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Hi! I’m José Guilherme de Almeida, a post-doctoral researcher with the Computational Clinical Imaging Group at the Champalimaud Foundation. I am interested in developing robust predictive methods for (semi-)automated diagnosis and prognosis from clinical images and data.

Previously, I did my PhD with Moritz Gerstung and George S. Vassiliou at the EMBL-EBI and my MSc thesis with Irina Moreira at Universidade de Coimbra.

I am interested in deep-learning, computer vision and computational oncobiology. I am also a big fan of data visualization (i.e. Pure Ideology!, one of my favourite projects) and do some musical production on my free time.

José Guilherme Almeida's Projects

bovw icon bovw

Leveraging keypoint detection and description methods for MRI classification.

clonal_dynamics icon clonal_dynamics

Code repository for the longitudinal and phylodynamic analysis in "The longitudinal dynamics and natural history of clonal haematopoiesis"

clonex icon clonex

Efficient Wright-Fisher simulations for intra-tumour population genetics

fan-tf-2 icon fan-tf-2

Implementation of Bug et al.'s feature-aware normalisation model in TF2

haemorasis icon haemorasis

Blood cell detection pipeline in peripheral blood smears

imdm icon imdm

A simple library to construct image data models for data testing and validation.

nnunet icon nnunet

Fork of nnUNet, focusing on improving performance of prediction

sondagens icon sondagens

Ferramenta para análise de sondagens (em português)

structural_biology icon structural_biology

Scripts developed for structural biology. Currently more of a side/spare-time project than any other thing.

tbca icon tbca

Code repository for the blood cell atlas (TBCA)

tf-u-net icon tf-u-net

Training, testing and inference implementations of a U-Net with a few add-ons.

torch_nlm icon torch_nlm

PyTorch-based implementation of non-local means with GPU support.

wbs-prediction icon wbs-prediction

Code repository for project focusing on blood cell detection and diagnostic prediction from peripheral blood slides

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