Carlos Santiago

Gonçalo P. Matos, Carlos Santiago, João P. Costeira et al.

Following crop growth through the vegetative cycle allows farmers to predict fruit setting and yield in early stages, but it is a laborious and non-scalable task if performed by a human who has to manually measure fruit sizes with a caliper or dendrometers. In recent years, computer vision has been used to automate several tasks in precision agriculture, such as detecting and counting fruits, and estimating their size. However, the fundamental problem of matching the exact same fruits from one video, collected on a given date, to the fruits visible in another video, collected on a later date, which is needed to track fruits' growth through time, remains to be solved. Few attempts were made, but they either assume that the camera always starts from the same known position and that there are sufficiently distinct features to match, or they used other sources of data like GPS. Here we propose a new paradigm to tackle this problem, based on constellations of 3D centroids, and introduce a descriptor for very sparse 3D point clouds that can be used to match fruits across videos. Matching constellations instead of individual fruits is key to deal with non-rigidity, occlusions and challenging imagery with few distinct visual features to track. The results show that the proposed method can be successfully used to match fruits across videos and through time, and also to build an orchard map and later use it to locate the camera pose in 6DoF, thus providing a method for autonomous navigation of robots in the orchard and for selective fruit picking, for example.

Rita Pereira, M. Rita Verdelho, Catarina Barata et al.

Whole Slide Imaging (WSI), which involves high-resolution digital scans of pathology slides, has become the gold standard for cancer diagnosis, but its gigapixel resolution and the scarcity of annotated datasets present challenges for deep learning models. Multiple Instance Learning (MIL), a widely-used weakly supervised approach, bypasses the need for patch-level annotations. However, conventional MIL methods overlook the spatial relationships between patches, which are crucial for tasks such as cancer grading and diagnosis. To address this, graph-based approaches have gained prominence by incorporating spatial information through node connections. Despite their potential, both MIL and graph-based models are vulnerable to learning spurious associations, like color variations in WSIs, affecting their robustness. In this dissertation, we conduct an extensive comparison of multiple graph construction techniques, MIL models, graph-MIL approaches, and interventional training, introducing a new framework, Graph-based Multiple Instance Learning with Interventional Training (GMIL-IT), for WSI classification. We evaluate their impact on model generalization through domain shift analysis and demonstrate that graph-based models alone achieve the generalization initially anticipated from interventional training. Our code is available here: github.com/ritamartinspereira/GMIL-IT

Rui Daniel, M. Rita Verdelho, Catarina Barata et al.

Deep Learning for medical imaging faces challenges in adapting and generalizing to new contexts. Additionally, it often lacks sufficient labeled data for specific tasks requiring significant annotation effort. Continual Learning (CL) tackles adaptability and generalizability by enabling lifelong learning from a data stream while mitigating forgetting of previously learned knowledge. Active Learning (AL) reduces the number of required annotations for effective training. This work explores both approaches (CAL) to develop a novel framework for robust medical image analysis. Based on the automatic recognition of shifts in image characteristics, Replay-Base Architecture for Context Adaptation (RBACA) employs a CL rehearsal method to continually learn from diverse contexts, and an AL component to select the most informative instances for annotation. A novel approach to evaluate CAL methods is established using a defined metric denominated IL-Score, which allows for the simultaneous assessment of transfer learning, forgetting, and final model performance. We show that RBACA works in domain and class-incremental learning scenarios, by assessing its IL-Score on the segmentation and diagnosis of cardiac images. The results show that RBACA outperforms a baseline framework without CAL, and a state-of-the-art CAL method across various memory sizes and annotation budgets. Our code is available in https://github.com/RuiDaniel/RBACA .