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Raquel de Melo Barbosa

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Open access 2026

AI-Based Whole Slide Image Analysis for Automated Breast Cancer Classification

Breast cancer remains a global health challenge, representing one of the most prevalent and deadly cancers worldwide. Histopathological analysis of biopsy specimens is the gold standard for diagnosis, but the increasing demand for assessments often surpasses the capacity of available pathologists. To address this challenge, this study proposes a lightweight framework for breast cancer classification from whole-slide images (WSIs) that decouples feature extraction, tile-to-slide aggregation, and classification. Tile-level descriptors are extracted using a pre-trained VGG19 network modified with a configurable max pooling layer that controls descriptor dimensionality. The resulting tile embeddings are summarized into compact slide-level representations by Incremental Uniform Attention (IUA), a non-parametric, permutation-invariant aggregation operator with linear time complexity and no trainable parameters. The slide descriptors are then classified using six conventional machine learning models. The framework was evaluated on $3{,}241$ WSIs from the TCGA-BRCA and HCMI-CMDC cohorts using a nested cross-validation protocol. In its most compact configuration, the pipeline reduced the stored feature representation from approximately 1.7 TB to 64 MB, corresponding to a reduction of more than $26{,}000\times $ , while preserving high predictive performance. Support Vector Machine yielded the most stable results across pooling configurations, whereas Logistic Regression achieved the highest overall performance in the most compact setting, with 99.7% accuracy, 99.8% F1-score, and 99.99% AUC. A theoretical analysis further shows that IUA has linear time and auxiliary-memory complexity with respect to the number of tiles per slide, in contrast to the quadratic complexity of self-attention-based Multiple Instance Learning (MIL) aggregators. These results indicate that compact, parameter-free aggregation can substantially reduce computational and storage costs, enabling large-scale WSI cohort analysis on conventional hardware.

Wysterlânya K. P. Barros, Raquel de Melo Barbosa, Marcelo A. C. Fernandes · 0 citations
Open access Jul 2026

Deep learning-based prediction of drug-target interactions between antiviral drugs and SARS-CoV-2 proteins using an image-based representation approach.

Drug repurposing offers a time-efficient strategy for identifying therapeutics against emerging pathogens such as SARS-CoV-2. In this study, we apply MPS2IT-DTI (Molecule and Protein Sequence to Image Transformer for Drug-Target Interaction), a deep learning framework that represents molecular (SMILES) and protein (FASTA) sequences as images using k-mer frequency encoding, enabling convolutional neural networks to capture spatial compositional patterns associated with biochemical interactions. A curated dataset (BindingDB-FDA) containing 83,165 binding interactions from 1640 FDA-approved ligands and 3270 targets was constructed from BindingDB, with binding scores derived from the KIBA scoring system. An enhanced variant, MPS2IT+MN, incorporating max-norm regularization, was introduced to improve generalization. The model was applied to predict binding affinities between 33 FDA-approved antiviral drugs and six key SARS-CoV-2 non-structural proteins. Results consistently identified five antivirals - MK-5172 (Grazoprevir), Simeprevir, Lopinavir, Etravirine, and Atazanavir - as top-ranked candidates across all targets. Comparative analysis with the MT-DTI model demonstrated competitive and, in several cases, superior ranking performance despite a simpler architecture. Importantly, these predictions are supported by independent experimental and clinical evidence, highlighting the potential of image-based representations as a computationally efficient and biologically meaningful approach for drug-target interaction prediction and drug repurposing.

Jackson G. de Souza, Marcelo A. C. Fernandes, Raquel de Melo Barbosa · 0 citations