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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
Posts
Drawing for Publications
Published:
This blogpost provides guidelines and best practices for creating figures, diagrams, and plots for scientific papers, particularly in the context of cheminformatics and related fields. The goal is to ensure that all figures are clear, consistent, and suitable for publication. This is mainly a collection of personal notes coming from experience with various tools and formats, and it is not exhaustive nor a definitive guide (Iām still learning myself!).
portfolio
Bioinformatics Course
Published:
Implementing sequence alignment, domain assignment, main chain tracing, and steric overlaps detection.
Image Analysis Course
Published:
MATLAB projects on SIFT, CNNs, image registration, and triangulation.
High Performance Computing Course
Published:
A series of assignments on OpenMP, Threads, and OpenCL.
Finite Element Method (FEM) using Python and CUDA
Published:
Implementing the FEM algorithm from scratch in Numba and CuPy.
projects
Mapping Multiple LSTM Models on FPGAs
Published:
In this work we introduce a novel framework for mapping multiple Long Short-Term Memory (LSTM) models onto FPGA devices. The proposed approach leverages Singular Value Decomposition (SVD)-based approximation and structured pruning to optimize the execution of multiple LSTMs in parallel, significantly improving performance and memory efficiency. Our FPGA-specific accelerator design features a custom dataflow architecture with dedicated SVD and non-linear kernels to handle LSTM gate computations efficiently. The framework achieves a 3Ć to 5Ć performance increase over traditional methods, with bounded accuracy loss, making it a scalable solution for high-performance applications requiring parallel LSTM execution.
Recommended citation: Your Name, You. (2024). "Paper Title Number 3." GitHub Journal of Bugs. 1(3).', link
publications
Mapping Multiple LSTM Models on FPGAs
Published in International Conference on Field-Programmable Technology (ICFPT), 2020
This paper introduces a framework for accelerating multiple Long Short-Term Memory (LSTM) models onto FPGA devices.
Recommended citation: Ribes, S., Trancoso, P., Sourdis, I., Bouganis, C.S., "Mapping Multiple LSTM Models on FPGAs", ICFPT 2020, link
Modeling PROTAC Degradation Activity with Machine Learning
Published in Artificial Intelligence in the Life Sciences, 2024
In this work, we propose an efficient and open-source machine learning strategy to predict the degradation activity of PROteolysis TArgeting Chimeras (PROTACs).
Recommended citation: Ribes, S., Nittinger, E., Tyrchan, C., Mercado, R., "Modeling PROTAC degradation activity with machine learning", Artificial Intelligence in the Life Sciences 2024, link
talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown files that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published:
This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.