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Publications

Publications by CTM

2024

An interpretable machine learning system for colorectal cancer diagnosis from pathology slides

Authors
Neto, PC; Montezuma, D; Oliveira, SP; Oliveira, D; Fraga, J; Monteiro, A; Monteiro, J; Ribeiro, L; Gonçalves, S; Reinhard, S; Zlobec, I; Pinto, IM; Cardoso, JS;

Publication
NPJ PRECISION ONCOLOGY

Abstract
Considering the profound transformation affecting pathology practice, we aimed to develop a scalable artificial intelligence (AI) system to diagnose colorectal cancer from whole-slide images (WSI). For this, we propose a deep learning (DL) system that learns from weak labels, a sampling strategy that reduces the number of training samples by a factor of six without compromising performance, an approach to leverage a small subset of fully annotated samples, and a prototype with explainable predictions, active learning features and parallelisation. Noting some problems in the literature, this study is conducted with one of the largest WSI colorectal samples dataset with approximately 10,500 WSIs. Of these samples, 900 are testing samples. Furthermore, the robustness of the proposed method is assessed with two additional external datasets (TCGA and PAIP) and a dataset of samples collected directly from the proposed prototype. Our proposed method predicts, for the patch-based tiles, a class based on the severity of the dysplasia and uses that information to classify the whole slide. It is trained with an interpretable mixed-supervision scheme to leverage the domain knowledge introduced by pathologists through spatial annotations. The mixed-supervision scheme allowed for an intelligent sampling strategy effectively evaluated in several different scenarios without compromising the performance. On the internal dataset, the method shows an accuracy of 93.44% and a sensitivity between positive (low-grade and high-grade dysplasia) and non-neoplastic samples of 0.996. On the external test samples varied with TCGA being the most challenging dataset with an overall accuracy of 84.91% and a sensitivity of 0.996.

2024

Comprehensive Review: Machine and Deep Learning in Brain Stroke Diagnosis

Authors
Fernandes, JND; Cardoso, VEM; Comesaña-Campos, A; Pinheira, A;

Publication
SENSORS

Abstract
Brain stroke, or a cerebrovascular accident, is a devastating medical condition that disrupts the blood supply to the brain, depriving it of oxygen and nutrients. Each year, according to the World Health Organization, 15 million people worldwide experience a stroke. This results in approximately 5 million deaths and another 5 million individuals suffering permanent disabilities. The complex interplay of various risk factors highlights the urgent need for sophisticated analytical methods to more accurately predict stroke risks and manage their outcomes. Machine learning and deep learning technologies offer promising solutions by analyzing extensive datasets including patient demographics, health records, and lifestyle choices to uncover patterns and predictors not easily discernible by humans. These technologies enable advanced data processing, analysis, and fusion techniques for a comprehensive health assessment. We conducted a comprehensive review of 25 review papers published between 2020 and 2024 on machine learning and deep learning applications in brain stroke diagnosis, focusing on classification, segmentation, and object detection. Furthermore, all these reviews explore the performance evaluation and validation of advanced sensor systems in these areas, enhancing predictive health monitoring and personalized care recommendations. Moreover, we also provide a collection of the most relevant datasets used in brain stroke analysis. The selection of the papers was conducted according to PRISMA guidelines. Furthermore, this review critically examines each domain, identifies current challenges, and proposes future research directions, emphasizing the potential of AI methods in transforming health monitoring and patient care.

2024

Optimized reconstruction of the absorption spectra of kidney tissues from the spectra of tissue components using the least squares method

Authors
Pinheiro, MR; Fernandes, LE; Carneiro, IC; Carvalho, SD; Henrique, RM; Tuchin, VV; Oliveira, HP; Oliveira, LM;

Publication
JOURNAL OF BIOPHOTONICS

Abstract
With the objective of developing new methods to acquire diagnostic information, the reconstruction of the broadband absorption coefficient spectra (mu a[lambda]) of healthy and chromophobe renal cell carcinoma kidney tissues was performed. By performing a weighted sum of the absorption spectra of proteins, DNA, oxygenated, and deoxygenated hemoglobin, lipids, water, melanin, and lipofuscin, it was possible to obtain a good match of the experimental mu a(lambda) of both kidney conditions. The weights used in those reconstructions were estimated using the least squares method, and assuming a total water content of 77% in both kidney tissues, it was possible to calculate the concentrations of the other tissue components. It has been shown that with the development of cancer, the concentrations of proteins, DNA, oxygenated hemoglobin, lipids, and lipofuscin increase, and the concentration of melanin decreases. Future studies based on minimally invasive spectral measurements will allow cancer diagnosis using the proposed approach.

2024

Light in evaluation of molecular diffusion in tissues: Discrimination of pathologies

Authors
Oliveira, LR; Pinheiro, MR; Tuchina, DK; Timoshina, PA; Carvalho, MI; Oliveira, LM;

Publication
ADVANCED DRUG DELIVERY REVIEWS

Abstract
The evaluation of the diffusion properties of different molecules in tissues is a subject of great interest in various fields, such as dermatology/cosmetology, clinical medicine, implantology and food preservation. In this review, a discussion of recent studies that used kinetic spectroscopy measurements to evaluate such diffusion properties in various tissues is made. By immersing ex vivo tissues in agents or by topical application of those agents in vivo, their diffusion properties can be evaluated by kinetic collimated transmittance or diffuse reflectance spectroscopy. Using this method, recent studies were able to discriminate the diffusion properties of agents between healthy and diseased tissues, especially in the cases of cancer and diabetes mellitus. In the case of cancer, it was also possible to evaluate an increase of 5% in the mobile water content from the healthy to the cancerous colorectal and kidney tissues. Considering the application of some agents to living organisms or food products to protect them from deterioration during low temperature preservation (cryopreservation), and knowing that such agent inclusion may be reversed, some studies in these fields are also discussed. Considering the broadband application of the optical spectroscopy evaluation of the diffusion properties of agents in tissues and the physiological diagnostic data that such method can acquire, further studies concerning the optimization of fruit sweetness or evaluation of poison diffusion in tissues or antidote application for treatment optimization purposes are indicated as future perspectives.

2024

Classification of healthy and cancerous colon tissues based on absorption coefficient spectra

Authors
Kupriyanov, V; Pinheiro, MR; Carvalho, SD; Carneiro, IC; Henrique, RM; Tuchin, VV; Oliveira, LM; Amouroux, M; Kistenev, Y; Blondel, W;

Publication
TISSUE OPTICS AND PHOTONICS III

Abstract
Colorectal cancer is the second most common cancer and the second with the highest associated deaths in the world. Methods used in clinical practice for colon cancer diagnosis are fairly effective but quite unpleasant and not always applicable in situations where the patient has symptoms of colonic obstruction. This problem can be solved by the use of optical methods that can be applied less invasively. This study presents the results of classification of cancerous and healthy colon tissue absorption coefficient spectra. The absorption coefficient was measured using direct calculations from the total reflectance and total transmittance spectra obtained ex vivo. Classification was performed using support vector machine, multilayer perceptron and linear discriminant analysis.

2024

Analysis of the experimental absorption spectrum of the rabbit lung and identification of its components

Authors
Pinheiro, MR; Tuchin, VV; Oliveira, LM;

Publication
JOURNAL OF BIOPHOTONICS

Abstract
The broadband absorption coefficient spectrum of the rabbit lung presents some particular characteristics that allow the identification of the chromophores in this tissue. By performing a weighted combination of the absorption spectra of water, hemoglobin, DNA, proteins and the pigments melanin and lipofuscin, it was possible to obtain a good match to the experimental absorption spectrum of the lung. Such reconstruction provided reasonable information about the contents of the tissue components in the lung tissue, and allowed to identify a similar accumulation of melanin and lipofuscin. The broadband absorption coefficient spectrum of the rabbit lung was reconstructed from the absorption spectra of tissue components. The similar accumulation of melanin and lipofuscin was retrieved from the broadband baseline in the absorption coefficient spectrum, and the calculation of the absorption fold ratios for proteins, DNA and hemoglobin provided good results. The method used is innovative and can be improved to allow the quantification of tissue components concentrations directly. image

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