Publications

2024

1. Distributed transformer for high order epistasis detection in large-scale datasets

   Miguel Graça, Ricardo Nobre, Leonel Sousa, and 1 more author

   Scientific Reports, 2024
2. IPU-EpiDet: Identifying Gene Interactions on Massively Parallel Graph-Based AI Accelerators

   Ricardo Nobre, Aleksandar Ilic, Sergio Santander-Jiménez, and 1 more author

   In 2024 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2024

2023

1. A Performance Modelling-Driven Approach to Hardware Resource Scaling

   Alexandre Rodrigues, Leonel Sousa, and Aleksandar Ilic

   In European Conference on Parallel Processing, 2023
2. Sparse-Aware CARM: Rooflining Locality of Sparse Computations

   Afonso Coutinho, Diogo Marques, Leonel Sousa, and 1 more author

   In European Conference on Parallel Processing, 2023
3. Interpreting High Order Epistasis Using Sparse Transformers

   Miguel Graça, Diogo Marques, Sergio Santander-Jiménez, and 2 more authors

   In Proceedings of the 8th ACM/IEEE International Conference on Connected Health: Applications, Systems and Engineering Technologies, 2023
4. Performance modelling-driven optimization of RISC-V hardware for efficient SpMV

   Alexandre Rodrigues, Leonel Sousa, and Aleksandar Ilic

   In International Conference on High Performance Computing, 2023

2022

1. Tensor-Accelerated Fourth-Order Epistasis Detection on GPUs

   Ricardo Nobre, Aleksandar Ilic, Sergio Santander-Jiménez, and 1 more author

   In Proceedings of the 51st International Conference on Parallel Processing, 2022
2. Unlocking Personalized Healthcare on Modern CPUs/GPUs: Three-way Gene Interaction Study

   Diogo Marques, Rafael Campos, Sergio Santander-Jiménez, and 3 more authors

   In 2022 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2022

2021

1. Mansard roofline model: Reinforcing the accuracy of the roofs

   Diogo Marques, Aleksandar Ilic, and Leonel Sousa

   ACM Transactions on Modeling and Performance Evaluation of Computing Systems, 2021
2. Fourth-order exhaustive epistasis detection for the xPU Era

   Ricardo Nobre, Aleksandar Ilic, Sergio Santander-Jiménez, and 1 more author

   In Proceedings of the 50th International Conference on Parallel Processing, 2021
3. HEDAcc: FPGA-based accelerator for high-order epistasis detection

   Gaspar Ribeiro, Nuno Neves, Sergio Santander-Jiménez, and 1 more author

   In 2021 IEEE 29th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM), 2021
4. Retargeting tensor accelerators for epistasis detection

   Ricardo Nobre, Aleksandar Ilic, Sergio Santander-Jiménez, and 1 more author

   IEEE Transactions on Parallel and Distributed Systems, 2021

2020

1. Heterogeneous CPU+ iGPU processing for efficient epistasis detection

   Rafael Campos, Diogo Marques, Sergio Santander-Jiménez, and 2 more authors

   In European conference on parallel processing, 2020
2. Application-driven cache-aware roofline model

   Diogo Marques, Aleksandar Ilic, Zakhar A Matveev, and 1 more author

   Future Generation Computer Systems, 2020
3. Exploring the binary precision capabilities of tensor cores for epistasis detection

   Ricardo Nobre, Aleksandar Ilic, Sergio Santander-Jiménez, and 1 more author

   In 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2020
4. Parallel evolutionary computation for multiobjective gene interaction analysis

   Francisco Gonçalves, Sergio Santander-Jiménez, Leonel Sousa, and 2 more authors

   Journal of Computational Science, 2020

2018

1. Cache-aware roofline model and medical image processing optimizations in gpus

   Estefania Serrano, Aleksandar Ilic, Leonel Sousa, and 2 more authors

   In International Conference on High Performance Computing, 2018
2. Modeling non-uniform memory access on large compute nodes with the cache-aware roofline model

   Nicolas Denoyelle, Brice Goglin, Aleksandar Ilic, and 2 more authors

   IEEE Transactions on Parallel and Distributed Systems, 2018

2017

1. Analyzing performance of multi-cores and applications with cache-aware roofline model

   Diogo Marques, Helder Duarte, Leonel Sousa, and 1 more author

   In 2017 international conference on high performance computing & simulation (HPCS), 2017
2. Performance analysis with cache-aware roofline model in intel advisor

   Diogo Marques, Helder Duarte, Aleksandar Ilic, and 4 more authors

   In 2017 International Conference on High Performance Computing & Simulation (HPCS), 2017
3. Exploring GPU performance, power and energy-efficiency bounds with Cache-aware Roofline Modeling

   André Lopes, Frederico Pratas, Leonel Sousa, and 1 more author

   In 2017 IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS), 2017

2016

1. Beyond the roofline: Cache-aware power and energy-efficiency modeling for multi-cores

   Aleksandar Ilic, Frederico Pratas, and Leonel Sousa

   IEEE Transactions on Computers, 2016

2013

1. Cache-aware roofline model: Upgrading the loft

   Aleksandar Ilic, Frederico Pratas, and Leonel Sousa

   IEEE Computer Architecture Letters, 2013