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Publications

Publications by CTM

2025

Transformer-Based Models for Probabilistic Time Series Forecasting with Explanatory Variables

Authors
Caetano, R; Oliveira, JM; Ramos, P;

Publication
MATHEMATICS

Abstract
Accurate demand forecasting is essential for retail operations as it directly impacts supply chain efficiency, inventory management, and financial performance. However, forecasting retail time series presents significant challenges due to their irregular patterns, hierarchical structures, and strong dependence on external factors such as promotions, pricing strategies, and socio-economic conditions. This study evaluates the effectiveness of Transformer-based architectures, specifically Vanilla Transformer, Informer, Autoformer, ETSformer, NSTransformer, and Reformer, for probabilistic time series forecasting in retail. A key focus is the integration of explanatory variables, such as calendar-related indicators, selling prices, and socio-economic factors, which play a crucial role in capturing demand fluctuations. This study assesses how incorporating these variables enhances forecast accuracy, addressing a research gap in the comprehensive evaluation of explanatory variables within multiple Transformer-based models. Empirical results, based on the M5 dataset, show that incorporating explanatory variables generally improves forecasting performance. Models leveraging these variables achieve up to 12.4% reduction in Normalized Root Mean Squared Error (NRMSE) and 2.9% improvement in Mean Absolute Scaled Error (MASE) compared to models that rely solely on past sales. Furthermore, probabilistic forecasting enhances decision making by quantifying uncertainty, providing more reliable demand predictions for risk management. These findings underscore the effectiveness of Transformer-based models in retail forecasting and emphasize the importance of integrating domain-specific explanatory variables to achieve more accurate, context-aware predictions in dynamic retail environments.

2025

Deep Learning-Driven Integration of Multimodal Data for Material Property Predictions

Authors
Costa, V; Oliveira, JM; Ramos, P;

Publication

Abstract
This study investigates the integration of deep learning for single-modality and multimodal data within materials science. Traditional methods for materials discovery are often resource-intensive and slow, prompting the exploration of machine learning to streamline the prediction of material properties. While single-modality models have been effective, they often miss the complexities inherent in material data. The paper explores multimodal data integration—combining text, images, and tabular data—and demonstrates its potential to improve predictive accuracy. Utilizing the Alexandria dataset, the research introduces a custom methodology involving multimodal data creation, model tuning with AutoGluon framework, and evaluation through targeted fusion techniques. Results reveal that multimodal approaches enhance predictive accuracy and efficiency, particularly when text and image data are integrated. However, challenges remain in predicting complex features like band gaps. Future directions include incorporating new data types and refining specialized models to improve materials discovery and innovation.

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

CNN explanation methods for ordinal regression tasks

Authors
Gómez, JB; Cruz, RPM; Cardoso, JS; Gutiérrez, PA; Martínez, CH;

Publication
Neurocomputing

Abstract

2025

CNN explanation methods for ordinal regression tasks

Authors
Barbero-Gómez, J; Cruz, RPM; Cardoso, JS; Gutiérrez, PA; Hervás-Martínez, C;

Publication
NEUROCOMPUTING

Abstract
The use of Convolutional Neural Network (CNN) models for image classification tasks has gained significant popularity. However, the lack of interpretability in CNN models poses challenges for debugging and validation. To address this issue, various explanation methods have been developed to provide insights into CNN models. This paper focuses on the validity of these explanation methods for ordinal regression tasks, where the classes have a predefined order relationship. Different modifications are proposed for two explanation methods to exploit the ordinal relationships between classes: Grad-CAM based on Ordinal Binary Decomposition (GradOBDCAM) and Ordinal Information Bottleneck Analysis (OIBA). The performance of these modified methods is compared to existing popular alternatives. Experimental results demonstrate that GradOBD-CAM outperforms other methods in terms of interpretability for three out of four datasets, while OIBA achieves superior performance compared to IBA.

2025

Learning Ordinality in Semantic Segmentation

Authors
Cruz, RPM; Cristino, R; Cardoso, JS;

Publication
IEEE ACCESS

Abstract
Semantic segmentation consists of predicting a semantic label for each image pixel. While existing deep learning approaches achieve high accuracy, they often overlook the ordinal relationships between classes, which can provide critical domain knowledge (e.g., the pupil lies within the iris, and lane markings are part of the road). This paper introduces novel methods for spatial ordinal segmentation that explicitly incorporate these inter-class dependencies. By treating each pixel as part of a structured image space rather than as an independent observation, we propose two regularization terms and a new metric to enforce ordinal consistency between neighboring pixels. Two loss regularization terms and one metric are proposed for structural ordinal segmentation, which penalizes predictions of non-ordinal adjacent classes. Five biomedical datasets and multiple configurations of autonomous driving datasets demonstrate the efficacy of the proposed methods. Our approach achieves improvements in ordinal metrics and enhances generalization, with up to a 15.7% relative increase in the Dice coefficient. Importantly, these benefits come without additional inference time costs. This work highlights the significance of spatial ordinal relationships in semantic segmentation and provides a foundation for further exploration in structured image representations.

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