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Publicações

Publicações por CTM

2025

Beyond Accuracy: The Role of Calibration in Computational Pathology

Autores
Nunes, JD; Montezuma, D; Oliveira, D; Pereira, T; Zlobec, I; Cardoso, JS;

Publicação
2025 INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS, IJCNN

Abstract
Deep learning in computational pathology (CPath) has rapidly advanced in recent years. Research has primarily focused on enhancing accuracy and interpretability across various histology image analysis tasks, from tile-level to slide-level foundation models and novel multiple instance learning (MIL) strategies. However, it is equally important for models to provide well-calibrated confidence estimates. Due to factors such as dataset bias, overfitting, and limited training data, existing models tend to be overly confident on test sets. Promising solutions to address this issue include temperature scaling, a post-hoc method that adjusts logits using a single scalar value. However, the role of calibration in CPath is yet to be clarified. In this study, we evaluate temperature scaling and linear temperature scaling for CPath tasks, analyzing their impact on recalibration in both in-domain and out-of-domain distributions. The results show the limitations of current probability calibration techniques and motivate future work.

2025

H&E to IHC virtual staining methods in breast cancer: an overview and benchmarking

Autores
Klöckner, P; Teixeira, J; Montezuma, D; Fraga, J; Horlings, HM; Cardoso, JS; Oliveira, SP;

Publicação
NPJ DIGITAL MEDICINE

Abstract
Immunohistochemistry (IHC) is crucial for the clinical categorisation of breast cancer cases. Deep generative models may offer a cost-effective alternative by virtually generating IHC images from hematoxylin and eosin samples. This review explores the state-of-the-art in virtual staining for breast cancer biomarkers (HER2, PgR, ER and Ki-67) and benchmarks several models on public datasets. It serves as a resource for researchers and clinicians interested in applying or developing virtual staining techniques.

2025

Intrinsically-Interpretable Siamese Networks for Identity Recognition

Autores
Rocha, MA; Cardoso, JS; Montenegro, H;

Publicação
2025 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS, ICCVW

Abstract
Deep learning models have excelled in computer vision tasks in the past decade, but their lack of transparency raises ethical and legal concerns, especially in high-stakes areas such as surveillance and law enforcement. As such, regulations like the European Union's General Data Protection Regulation are now demanding interpretable Artificial Intelligence systems. This paper focuses on automatic face recognition, where existing systems lack interpretability and research into explainable alternatives is limited. To address this gap, we propose two interpretable facial verification models based on Siamese Networks that match and compare semantically-aligned local regions in the images. Experiments show these models rival and even outperform traditional baselines while offering clearer, more accountable explanations, advancing ethical and legally compliant facial recognition.

2025

GANs vs. Diffusion Models for virtual staining with the HER2match dataset

Autores
Klöckner, P; Teixeira, J; Montezuma, D; Cardoso, JS; Horlings, HM; de Oliveira, SP;

Publicação
CoRR

Abstract

2025

Evaluating Dense Model-based Approaches for Multimodal Medical Case Retrieval

Autores
Pires, C; Nunes, S; Teixeira, LF;

Publicação
Inf. Retr. Res. J.

Abstract
Medical case retrieval plays a crucial role in clinical decision-making by enabling healthcare professionals to find relevant cases based on patient records, diagnostic images, and textual descriptions. Given the inherently multimodal nature of medical data, effective retrieval requires models that can bridge the gap between different modalities. Traditional retrieval approaches often rely on unimodal representations, limiting their ability to capture cross-modal relationships. Recent advances in dense model-based techniques have shown promise in overcoming these limitations by encoding multimodal information into a shared latent space, facilitating retrieval based on semantic similarity. This paper investigates the potential of dense models to enhance multimodal search systems. We evaluate various dense model-based approaches to assess which model characteristics have the greatest impact on retrieval effectiveness, using the medical case-based retrieval task from ImageCLEFmed 2013 as a benchmark. Our findings indicate that different dense model approaches substantially impact retrieval effectiveness, and that applying the CombMAX fusion methodto combine their output results further improves effectiveness. Extending context length, however, yielded mixed results depending on the input data. Additionally, domain-specific models—those trained on medical data—outperformed general models trained on broad, non-specialized datasets within their respective fields. Furthermore, when text is the dominant information source, text-only models surpassed multimodal models

2025

Expanding Relevance Judgments for Medical Case-based Retrieval Task with Multimodal LLMs

Autores
Pires, C; Nunes, S; Teixeira, LF;

Publicação
CoRR

Abstract

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