Pablo Arbeláez

Cristhian Forigua, Maria Escobar, Jordi Pont-Tuset et al.

We present EgoCOL, an egocentric camera pose estimation method for open-world 3D object localization. Our method leverages sparse camera pose reconstructions in a two-fold manner, video and scan independently, to estimate the camera pose of egocentric frames in 3D renders with high recall and precision. We extensively evaluate our method on the Visual Query (VQ) 3D object localization Ego4D benchmark. EgoCOL can estimate 62% and 59% more camera poses than the Ego4D baseline in the Ego4D Visual Queries 3D Localization challenge at CVPR 2023 in the val and test sets, respectively. Our code is publicly available at https://github.com/BCV-Uniandes/EgoCOL

Adrito Das, Danyal Z. Khan, Dimitrios Psychogyios et al.

The field of computer vision applied to videos of minimally invasive surgery is ever-growing. Workflow recognition pertains to the automated recognition of various aspects of a surgery: including which surgical steps are performed; and which surgical instruments are used. This information can later be used to assist clinicians when learning the surgery; during live surgery; and when writing operation notes. The Pituitary Vision (PitVis) 2023 Challenge tasks the community to step and instrument recognition in videos of endoscopic pituitary surgery. This is a unique task when compared to other minimally invasive surgeries due to the smaller working space, which limits and distorts vision; and higher frequency of instrument and step switching, which requires more precise model predictions. Participants were provided with 25-videos, with results presented at the MICCAI-2023 conference as part of the Endoscopic Vision 2023 Challenge in Vancouver, Canada, on 08-Oct-2023. There were 18-submissions from 9-teams across 6-countries, using a variety of deep learning models. A commonality between the top performing models was incorporating spatio-temporal and multi-task methods, with greater than 50% and 10% macro-F1-score improvement over purely spacial single-task models in step and instrument recognition respectively. The PitVis-2023 Challenge therefore demonstrates state-of-the-art computer vision models in minimally invasive surgery are transferable to a new dataset, with surgery specific techniques used to enhance performance, progressing the field further. Benchmark results are provided in the paper, and the dataset is publicly available at: https://doi.org/10.5522/04/26531686.

Natalia Valderrama, Paola Ruiz Puentes, Isabela Hernández et al.

Most benchmarks for studying surgical interventions focus on a specific challenge instead of leveraging the intrinsic complementarity among different tasks. In this work, we present a new experimental framework towards holistic surgical scene understanding. First, we introduce the Phase, Step, Instrument, and Atomic Visual Action recognition (PSI-AVA) Dataset. PSI-AVA includes annotations for both long-term (Phase and Step recognition) and short-term reasoning (Instrument detection and novel Atomic Action recognition) in robot-assisted radical prostatectomy videos. Second, we present Transformers for Action, Phase, Instrument, and steps Recognition (TAPIR) as a strong baseline for surgical scene understanding. TAPIR leverages our dataset's multi-level annotations as it benefits from the learned representation on the instrument detection task to improve its classification capacity. Our experimental results in both PSI-AVA and other publicly available databases demonstrate the adequacy of our framework to spur future research on holistic surgical scene understanding.

Angela Castillo, Maria Escobar, Guillaume Jeanneret et al.

Mixed reality applications require tracking the user's full-body motion to enable an immersive experience. However, typical head-mounted devices can only track head and hand movements, leading to a limited reconstruction of full-body motion due to variability in lower body configurations. We propose BoDiffusion -- a generative diffusion model for motion synthesis to tackle this under-constrained reconstruction problem. We present a time and space conditioning scheme that allows BoDiffusion to leverage sparse tracking inputs while generating smooth and realistic full-body motion sequences. To the best of our knowledge, this is the first approach that uses the reverse diffusion process to model full-body tracking as a conditional sequence generation task. We conduct experiments on the large-scale motion-capture dataset AMASS and show that our approach outperforms the state-of-the-art approaches by a significant margin in terms of full-body motion realism and joint reconstruction error.

Zalan Fabian, Zhongqi Miao, Chunyuan Li et al.

Due to deteriorating environmental conditions and increasing human activity, conservation efforts directed towards wildlife is crucial. Motion-activated camera traps constitute an efficient tool for tracking and monitoring wildlife populations across the globe. Supervised learning techniques have been successfully deployed to analyze such imagery, however training such techniques requires annotations from experts. Reducing the reliance on costly labelled data therefore has immense potential in developing large-scale wildlife tracking solutions with markedly less human labor. In this work we propose WildMatch, a novel zero-shot species classification framework that leverages multimodal foundation models. In particular, we instruction tune vision-language models to generate detailed visual descriptions of camera trap images using similar terminology to experts. Then, we match the generated caption to an external knowledge base of descriptions in order to determine the species in a zero-shot manner. We investigate techniques to build instruction tuning datasets for detailed animal description generation and propose a novel knowledge augmentation technique to enhance caption quality. We demonstrate the performance of WildMatch on a new camera trap dataset collected in the Magdalena Medio region of Colombia.

Maria Escobar, Laura Daza, Cristina González et al.

We implemented Video Swin Transformer as a base architecture for the tasks of Point-of-No-Return temporal localization and Object State Change Classification. Our method achieved competitive performance on both challenges.

Natalia Valderrama, Ioannis Pitsiorlas, Luisa Vargas et al.

We propose the first joint-task learning framework for brain and vessel segmentation (JoB-VS) from Time-of-Flight Magnetic Resonance images. Unlike state-of-the-art vessel segmentation methods, our approach avoids the pre-processing step of implementing a model to extract the brain from the volumetric input data. Skipping this additional step makes our method an end-to-end vessel segmentation framework. JoB-VS uses a lattice architecture that favors the segmentation of structures of different scales (e.g., the brain and vessels). Its segmentation head allows the simultaneous prediction of the brain and vessel mask. Moreover, we generate data augmentation with adversarial examples, which our results demonstrate to enhance the performance. JoB-VS achieves 70.03% mean AP and 69.09% F1-score in the OASIS-3 dataset and is capable of generalizing the segmentation in the IXI dataset. These results show the adequacy of JoB-VS for the challenging task of vessel segmentation in complete TOF-MRA images.

Nicolás Ayobi, Alejandra Pérez-Rondón, Santiago Rodríguez et al.

We propose Masked-Attention Transformers for Surgical Instrument Segmentation (MATIS), a two-stage, fully transformer-based method that leverages modern pixel-wise attention mechanisms for instrument segmentation. MATIS exploits the instance-level nature of the task by employing a masked attention module that generates and classifies a set of fine instrument region proposals. Our method incorporates long-term video-level information through video transformers to improve temporal consistency and enhance mask classification. We validate our approach in the two standard public benchmarks, Endovis 2017 and Endovis 2018. Our experiments demonstrate that MATIS' per-frame baseline outperforms previous state-of-the-art methods and that including our temporal consistency module boosts our model's performance further.

Cristina González, Nicolás Ayobi, Felipe Escallón et al.

This paper introduces a novel benchmark to study the impact and relationship of built environment elements on pedestrian collision prediction, intending to enhance environmental awareness in autonomous driving systems to prevent pedestrian injuries actively. We introduce a built environment detection task in large-scale panoramic images and a detection-based pedestrian collision frequency prediction task. We propose a baseline method that incorporates a collision prediction module into a state-of-the-art detection model to tackle both tasks simultaneously. Our experiments demonstrate a significant correlation between object detection of built environment elements and pedestrian collision frequency prediction. Our results are a stepping stone towards understanding the interdependencies between built environment conditions and pedestrian safety.

Daniela Ruiz, Juan Sebastián Ulloa, Zhongqi Miao et al.

Passive acoustic monitoring enables continuous, non-invasive biodiversity assessment across diverse ecosystems. The scale of these datasets has driven the adoption of machine learning, with supervised approaches showing strong performance. However, supervised methods require time-resolved annotated datasets, which remain scarce, especially in complex tropical soundscapes. We present PteroSet, a curated dataset of strongly annotated Neotropical bird vocalizations recorded in Puerto Asis (Putumayo) and Pivijay (Magdalena), Colombia, between 2023 and 2025. The dataset comprises 563 recordings (73.62 h) and 15,372 time-frequency annotations, including 6,702 events identified to the species level across 168 species. We release the annotations in a COCO-inspired JSON schema that unifies audio files, taxonomic categories, and labels for machine learning workflows. Beyond providing annotated data, PteroSet serves as a realistic benchmark that highlights key characteristics of tropical soundscapes, including acoustic co-occurrence and domain shift across recording sites. We provide a deep learning baseline for binary bird detection, demonstrating PteroSet's usability and the challenges it presents.

Alejandra Pérez, Santiago Rodríguez, Nicolás Ayobi et al.

Phase recognition in surgical videos is crucial for enhancing computer-aided surgical systems as it enables automated understanding of sequential procedural stages. Existing methods often rely on fixed temporal windows for video analysis to identify dynamic surgical phases. Thus, they struggle to simultaneously capture short-, mid-, and long-term information necessary to fully understand complex surgical procedures. To address these issues, we propose Multi-Scale Transformers for Surgical Phase Recognition (MuST), a novel Transformer-based approach that combines a Multi-Term Frame encoder with a Temporal Consistency Module to capture information across multiple temporal scales of a surgical video. Our Multi-Term Frame Encoder computes interdependencies across a hierarchy of temporal scales by sampling sequences at increasing strides around the frame of interest. Furthermore, we employ a long-term Transformer encoder over the frame embeddings to further enhance long-term reasoning. MuST achieves higher performance than previous state-of-the-art methods on three different public benchmarks.

Sebastian Ojeda, Rafael Velasquez, Nicolás Aparicio et al.

Antimicrobial peptides have emerged as promising molecules to combat antimicrobial resistance. However, fragmented datasets, inconsistent annotations, and the lack of standardized benchmarks hinder computational approaches and slow down the discovery of new candidates. To address these challenges, we present the Expanded Standardized Collection for Antimicrobial Peptide Evaluation (ESCAPE), an experimental framework integrating over 80.000 peptides from 27 validated repositories. Our dataset separates antimicrobial peptides from negative sequences and incorporates their functional annotations into a biologically coherent multilabel hierarchy, capturing activities across antibacterial, antifungal, antiviral, and antiparasitic classes. Building on ESCAPE, we propose a transformer-based model that leverages sequence and structural information to predict multiple functional activities of peptides. Our method achieves up to a 2.56% relative average improvement in mean Average Precision over the second-best method adapted for this task, establishing a new state-of-the-art multilabel peptide classification. ESCAPE provides a comprehensive and reproducible evaluation framework to advance AI-driven antimicrobial peptide research.

Juanita Puentes, Angela Castillo, Wilmar Osejo et al.

Online violence against children has increased globally recently, demanding urgent attention. Competent authorities manually analyze abuse complaints to comprehend crime dynamics and identify patterns. However, the manual analysis of these complaints presents a challenge because it exposes analysts to harmful content during the review process. Given these challenges, we present a novel solution, an automated tool designed to analyze children's sexual abuse reports comprehensively. By automating the analysis process, our tool significantly reduces the risk of exposure to harmful content by categorizing the reports on three dimensions: Subject, Degree of Criminality, and Damage. Furthermore, leveraging our multidisciplinary team's expertise, we introduce a novel approach to annotate the collected data, enabling a more in-depth analysis of the reports. This approach improves the comprehension of fundamental patterns and trends, enabling law enforcement agencies and policymakers to create focused strategies in the fight against children's violence.

Isai Daniel Chacón, Paola Ruiz Puentes, Jillian Pearse et al.

Petrography is a branch of geology that analyzes the mineralogical composition of rocks from microscopical thin section samples. It is essential for understanding rock properties across geology, archaeology, engineering, mineral exploration, and the oil industry. However, petrography is a labor-intensive task requiring experts to conduct detailed visual examinations of thin section samples through optical polarization microscopes, thus hampering scalability and highlighting the need for automated techniques. To address this challenge, we introduce the Large-scale Imaging and Thin section Optical-polarization Set (LITHOS), the largest and most diverse publicly available experimental framework for automated petrography. LITHOS includes 211,604 high-resolution RGB patches of polarized light and 105,802 expert-annotated grains across 25 mineral categories. Each annotation consists of the mineral class, spatial coordinates, and expert-defined major and minor axes represented as intersecting vector paths, capturing grain geometry and orientation. We evaluate multiple deep learning techniques for mineral classification in LITHOS and propose a dual-encoder transformer architecture that integrates both polarization modalities as a strong baseline for future reference. Our method consistently outperforms single-polarization models, demonstrating the value of polarization synergy in mineral classification. We have made the LITHOS Benchmark publicly available, comprising our dataset, code, and pretrained models, to foster reproducibility and further research in automated petrographic analysis.

Gabriel Pérez S, Juan C. Pérez, Motasem Alfarra et al.

This paper presents preliminary work on a novel connection between certified robustness in machine learning and the modeling of 3D objects. We highlight an intriguing link between the Maximal Certified Radius (MCR) of a classifier representing a space's occupancy and the space's Signed Distance Function (SDF). Leveraging this relationship, we propose to use the certification method of randomized smoothing (RS) to compute SDFs. Since RS' high computational cost prevents its practical usage as a way to compute SDFs, we propose an algorithm to efficiently run RS in low-dimensional applications, such as 3D space, by expressing RS' fundamental operations as Gaussian smoothing on pre-computed voxel grids. Our approach offers an innovative and practical tool to compute SDFs, validated through proof-of-concept experiments in novel view synthesis. This paper bridges two previously disparate areas of machine learning, opening new avenues for further exploration and potential cross-domain advancements.

Gabriel Mejia, Daniela Ruiz, Paula Cárdenas et al.

Spatial Transcriptomics is a novel technology that aligns histology images with spatially resolved gene expression profiles. Although groundbreaking, it struggles with gene capture yielding high corruption in acquired data. Given potential applications, recent efforts have focused on predicting transcriptomic profiles solely from histology images. However, differences in databases, preprocessing techniques, and training hyperparameters hinder a fair comparison between methods. To address these challenges, we present a systematically curated and processed database collected from 26 public sources, representing an 8.6-fold increase compared to previous works. Additionally, we propose a state-of-the-art transformer based completion technique for inferring missing gene expression, which significantly boosts the performance of transcriptomic profile predictions across all datasets. Altogether, our contributions constitute the most comprehensive benchmark of gene expression prediction from histology images to date and a stepping stone for future research on spatial transcriptomics.

Daniela Vega, Hannah V. Ceballos, Javier S. Vera et al.

Prenatal diagnosis of Congenital Heart Diseases (CHDs) holds great potential for Artificial Intelligence (AI)-driven solutions. However, collecting high-quality diagnostic data remains difficult due to the rarity of these conditions, resulting in imbalanced and low-quality datasets that hinder model performance. Moreover, no public efforts have been made to integrate multiple sources of information, such as imaging and clinical data, further limiting the ability of AI models to support and enhance clinical decision-making. To overcome these challenges, we introduce the Congenital Anomaly Recognition with Diagnostic Images and Unified Medical records (CARDIUM) dataset, the first publicly available multimodal dataset consolidating fetal ultrasound and echocardiographic images along with maternal clinical records for prenatal CHD detection. Furthermore, we propose a robust multimodal transformer architecture that incorporates a cross-attention mechanism to fuse feature representations from image and tabular data, improving CHD detection by 11% and 50% over image and tabular single-modality approaches, respectively, and achieving an F1 score of 79.8 $\pm$ 4.8% in the CARDIUM dataset. We will publicly release our dataset and code to encourage further research on this unexplored field. Our dataset and code are available at https://github.com/BCV-Uniandes/Cardium, and at the project website https://bcv-uniandes.github.io/CardiumPage/

Andrés Romero, Pablo Arbeláez, Luc Van Gool et al.

Cross-domain mapping has been a very active topic in recent years. Given one image, its main purpose is to translate it to the desired target domain, or multiple domains in the case of multiple labels. This problem is highly challenging due to three main reasons: (i) unpaired datasets, (ii) multiple attributes, and (iii) the multimodality (e.g., style) associated with the translation. Most of the existing state-of-the-art has focused only on two reasons, i.e. either on (i) and (ii), or (i) and (iii). In this work, we propose a joint framework (i, ii, iii) of diversity and multi-mapping image-to-image translations, using a single generator to conditionally produce countless and unique fake images that hold the underlying characteristics of the source image. Our system does not use style regularization, instead, it uses an embedding representation that we call domain embedding for both domain and style. Extensive experiments over different datasets demonstrate the effectiveness of our proposed approach in comparison with the state-of-the-art in both multi-label and multimodal problems. Additionally, our method is able to generalize under different scenarios: continuous style interpolation, continuous label interpolation, and fine-grained mapping. Code and pretrained models are available at https://github.com/BCV-Uniandes/SMIT.

Angela Castillo, Jonas Kohler, Juan C. Pérez et al.

This paper presents a comprehensive study on the role of Classifier-Free Guidance (CFG) in text-conditioned diffusion models from the perspective of inference efficiency. In particular, we relax the default choice of applying CFG in all diffusion steps and instead search for efficient guidance policies. We formulate the discovery of such policies in the differentiable Neural Architecture Search framework. Our findings suggest that the denoising steps proposed by CFG become increasingly aligned with simple conditional steps, which renders the extra neural network evaluation of CFG redundant, especially in the second half of the denoising process. Building upon this insight, we propose "Adaptive Guidance" (AG), an efficient variant of CFG, that adaptively omits network evaluations when the denoising process displays convergence. Our experiments demonstrate that AG preserves CFG's image quality while reducing computation by 25%. Thus, AG constitutes a plug-and-play alternative to Guidance Distillation, achieving 50% of the speed-ups of the latter while being training-free and retaining the capacity to handle negative prompts. Finally, we uncover further redundancies of CFG in the first half of the diffusion process, showing that entire neural function evaluations can be replaced by simple affine transformations of past score estimates. This method, termed LinearAG, offers even cheaper inference at the cost of deviating from the baseline model. Our findings provide insights into the efficiency of the conditional denoising process that contribute to more practical and swift deployment of text-conditioned diffusion models.

Soumick Chatterjee, Hendrik Mattern, Marc Dörner et al.

The human brain receives nutrients and oxygen through an intricate network of blood vessels. Pathology affecting small vessels, at the mesoscopic scale, represents a critical vulnerability within the cerebral blood supply and can lead to severe conditions, such as Cerebral Small Vessel Diseases. The advent of 7 Tesla MRI systems has enabled the acquisition of higher spatial resolution images, making it possible to visualise such vessels in the brain. However, the lack of publicly available annotated datasets has impeded the development of robust, machine learning-driven segmentation algorithms. To address this, the SMILE-UHURA challenge was organised. This challenge, held in conjunction with the ISBI 2023, in Cartagena de Indias, Colombia, aimed to provide a platform for researchers working on related topics. The SMILE-UHURA challenge addresses the gap in publicly available annotated datasets by providing an annotated dataset of Time-of-Flight angiography acquired with 7T MRI. This dataset was created through a combination of automated pre-segmentation and extensive manual refinement. In this manuscript, sixteen submitted methods and two baseline methods are compared both quantitatively and qualitatively on two different datasets: held-out test MRAs from the same dataset as the training data (with labels kept secret) and a separate 7T ToF MRA dataset where both input volumes and labels are kept secret. The results demonstrate that most of the submitted deep learning methods, trained on the provided training dataset, achieved reliable segmentation performance. Dice scores reached up to 0.838 $\pm$ 0.066 and 0.716 $\pm$ 0.125 on the respective datasets, with an average performance of up to 0.804 $\pm$ 0.15.

Daniela Ruiz, Paula Cárdenas, Leonardo Manrique et al.

Spatial Transcriptomics is a groundbreaking technology that integrates histology images with spatially resolved gene expression profiles. Among the various Spatial Transcriptomics techniques available, Visium has emerged as the most widely adopted. However, its accessibility is limited by high costs, the need for specialized expertise, and slow clinical integration. Additionally, gene capture inefficiencies lead to significant dropout, corrupting acquired data. To address these challenges, the deep learning community has explored the gene expression prediction task directly from histology images. Yet, inconsistencies in datasets, preprocessing, and training protocols hinder fair comparisons between models. To bridge this gap, we introduce SpaRED, a systematically curated database comprising 26 public datasets, providing a standardized resource for model evaluation. We further propose SpaCKLE, a state-of-the-art transformer-based gene expression completion model that reduces mean squared error by over 82.5% compared to existing approaches. Finally, we establish the SpaRED benchmark, evaluating eight state-of-the-art prediction models on both raw and SpaCKLE-completed data, demonstrating SpaCKLE substantially improves the results across all the gene expression prediction models. Altogether, our contributions constitute the most comprehensive benchmark of gene expression prediction from histology images to date and a stepping stone for future research on Spatial Transcriptomics.

Paula Cárdenas, Leonardo Manrique, Daniela Vega et al.

Computer Vision has proven to be a powerful tool for analyzing Spatial Transcriptomics (ST) data. However, current models that predict spatially resolved gene expression from histopathology images suffer from significant limitations due to data dropout. Most existing approaches rely on single-cell RNA sequencing references, making them dependent on alignment quality and external datasets while also risking batch effects and inherited dropout. In this paper, we address these limitations by introducing LGDiST, the first reference-free latent gene diffusion model for ST data dropout. We show that LGDiST outperforms the previous state-of-the-art in gene expression completion, with an average Mean Squared Error that is 18% lower across 26 datasets. Furthermore, we demonstrate that completing ST data with LGDiST improves gene expression prediction performance on six state-of-the-art methods up to 10% in MSE. A key innovation of LGDiST is using context genes previously considered uninformative to build a rich and biologically meaningful genetic latent space. Our experiments show that removing key components of LGDiST, such as the context genes, the ST latent space, and the neighbor conditioning, leads to considerable drops in performance. These findings underscore that the full architecture of LGDiST achieves substantially better performance than any of its isolated components.

Tobias Rueckert, David Rauber, Raphaela Maerkl et al.

Reliable recognition and localization of surgical instruments in endoscopic video recordings are foundational for a wide range of applications in computer- and robot-assisted minimally invasive surgery (RAMIS), including surgical training, skill assessment, and autonomous assistance. However, robust performance under real-world conditions remains a significant challenge. Incorporating surgical context - such as the current procedural phase - has emerged as a promising strategy to improve robustness and interpretability. To address these challenges, we organized the Surgical Procedure Phase, Keypoint, and Instrument Recognition (PhaKIR) sub-challenge as part of the Endoscopic Vision (EndoVis) challenge at MICCAI 2024. We introduced a novel, multi-center dataset comprising thirteen full-length laparoscopic cholecystectomy videos collected from three distinct medical institutions, with unified annotations for three interrelated tasks: surgical phase recognition, instrument keypoint estimation, and instrument instance segmentation. Unlike existing datasets, ours enables joint investigation of instrument localization and procedural context within the same data while supporting the integration of temporal information across entire procedures. We report results and findings in accordance with the BIAS guidelines for biomedical image analysis challenges. The PhaKIR sub-challenge advances the field by providing a unique benchmark for developing temporally aware, context-driven methods in RAMIS and offers a high-quality resource to support future research in surgical scene understanding.

Nicolás Ayobi, Santiago Rodríguez, Alejandra Pérez et al.

This paper presents the Holistic and Multi-Granular Surgical Scene Understanding of Prostatectomies (GraSP) dataset, a curated benchmark that models surgical scene understanding as a hierarchy of complementary tasks with varying levels of granularity. Our approach enables a multi-level comprehension of surgical activities, encompassing long-term tasks such as surgical phases and steps recognition and short-term tasks including surgical instrument segmentation and atomic visual actions detection. To exploit our proposed benchmark, we introduce the Transformers for Actions, Phases, Steps, and Instrument Segmentation (TAPIS) model, a general architecture that combines a global video feature extractor with localized region proposals from an instrument segmentation model to tackle the multi-granularity of our benchmark. Through extensive experimentation, we demonstrate the impact of including segmentation annotations in short-term recognition tasks, highlight the varying granularity requirements of each task, and establish TAPIS's superiority over previously proposed baselines and conventional CNN-based models. Additionally, we validate the robustness of our method across multiple public benchmarks, confirming the reliability and applicability of our dataset. This work represents a significant step forward in Endoscopic Vision, offering a novel and comprehensive framework for future research towards a holistic understanding of surgical procedures.

Gabriel Mejia, Paula Cárdenas, Daniela Ruiz et al.

Spatial transcriptomics is an emerging technology that aligns histopathology images with spatially resolved gene expression profiling. It holds the potential for understanding many diseases but faces significant bottlenecks such as specialized equipment and domain expertise. In this work, we present SEPAL, a new model for predicting genetic profiles from visual tissue appearance. Our method exploits the biological biases of the problem by directly supervising relative differences with respect to mean expression, and leverages local visual context at every coordinate to make predictions using a graph neural network. This approach closes the gap between complete locality and complete globality in current methods. In addition, we propose a novel benchmark that aims to better define the task by following current best practices in transcriptomics and restricting the prediction variables to only those with clear spatial patterns. Our extensive evaluation in two different human breast cancer datasets indicates that SEPAL outperforms previous state-of-the-art methods and other mechanisms of including spatial context.

Juan C. Pérez, Motasem Alfarra, Ali Thabet et al.

Deep Neural Networks (DNNs) lack robustness against imperceptible perturbations to their input. Face Recognition Models (FRMs) based on DNNs inherit this vulnerability. We propose a methodology for assessing and characterizing the robustness of FRMs against semantic perturbations to their input. Our methodology causes FRMs to malfunction by designing adversarial attacks that search for identity-preserving modifications to faces. In particular, given a face, our attacks find identity-preserving variants of the face such that an FRM fails to recognize the images belonging to the same identity. We model these identity-preserving semantic modifications via direction- and magnitude-constrained perturbations in the latent space of StyleGAN. We further propose to characterize the semantic robustness of an FRM by statistically describing the perturbations that induce the FRM to malfunction. Finally, we combine our methodology with a certification technique, thus providing (i) theoretical guarantees on the performance of an FRM, and (ii) a formal description of how an FRM may model the notion of face identity.

Angela Castillo, María Escobar, Juan C. Pérez et al.

Real-world Super-Resolution (SR) has been traditionally tackled by first learning a specific degradation model that resembles the noise and corruption artifacts in low-resolution imagery. Thus, current methods lack generalization and lose their accuracy when tested on unseen types of corruption. In contrast to the traditional proposal, we present Robust Super-Resolution (RSR), a method that leverages the generalization capability of adversarial attacks to tackle real-world SR. Our novel framework poses a paradigm shift in the development of real-world SR methods. Instead of learning a dataset-specific degradation, we employ adversarial attacks to create difficult examples that target the model's weaknesses. Afterward, we use these adversarial examples during training to improve our model's capacity to process noisy inputs. We perform extensive experimentation on synthetic and real-world images and empirically demonstrate that our RSR method generalizes well across datasets without re-training for specific noise priors. By using a single robust model, we outperform state-of-the-art specialized methods on real-world benchmarks.

Juan C. Pérez, Motasem Alfarra, Guillaume Jeanneret et al.

Deep learning models are prone to being fooled by imperceptible perturbations known as adversarial attacks. In this work, we study how equipping models with Test-time Transformation Ensembling (TTE) can work as a reliable defense against such attacks. While transforming the input data, both at train and test times, is known to enhance model performance, its effects on adversarial robustness have not been studied. Here, we present a comprehensive empirical study of the impact of TTE, in the form of widely-used image transforms, on adversarial robustness. We show that TTE consistently improves model robustness against a variety of powerful attacks without any need for re-training, and that this improvement comes at virtually no trade-off with accuracy on clean samples. Finally, we show that the benefits of TTE transfer even to the certified robustness domain, in which TTE provides sizable and consistent improvements.

Laura Daza, Juan C. Pérez, Pablo Arbeláez

The reliability of Deep Learning systems depends on their accuracy but also on their robustness against adversarial perturbations to the input data. Several attacks and defenses have been proposed to improve the performance of Deep Neural Networks under the presence of adversarial noise in the natural image domain. However, robustness in computer-aided diagnosis for volumetric data has only been explored for specific tasks and with limited attacks. We propose a new framework to assess the robustness of general medical image segmentation systems. Our contributions are two-fold: (i) we propose a new benchmark to evaluate robustness in the context of the Medical Segmentation Decathlon (MSD) by extending the recent AutoAttack natural image classification framework to the domain of volumetric data segmentation, and (ii) we present a novel lattice architecture for RObust Generic medical image segmentation (ROG). Our results show that ROG is capable of generalizing across different tasks of the MSD and largely surpasses the state-of-the-art under sophisticated adversarial attacks.

Arnaud Huaulmé, Duygu Sarikaya, Kévin Le Mut et al.

The "MIcro-Surgical Anastomose Workflow recognition on training sessions" (MISAW) challenge provided a data set of 27 sequences of micro-surgical anastomosis on artificial blood vessels. This data set was composed of videos, kinematics, and workflow annotations described at three different granularity levels: phase, step, and activity. The participants were given the option to use kinematic data and videos to develop workflow recognition models. Four tasks were proposed to the participants: three of them were related to the recognition of surgical workflow at three different granularity levels, while the last one addressed the recognition of all granularity levels in the same model. One ranking was made for each task. We used the average application-dependent balanced accuracy (AD-Accuracy) as the evaluation metric. This takes unbalanced classes into account and it is more clinically relevant than a frame-by-frame score. Six teams, including a non-competing team, participated in at least one task. All models employed deep learning models, such as CNN or RNN. The best models achieved more than 95% AD-Accuracy for phase recognition, 80% for step recognition, 60% for activity recognition, and 75% for all granularity levels. For high levels of granularity (i.e., phases and steps), the best models had a recognition rate that may be sufficient for applications such as prediction of remaining surgical time or resource management. However, for activities, the recognition rate was still low for applications that can be employed clinically. The MISAW data set is publicly available to encourage further research in surgical workflow recognition. It can be found at www.synapse.org/MISAW

Cristina González, María Escobar, Laura Daza et al.

Bone Age Assessment (BAA) is a task performed by radiologists to diagnose abnormal growth in a child. In manual approaches, radiologists take into account different identity markers when calculating bone age, i.e., chronological age and gender. However, the current automated Bone Age Assessment methods do not completely exploit the information present in the patient's metadata. With this lack of available methods as motivation, we present SIMBA: Specific Identity Markers for Bone Age Assessment. SIMBA is a novel approach for the task of BAA based on the use of identity markers. For this purpose, we build upon the state-of-the-art model, fusing the information present in the identity markers with the visual features created from the original hand radiograph. We then use this robust representation to estimate the patient's relative bone age: the difference between chronological age and bone age. We validate SIMBA on the Radiological Hand Pose Estimation dataset and find that it outperforms previous state-of-the-art methods. SIMBA sets a trend of a new wave of Computer-aided Diagnosis methods that incorporate all of the data that is available regarding a patient. To promote further research in this area and ensure reproducibility we will provide the source code as well as the pre-trained models of SIMBA.

Mauricio Neira, Catalina Gómez, John F. Suárez-Pérez et al.

We introduce MANTRA, an annotated dataset of 4869 transient and 71207 non-transient object lightcurves built from the Catalina Real Time Transient Survey. We provide public access to this dataset as a plain text file to facilitate standardized quantitative comparison of astronomical transient event recognition algorithms. Some of the classes included in the dataset are: supernovae, cataclysmic variables, active galactic nuclei, high proper motion stars, blazars and flares. As an example of the tasks that can be performed on the dataset we experiment with multiple data pre-processing methods, feature selection techniques and popular machine learning algorithms (Support Vector Machines, Random Forests and Neural Networks). We assess quantitative performance in two classification tasks: binary (transient/non-transient) and eight-class classification. The best performing algorithm in both tasks is the Random Forest Classifier. It achieves an F1-score of 96.25% in the binary classification and 52.79% in the eight-class classification. For the eight-class classification, non-transients ( 96.83% ) is the class with the highest F1-score, while the lowest corresponds to high-proper-motion stars ( 16.79% ); for supernovae it achieves a value of 54.57% , close to the average across classes. The next release of MANTRA includes images and benchmarks with deep learning models.

Motasem Alfarra, Juan C. Pérez, Adel Bibi et al.

This paper studies how encouraging semantically-aligned features during deep neural network training can increase network robustness. Recent works observed that Adversarial Training leads to robust models, whose learnt features appear to correlate with human perception. Inspired by this connection from robustness to semantics, we study the complementary connection: from semantics to robustness. To do so, we provide a robustness certificate for distance-based classification models (clustering-based classifiers). Moreover, we show that this certificate is tight, and we leverage it to propose ClusTR (Clustering Training for Robustness), a clustering-based and adversary-free training framework to learn robust models. Interestingly, \textit{ClusTR} outperforms adversarially-trained networks by up to $4\%$ under strong PGD attacks.

Catalina Gómez, Mauricio Neira, Marcela Hernández Hoyos et al.

Supervised classification of temporal sequences of astronomical images into meaningful transient astrophysical phenomena has been considered a hard problem because it requires the intervention of human experts. The classifier uses the expert's knowledge to find heuristic features to process the images, for instance, by performing image subtraction or by extracting sparse information such as flux time series, also known as light curves. We present a successful deep learning approach that learns directly from imaging data. Our method models explicitly the spatio-temporal patterns with Deep Convolutional Neural Networks and Gated Recurrent Units. We train these deep neural networks using 1.3 million real astronomical images from the Catalina Real-Time Transient Survey to classify the sequences into five different types of astronomical transient classes. The TAO-Net (for Transient Astronomical Objects Network) architecture outperforms the results from random forest classification on light curves by 10 percentage points as measured by the F1 score for each class; the average F1 over classes goes from $45\%$ with random forest classification to $55\%$ with TAO-Net. This achievement with TAO-Net opens the possibility to develop new deep learning architectures for early transient detection. We make available the training dataset and trained models of TAO-Net to allow for future extensions of this work.

Tobias Ross, Annika Reinke, Peter M. Full et al.

Intraoperative tracking of laparoscopic instruments is often a prerequisite for computer and robotic-assisted interventions. While numerous methods for detecting, segmenting and tracking of medical instruments based on endoscopic video images have been proposed in the literature, key limitations remain to be addressed: Firstly, robustness, that is, the reliable performance of state-of-the-art methods when run on challenging images (e.g. in the presence of blood, smoke or motion artifacts). Secondly, generalization; algorithms trained for a specific intervention in a specific hospital should generalize to other interventions or institutions. In an effort to promote solutions for these limitations, we organized the Robust Medical Instrument Segmentation (ROBUST-MIS) challenge as an international benchmarking competition with a specific focus on the robustness and generalization capabilities of algorithms. For the first time in the field of endoscopic image processing, our challenge included a task on binary segmentation and also addressed multi-instance detection and segmentation. The challenge was based on a surgical data set comprising 10,040 annotated images acquired from a total of 30 surgical procedures from three different types of surgery. The validation of the competing methods for the three tasks (binary segmentation, multi-instance detection and multi-instance segmentation) was performed in three different stages with an increasing domain gap between the training and the test data. The results confirm the initial hypothesis, namely that algorithm performance degrades with an increasing domain gap. While the average detection and segmentation quality of the best-performing algorithms is high, future research should concentrate on detection and segmentation of small, crossing, moving and transparent instrument(s) (parts).

Juan C. Pérez, Motasem Alfarra, Guillaume Jeanneret et al.

We revisit the benefits of merging classical vision concepts with deep learning models. In particular, we explore the effect on robustness against adversarial attacks of replacing the first layers of various deep architectures with Gabor layers, i.e. convolutional layers with filters that are based on learnable Gabor parameters. We observe that architectures enhanced with Gabor layers gain a consistent boost in robustness over regular models and preserve high generalizing test performance, even though these layers come at a negligible increase in the number of parameters. We then exploit the closed form expression of Gabor filters to derive an expression for a Lipschitz constant of such filters, and harness this theoretical result to develop a regularizer we use during training to further enhance network robustness. We conduct extensive experiments with various architectures (LeNet, AlexNet, VGG16 and WideResNet) on several datasets (MNIST, SVHN, CIFAR10 and CIFAR100) and demonstrate large empirical robustness gains. Furthermore, we experimentally show how our regularizer provides consistent robustness improvements.

Edgar Margffoy-Tuay, Juan C. Pérez, Emilio Botero et al.

We address the problem of segmenting an object given a natural language expression that describes it. Current techniques tackle this task by either (\textit{i}) directly or recursively merging linguistic and visual information in the channel dimension and then performing convolutions; or by (\textit{ii}) mapping the expression to a space in which it can be thought of as a filter, whose response is directly related to the presence of the object at a given spatial coordinate in the image, so that a convolution can be applied to look for the object. We propose a novel method that integrates these two insights in order to fully exploit the recursive nature of language. Additionally, during the upsampling process, we take advantage of the intermediate information generated when downsampling the image, so that detailed segmentations can be obtained. We compare our method against the state-of-the-art approaches in four standard datasets, in which it surpasses all previous methods in six of eight of the splits for this task.

Jordi Pont-Tuset, Federico Perazzi, Sergi Caelles et al.

We present the 2017 DAVIS Challenge on Video Object Segmentation, a public dataset, benchmark, and competition specifically designed for the task of video object segmentation. Following the footsteps of other successful initiatives, such as ILSVRC and PASCAL VOC, which established the avenue of research in the fields of scene classification and semantic segmentation, the DAVIS Challenge comprises a dataset, an evaluation methodology, and a public competition with a dedicated workshop co-located with CVPR 2017. The DAVIS Challenge follows up on the recent publication of DAVIS (Densely-Annotated VIdeo Segmentation), which has fostered the development of several novel state-of-the-art video object segmentation techniques. In this paper we describe the scope of the benchmark, highlight the main characteristics of the dataset, define the evaluation metrics of the competition, and present a detailed analysis of the results of the participants to the challenge.

Kevis-Kokitsi Maninis, Jordi Pont-Tuset, Pablo Arbeláez et al.

We present Convolutional Oriented Boundaries (COB), which produces multiscale oriented contours and region hierarchies starting from generic image classification Convolutional Neural Networks (CNNs). COB is computationally efficient, because it requires a single CNN forward pass for multi-scale contour detection and it uses a novel sparse boundary representation for hierarchical segmentation; it gives a significant leap in performance over the state-of-the-art, and it generalizes very well to unseen categories and datasets. Particularly, we show that learning to estimate not only contour strength but also orientation provides more accurate results. We perform extensive experiments for low-level applications on BSDS, PASCAL Context, PASCAL Segmentation, and NYUD to evaluate boundary detection performance, showing that COB provides state-of-the-art contours and region hierarchies in all datasets. We also evaluate COB on high-level tasks when coupled with multiple pipelines for object proposals, semantic contours, semantic segmentation, and object detection on MS-COCO, SBD, and PASCAL; showing that COB also improves the results for all tasks.

Kevis-Kokitsi Maninis, Jordi Pont-Tuset, Pablo Arbeláez et al.

This paper presents Deep Retinal Image Understanding (DRIU), a unified framework of retinal image analysis that provides both retinal vessel and optic disc segmentation. We make use of deep Convolutional Neural Networks (CNNs), which have proven revolutionary in other fields of computer vision such as object detection and image classification, and we bring their power to the study of eye fundus images. DRIU uses a base network architecture on which two set of specialized layers are trained to solve both the retinal vessel and optic disc segmentation. We present experimental validation, both qualitative and quantitative, in four public datasets for these tasks. In all of them, DRIU presents super-human performance, that is, it shows results more consistent with a gold standard than a second human annotator used as control.

Kevis-Kokitsi Maninis, Jordi Pont-Tuset, Pablo Arbeláez et al.

We present Convolutional Oriented Boundaries (COB), which produces multiscale oriented contours and region hierarchies starting from generic image classification Convolutional Neural Networks (CNNs). COB is computationally efficient, because it requires a single CNN forward pass for contour detection and it uses a novel sparse boundary representation for hierarchical segmentation; it gives a significant leap in performance over the state-of-the-art, and it generalizes very well to unseen categories and datasets. Particularly, we show that learning to estimate not only contour strength but also orientation provides more accurate results. We perform extensive experiments on BSDS, PASCAL Context, PASCAL Segmentation, and MS-COCO, showing that COB provides state-of-the-art contours, region hierarchies, and object proposals in all datasets.

Jordi Pont-Tuset, Pablo Arbeláez, Luc Van Gool

The recently presented COCO detection challenge will most probably be the reference benchmark in object detection in the next years. COCO is two orders of magnitude larger than Pascal and has four times the number of categories; so in all likelihood researchers will be faced with a number of new challenges. At this point, without any finished round of the competition, it is difficult for researchers to put their techniques in context, or in other words, to know how good their results are. In order to give a little context, this note evaluates a hypothetical object detector consisting in an oracle picking the best object proposal from a state-of-the-art technique. This oracle achieves a AP=0.292 in segmented objects and AP=0.317 in bounding boxes, showing that indeed the database is challenging, given that this value is the best one can expect if working on object proposals without refinement.

Saurabh Gupta, Pablo Arbeláez, Ross Girshick et al.

The goal of this work is to replace objects in an RGB-D scene with corresponding 3D models from a library. We approach this problem by first detecting and segmenting object instances in the scene using the approach from Gupta et al. [13]. We use a convolutional neural network (CNN) to predict the pose of the object. This CNN is trained using pixel normals in images containing rendered synthetic objects. When tested on real data, it outperforms alternative algorithms trained on real data. We then use this coarse pose estimate along with the inferred pixel support to align a small number of prototypical models to the data, and place the model that fits the best into the scene. We observe a 48% relative improvement in performance at the task of 3D detection over the current state-of-the-art [33], while being an order of magnitude faster at the same time.

Bharath Hariharan, Pablo Arbeláez, Ross Girshick et al.

Recognition algorithms based on convolutional networks (CNNs) typically use the output of the last layer as feature representation. However, the information in this layer may be too coarse to allow precise localization. On the contrary, earlier layers may be precise in localization but will not capture semantics. To get the best of both worlds, we define the hypercolumn at a pixel as the vector of activations of all CNN units above that pixel. Using hypercolumns as pixel descriptors, we show results on three fine-grained localization tasks: simultaneous detection and segmentation[22], where we improve state-of-the-art from 49.7[22] mean AP^r to 60.0, keypoint localization, where we get a 3.3 point boost over[20] and part labeling, where we show a 6.6 point gain over a strong baseline.

Saurabh Gupta, Ross Girshick, Pablo Arbeláez et al.

In this paper we study the problem of object detection for RGB-D images using semantically rich image and depth features. We propose a new geocentric embedding for depth images that encodes height above ground and angle with gravity for each pixel in addition to the horizontal disparity. We demonstrate that this geocentric embedding works better than using raw depth images for learning feature representations with convolutional neural networks. Our final object detection system achieves an average precision of 37.3%, which is a 56% relative improvement over existing methods. We then focus on the task of instance segmentation where we label pixels belonging to object instances found by our detector. For this task, we propose a decision forest approach that classifies pixels in the detection window as foreground or background using a family of unary and binary tests that query shape and geocentric pose features. Finally, we use the output from our object detectors in an existing superpixel classification framework for semantic scene segmentation and achieve a 24% relative improvement over current state-of-the-art for the object categories that we study. We believe advances such as those represented in this paper will facilitate the use of perception in fields like robotics.

Bharath Hariharan, Pablo Arbeláez, Ross Girshick et al.

We aim to detect all instances of a category in an image and, for each instance, mark the pixels that belong to it. We call this task Simultaneous Detection and Segmentation (SDS). Unlike classical bounding box detection, SDS requires a segmentation and not just a box. Unlike classical semantic segmentation, we require individual object instances. We build on recent work that uses convolutional neural networks to classify category-independent region proposals (R-CNN [16]), introducing a novel architecture tailored for SDS. We then use category-specific, top- down figure-ground predictions to refine our bottom-up proposals. We show a 7 point boost (16% relative) over our baselines on SDS, a 5 point boost (10% relative) over state-of-the-art on semantic segmentation, and state-of-the-art performance in object detection. Finally, we provide diagnostic tools that unpack performance and provide directions for future work.