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Publications

Publications by CTM

2025

A survey on cell nuclei instance segmentation and classification: Leveraging context and attention

Authors
Nunes, JD; Montezuma, D; Oliveira, D; Pereira, T; Cardoso, JS;

Publication
MEDICAL IMAGE ANALYSIS

Abstract
Nuclear-derived morphological features and biomarkers provide relevant insights regarding the tumour microenvironment, while also allowing diagnosis and prognosis in specific cancer types. However, manually annotating nuclei from the gigapixel Haematoxylin and Eosin (H&E)-stained Whole Slide Images (WSIs) is a laborious and costly task, meaning automated algorithms for cell nuclei instance segmentation and classification could alleviate the workload of pathologists and clinical researchers and at the same time facilitate the automatic extraction of clinically interpretable features for artificial intelligence (AI) tools. But due to high intra- and inter-class variability of nuclei morphological and chromatic features, as well as H&Estains susceptibility to artefacts, state-of-the-art algorithms cannot correctly detect and classify instances with the necessary performance. In this work, we hypothesize context and attention inductive biases in artificial neural networks (ANNs) could increase the performance and generalization of algorithms for cell nuclei instance segmentation and classification. To understand the advantages, use-cases, and limitations of context and attention-based mechanisms in instance segmentation and classification, we start by reviewing works in computer vision and medical imaging. We then conduct a thorough survey on context and attention methods for cell nuclei instance segmentation and classification from H&E-stained microscopy imaging, while providing a comprehensive discussion of the challenges being tackled with context and attention. Besides, we illustrate some limitations of current approaches and present ideas for future research. As a case study, we extend both a general (Mask-RCNN) and a customized (HoVer-Net) instance segmentation and classification methods with context- and attention-based mechanisms and perform a comparative analysis on a multicentre dataset for colon nuclei identification and counting. Although pathologists rely on context at multiple levels while paying attention to specific Regions of Interest (RoIs) when analysing and annotating WSIs, our findings suggest translating that domain knowledge into algorithm design is no trivial task, but to fully exploit these mechanisms in ANNs, the scientific understanding of these methods should first be addressed.

2025

Causal representation learning through higher-level information extraction

Authors
Silva, F; Oliveira, HP; Pereira, T;

Publication
ACM COMPUTING SURVEYS

Abstract
The large gap between the generalization level of state-of-the-art machine learning and human learning systems calls for the development of artificial intelligence (AI) models that are truly inspired by human cognition. In tasks related to image analysis, searching for pixel-level regularities has reached a power of information extraction still far from what humans capture with image-based observations. This leads to poor generalization when even small shifts occur at the level of the observations. We explore a perspective on this problem that is directed to learning the generative process with causality-related foundations, using models capable of combining symbolic manipulation, probabilistic reasoning, and pattern recognition abilities. We briefly review and explore connections of research from machine learning, cognitive science, and related fields of human behavior to support our perspective for the direction to more robust and human-like artificial learning systems.

2025

Evaluation of Lyrics Extraction from Folk Music Sheets Using Vision Language Models (VLMs)

Authors
Sales Mendes, A; Lozano Murciego, Á; Silva, LA; Jiménez Bravo, M; Navarro Cáceres, M; Bernardes, G;

Publication
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Abstract
Monodic folk music has traditionally been preserved in physical documents. It constitutes a vast archive that needs to be digitized to facilitate comprehensive analysis using AI techniques. A critical component of music score digitization is the transcription of lyrics, an extensively researched process in Optical Character Recognition (OCR) and document layout analysis. These fields typically require the development of specific models that operate in several stages: first, to detect the bounding boxes of specific texts, then to identify the language, and finally, to recognize the characters. Recent advances in vision language models (VLMs) have introduced multimodal capabilities, such as processing images and text, which are competitive with traditional OCR methods. This paper proposes an end-to-end system for extracting lyrics from images of handwritten musical scores. We aim to evaluate the performance of two state-of-the-art VLMs to determine whether they can eliminate the need to develop specialized text recognition and OCR models for this task. The results of the study, obtained from a dataset in a real-world application environment, are presented along with promising new research directions in the field. This progress contributes to preserving cultural heritage and opens up new possibilities for global analysis and research in folk music. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

2025

Model compression techniques in biometrics applications: A survey

Authors
Caldeira, E; Neto, PC; Huber, M; Damer, N; Sequeira, AF;

Publication
INFORMATION FUSION

Abstract
The development of deep learning algorithms has extensively empowered humanity's task automatization capacity. However, the huge improvement in the performance of these models is highly correlated with their increasing level of complexity, limiting their usefulness in human-oriented applications, which are usually deployed in resource-constrained devices. This led to the development of compression techniques that drastically reduce the computational and memory costs of deep learning models without significant performance degradation. These compressed models are especially essential when implementing multi-model fusion solutions where multiple models are required to operate simultaneously. This paper aims to systematize the current literature on this topic by presenting a comprehensive survey of model compression techniques in biometrics applications, namely quantization, knowledge distillation and pruning. We conduct a critical analysis of the comparative value of these techniques, focusing on their advantages and disadvantages and presenting suggestions for future work directions that can potentially improve the current methods. Additionally, we discuss and analyze the link between model bias and model compression, highlighting the need to direct compression research toward model fairness in future works.

2024

Incremental Redundancy HARQ Communication Schemes applied to Energy Efficient IoT Systems

Authors
Silva, SM; Almeida, NT;

Publication
2024 IEEE 22ND MEDITERRANEAN ELECTROTECHNICAL CONFERENCE, MELECON 2024

Abstract
The rapid proliferation of Internet of Things (IoT) systems, encompassing a wide range of devices and sensors with limited battery life, has highlighted the critical need for energy-efficient solutions to extend the operational lifespan of these battery-powered devices. One effective strategy for reducing energy consumption is minimizing the number and size of retransmitted packets in case of communication errors. Among the potential solutions, Incremental Redundancy Hybrid Automatic Repeat reQuest (IR-HARQ) communication schemes have emerged as particularly compelling options by adopting the best aspects of error control, namely, automatic repetition and variable redundancy. This work addresses the challenge by developing a simulator capable of executing and analysing several (H)ARQ schemes using different channel models, such as the Additive White Gaussian Noise (AWGN) and Gilbert-Elliott (GE) models. The primary objective is to compare their performance across multiple metrics, enabling a thorough evaluation of their capabilities. The results indicate that IR-HARQ outperforms alternative methods, especially in the presence of burst errors. Furthermore, its potential for further adaptation and enhancement opens up new ways for optimizing energy consumption and extending the lifespan of battery-powered IoT devices.

2024

Memory Optimization for FPGA Implementation of Correlation-Based Beamforming

Authors
Avelar, H; Ferreira, JC;

Publication
2024 IEEE 22ND MEDITERRANEAN ELECTROTECHNICAL CONFERENCE, MELECON 2024

Abstract
This paper proposes a method to avoid using a CORDIC or external memory to process the steering vectors to calculate the pseudospectrum of correlation-based beamforming algorithms. We show that if we decompose the steering vector equation, the size of the matrix to be saved in memory becomes independent of the antenna array size. Besides, the amount of data needed is small enough to be saved in the internal block RAMs of the FPGA SoC. Besides, this method greatly reduces the number of memory accesses, by offloading some processing to hardware, while keeping the frequency at 300MHz with a precision of 0.25 degrees. Finally, we show that this approach is scalable since the complexity grows logarithmically for bigger arrays, and the symmetry in the matrices obtained allows even more compact data.

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