Research Publications Archive - Biomedical Computer Vision

Publications

Our publications by year

Benchmarking Open-ended Segmentation

ICLR (2026)

Heartbeat: a multimodal dataset of fetal echocardiography and clinical metadata for early detection of congenital heart disease

Frontiers in Cardiovascular Medicine (2026)

New frontiers in artificial intelligence for biodiversity research and conservation with multimodal language models

Methods in Ecology and Evolution (2026)

Comparative validation of surgical phase recognition, instrument keypoint estimation, and instrument instance segmentation in endoscopy: Results of the PhaKIR 2024 challenge

Medical Image Analysis (2026)

Early Prediction of MMSE & CSI-D Scores with AI

Alzheimer’s & Dementia (2025)

Multimodal Interpretable Transformer for AD

Alzheimer’s & Dementia (2025)

A Standardized Benchmark for Multilabel Antimicrobial Peptide Classification

NeurIPS Datasets & Benchmarks Track (2025)

Towards Automated Petrography

NeurIPS Datasets & Benchmarks Track (2025)

Completing spatial transcriptomics data for gene expression prediction benchmarking

Medical Image Analysis (2025)

Pixel-wise recognition for holistic surgical scene understanding

Medical Image Analysis (2025)

Pitvis-2023 challenge: Workflow recognition in videos of endoscopic pituitary surgery

Medical Image Analysis (2025)

A new benchmark for machine learning applied to powder X-ray diffraction

Scientific Data (2025)

Adaptive guidance: Training-free acceleration of conditional diffusion models

AAAI (2025)

Deep-TAO: The Deep Learning Transient Astronomical Object data set for Astronomical Transient Event Classification

arXiv (2025)

Egocast: Forecasting egocentric human pose in the wild

WACV (2025)

Invited commentary: deep learning—methods to amplify epidemiologic data collection and analyses

American journal of epidemiology (2025)

CARDIUM: Congenital Anomaly Recognition with Diagnostic Images and Unified Medical records

Third Workshop on Computer Vision for Automated Medical Diagnosis – ICCV (2025)

Latent Gene Diffusion for Spatial Transcriptomics Completion

Third Workshop on Computer Vision for Automated Medical Diagnosis – ICCV (2025 – Oral)

Artificial intelligence for the discovery of antimicrobial peptides

Antimicrobial Peptides (2025)

Computational tools for handling large databases of biological relevance

Antimicrobial Peptides (2025)

SMILE-UHURA Challenge–Small Vessel Segmentation at Mesoscopic Scale from Ultra-High Resolution 7T Magnetic Resonance Angiograms

arXiv (2024)

Multi-center fetal brain tissue annotation (feta) challenge 2022 results

IEEE transactions on medical imaging (2024)

Enhancing gene expression prediction from histology images with spatial transcriptomics completion

MICCAI (2024)

Ego-exo4d: Understanding skilled human activity from first-and third-person perspectives

CVPR (2024)

MuST: Multi-scale Transformers for Surgical Phase Recognition

MICCAI (2024)

Nuclei detection and segmentation of histopathological images using a feature pyramidal network variant of a mask R-CNN

Bioengineering (2024)

Deep Learning at the Intersection: Certified Robustness as a Tool for 3D Vision

arXiv (2024)

Road traffic injuries and the built environment in Bogotá, Colombia, 2015–2019: a cross-sectional analysis

Journal of urban health (2024)

Pytorch-wildlife: A collaborative deep learning framework for conservation

arXiv (2024)

Antimicrobial activities of casein

Casein (2024)

Styleavatar: Stylizing animatable head avatars

WACV (2024)

Sar-rarp50: Segmentation of surgical instrumentation and action recognition on robot-assisted radical prostatectomy challenge

arXiv (2023)

Knowledge Augmented Instruction Tuning for Zero-shot Animal Species Recognition

NeurIPS Workshop on Instruction Tuning and Instruction Following (2023)

Multimodal foundation models for zero-shot animal species recognition in camera trap images

arXiv (2023)

EgoCOL: Egocentric Camera pose estimation for Open-world 3D object Localization@ Ego4D challenge 2023

arXiv (2023)

Piglet: Pixel-level grounding of language expressions with transformers

IEEE Transactions on Pattern Analysis and Machine Intelligence (2023)

3D visualization, skeletonization and branching analysis of blood vessels in angiogenesis

International journal of molecular sciences (2023)

Fest: Learning spatio-temporal priors for fetal brain mri segmentation

ISBI (2023)

JOB-VS: Joint brain-vessel segmentation in TOF-MRA images

ISBI (2023)

Matis: Masked-attention transformers for surgical instrument segmentation

ISBI (2023)

SEPAL: spatial gene expression prediction from local graphs

ICCV workshop of Computer Vision for Automated Medical Diagnosis (2023 – Oral)

STRIDE: Street View-based Environmental Feature Detection and Pedestrian Collision Prediction

IEEE/CVF Interancional Conference on Computer Vision Workshops (ICCVW – 2023)

Guarding the guardians: Automated analysis of online child sexual abuse

Artificial Intelligence (AI) and Humanitarian Assistance and Disaster Recovery (HADR) Workshop, ICCV 2023

Towards characterizing the semantic robustness of face recognition

IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW – 2023)

Bodiffusion: Diffusing sparse observations for full-body human motion synthesis

Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV) Workshops (2023)

430 training neural networks to identify built environment features for pedestrian safety

Injury prevention (2022)

Adversarially robust panoptic segmentation (ARPaS) benchmark

ECCV (2022)

SuperFormer: Volumetric Transformer Architectures for MRI Super-Resolution

International workshop on simulation and synthesis in medical imaging (2022)

CanDLE: Illuminating Biases in Transcriptomic Pan-Cancer Diagnosis

Computational Mathematics Modeling in Cancer Analysis (CMMCA – 2022)

Towards holistic surgical scene understanding

MICCAI (2022)

QU-BraTS: MICCAI BraTS 2020 challenge on quantifying uncertainty in brain tumor segmentation-analysis of ranking scores and benchmarking results

The journal of machine learning for biomedical imaging (2022)

Video swin transformers for egocentric video understanding@ ego4d challenges 2022

arXiv (2022)

The medical segmentation decathlon

Nature communications (2022)

Rational discovery of antimicrobial peptides by means of artificial intelligence

Membranes (2022)

Around the world in 3,000 hours of egocentric video

CVPR (2022)

Multi-view dynamic facial action unit detection

Image and Vision Computing (2022)

Predicting target–ligand interactions with graph convolutional networks for interpretable pharmaceutical discovery

Scientific reports (2022)

Surgical instrument grounding for robot-assisted interventions

Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization (2022)

Smart pooling: AI-powered COVID-19 informative group testing

Scientific Reports (2022)

Towards Assessing and Characterizing the Semantic Robustness of Face Recognition

arXiv (2022)

Adversarially Robust Panoptic Segmentation (ARPaS) Benchmark

Computer Vision – ECCV 2022 Workshops (ECCV 2022)

Micro-surgical anastomose workflow recognition challenge report

Computer Methods and Programs in Biomedicine (2021)

SAMA: Spatially-Aware Multimodal Network with Attention For Early Lung Cancer Diagnosis

International Workshop on Multimodal Learning for Clinical Decision Support (2021)

Towards robust general medical image segmentation

MICCAI (2021)

MAIN: Multi-attention instance network for video segmentation

Computer Vision and Image Understanding (2021)

Lung nodule malignancy prediction in sequential ct scans: Summary of isbi 2018 challenge

IEEE transactions on medical imaging (2021)

Comparative validation of multi-instance instrument segmentation in endoscopy: Results of the ROBUST-MIS 2019 challenge

Medical image analysis (2021)

PharmaNet: Pharmaceutical discovery with deep recurrent neural networks

Plos one (2021)

Panoptic narrative grounding

Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV – 2021)

Generalized real-world super-resolution through adversarial robustness

Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV 2021)

A hierarchical assessment of adversarial severity

Proceedings of the IEEE/CVF international conference on computer vision (ICCV – 2021)

Enhancing adversarial robustness via test-time transformation ensembling

Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV – 2021)

APES: Audiovisual person search in untrimmed video

Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (ICCV – 2021)

Baod: budget-aware object detection

Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (ICCV – 2021)

Automatic seizure detection based on imaged-EEG signals through fully convolutional networks

Scientific reports (2020)

Classifying image sequences of astronomical transients with deep neural networks

Monthly Notices of the Royal Astronomical Society (2020)

Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches

Antibiotics (2020)

Cerberus: A multi-headed network for brain tumor segmentation

International MICCAI Brainlesion Workshop (2020)

LUCAS: LUng CAncer screening with multimodal biomarkers

Workshop on Clinical Image-Based Procedures (2020)

Isinet: an instance-based approach for surgical instrument segmentation

International conference on medical image computing and computer-assisted intervention (2020)

SIMBA: Specific identity markers for bone age assessment

International conference on medical image computing and computer-assisted intervention (2020)

UltraGAN: ultrasound enhancement through adversarial generation

International Workshop on Simulation and Synthesis in Medical Imaging (2020)

MANTRA: A Machine-learning Reference Light-curve Data Set for Astronomical Transient Event Recognition

The Astrophysical Journal Supplement Series (2020)

Automated lung cancer diagnosis using three-dimensional convolutional neural networks

Medical & biological engineering & computing (2020)

An image J plugin for the high throughput image analysis of in vitro scratch wound healing assays

PloS one (2020)

Smart pooling: AI-powered COVID-19 testing

medrxiv (2020)

Rethinking Clustering for Robustness

arXiv (2020)

Clustr: Clustering training for robustness

arXiv (2020)

El papel de la ingeniería en la pandemia de COVID-19

Revista de Ingeniería (2020)

Robust medical instrument segmentation challenge 2019

arXiv (2020)

Learning to segment brain tumors

15th International Symposium on Medical Information Processing and Analysis (2020)

An empirical study on global bone age assessment

15th International Symposium on Medical Information Processing and Analysis (2020)

Precise human pose estimation based on two-dimensional images for kinematic analysis

15th International Symposium on Medical Information Processing and Analysis (2020)

Universidad de los Andes at ActivityNet Challenge 2020-Task B Active Speaker Detection (AVA)

The ActivityNet Large-Scale Activity Recognition Challenge (2020)

Active speakers in context

CVPR (2020)

Gabor Layers Enhance Network Robustness

ECCV (2020)

Hand pose estimation for pediatric bone age assessment

MICCAI (2019)

Smit: Stochastic multi-label image-to-image translation

Proceedings of the IEEE/CVF International Conference on Computer Vision Workshops (2019)

Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge

arXiv (2018)

ISLES 2016 and 2017-benchmarking ischemic stroke lesion outcome prediction based on multispectral MRI

Frontiers in neurology (2018)

An uncertainty-aware visual system for image pre-processing

Journal of Imaging (2018)

Dynamic Multimodal Instance Segmentation guided by natural language queries

ECCV (2018)

Automated/Quantitative assessment of anatomical specimen preservation techniques using machine learning.

The FASEB Journal (2018)

Light-sheet enhanced resolution of light field microscopy for rapid imaging of large volumes

Three-dimensional and multidimensional microscopy: image acquisition and processing XXV (2018)

ISLES 2016 and 2017-benchmarking ischemic stroke lesion outcome prediction based on multispectral MRI. Front Neurol 9: 679

(2018)

2017 Index IEEE Transactions on Pattern Analysis and Machine Intelligence Vol. 39

IEEE Transactions on Pattern Analysis and Machine Intelligence (2018)

Bone age detection via carpogram analysis using convolutional neural networks

13th International Conference on Medical Information Processing and Analysis (2017)

Volumetric multimodality neural network for brain tumor segmentation

13th international conference on medical information processing and analysis (2017)

Learning to segment mouse embryo cells

13th International Conference on Medical Information Processing and Analysis (2017)

Automated detection of lung nodules with three-dimensional convolutional neural networks

13th international conference on medical information processing and analysis (2017)

Automatic diabetic retinopathy classification

13th international conference on medical information processing and analysis (2017)

Volumetric multimodality neural network for brain tumor segmentation

Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series (2017)

Brain tumor segmentation and parsing on MRIs using multiresolution neural networks

International MICCAI Brainlesion Workshop (2017)

Convolutional oriented boundaries: From image segmentation to high-level tasks

IEEE transactions on pattern analysis and machine intelligence (2017)

The 2017 davis challenge on video object segmentation

arXiv (2017)

Object Instance Segmentation and Fine-Grained Localization using Hypercolumns

IEEE transactions on pattern analysis and machine intelligence (2017)

Intuitive error space exploration of medical image data in clinical daily routine

(2017)

Multiscale combinatorial grouping for image segmentation and object proposal generation

IEEE transactions on pattern analysis and machine intelligence (2017)

Preliminary Design, Production and Characterization of a Coral and Alginate Composite for Bone Engineering

TISSUE ENGINEERING PART A (2016)

Deep retinal image understanding

International conference on medical image computing and computer-assisted intervention (2016)

Convolutional oriented boundaries

ECCV (2016)

Multispectral image segmentation based on Cartesian complexes and their associated oriented matroids

GEOBIA 2016 : Solutions and Synergies (2016)

Analysis of PHOW representations for Alzheimer disease classification on brain structural MRI

IEEE 13th International Symposium on Biomedical Imaging (ISBI) (2016)

The three R’s of computer vision: Recognition, reconstruction and reorganization

Pattern Recognition Letters (2016)

Oracle MCG: A first peek into COCO Detection Challenges

arXiv (2015)

Indoor Scene Understanding from RGB-D Images

Digest of Technical Papers-SID International Symposium (2015)

I1.4: Invited Paper: Indoor Scene Understanding from RGB‐D Images

SID Symposium Digest of Technical Papers (2015)

Indoor scene understanding with rgb-d images: Bottom-up segmentation, object detection and semantic segmentation

International Journal of Computer Vision (2015)

Inferring 3d object pose in RGB-D images

arXiv (2015)

Learning to Segment Moving Objects in Videos

CVPR (2015)

Aligning 3D models to RGB-D images of cluttered scenes

CVPR (2015)

Hypercolumns for object segmentation and fine-grained localization

CVPR (2015)

Learning rich features from RGB-D images for object detection and segmentation

ECCV (2014)

Simultaneous detection and segmentation

ECCV (2014)

Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs

Journal of Structural Biology (2014)

A discriminant multi-scale histopathology descriptor using dictionary learning

Medical Imaging 2014: Digital Pathology (2014)

Spatio-temporal moving object proposals

arXiv (2014)

Grouping-based low-rank trajectory completion and 3D reconstruction

NeurIPS (2014)

Multiscale combinatorial grouping

CVPR (2014)

Optimal and fast rotational alignment of volumes with missing data in Fourier space

Journal of Structural Biology (2013)

Volumetric semantic segmentation using pyramid context features

Proceedings of the IEEE international conference on computer vision (2013)

Perceptual organization and recognition of indoor scenes from RGB-D images

Proceedings of the IEEE conference on computer vision and pattern recognition (2013)

Articulated pose estimation using discriminative armlet classifiers

Proceedings of the IEEE conference on computer vision and pattern recognition (2013)

Automated tuberculosis diagnosis using fluorescence images from a mobile microscope

International conference on medical image computing and computer-assisted intervention (2012)

Electron microscopy of biotinylated protein complexes bound to streptavidin monolayer crystals

Journal of structural biology (2012)

Semantic segmentation using regions and parts

CVPR (2012)

2011 Index IEEE Transactions on Pattern Analysis and Machine Intelligence Vol. 33

IEEE Transactions on Pattern Analysis and Machine Intelligence (2011)

Semantic contours from inverse detectors

CVPR (2012)

Experimental evaluation of support vector machine-based and correlation-based approaches to automatic particle selection

Journal of Structural Biology (2011)

Occlusion boundary detection and figure/ground assignment from optical flow

CVPR (2011)

Finding semantic structures in image hierarchies using Laplacian graph energy

ECCV (2010)

Contour detection and hierarchical image segmentation

IEEE transactions on pattern analysis and machine intelligence (2010)

Context by region ancestry

IEEE 12th International Conference on Computer Vision (2009)

Recognition using regions

CVPR (2009)

From contours to regions: An empirical evaluation

CVPR (2009)

Constrained image segmentation from hierarchical boundaries

CVPR (2008)

Using contours to detect and localize junctions in natural images

CVPR (2008)

The Berkeley segmentation dataset and benchmark

(2007)

A metric approach to vector-valued image segmentation

International Journal of Computer Vision (2006)

Boundary extraction in natural images using ultrametric contour maps

onference on Computer Vision and Pattern Recognition Workshop (CVPRW’06) (2006)

Segmentation d’images couleur par partitions de Voronoï

Traitement du signal (2004)

Energy partitions and image segmentation

Journal of Mathematical Imaging and Vision (2004)

Path variation and image segmentation

International Workshop on Energy Minimization Methods in Computer Vision and Pattern Recognition (2003)

The extrema edges

International Conference on Scale-Space Theories in Computer Vision (2003)