apostolos Dollas
2009	A	`conf`	Exploring FPGAs for accelerating the phylogenetic likelihood function. IPDPS Nikolaos Alachiotis, Euripides Sotiriades, Apostolos Dollas, Alexandros Stamatakis