Breast cancer is a prominent health concern worldwide, currently being the secondmost common and second-deadliest type of cancer in women. While current breast cancer diagnosis mainly relies on mammography imaging, in recent years the use of thermography for breast cancer imaging has been garnering growing popularity. Thermographic imaging relies on infrared cameras to capture body-emitted heat distributions. While these heat signatures have proven useful for computer-vision systems for accurate breast cancer segmentation and classification, prior work often relies on handcrafted feature engineering or complex architectures, potentially limiting the comparability and applicability of these methods. In this work, we present a novel algorithm for both breast cancer classification and segmentation. Rather than focusing efforts on manual feature and architecture engineering, our algorithm focuses on leveraging an informative, learned feature space, thus making our solution simpler to use and extend to other frameworks and downstream tasks, as well as more applicable to data-scarce settings. Our classification produces SOTA results, while we are the first work to produce segmentation regions studied in this paper.
Accurate screening of cancer types is crucial for effective cancer detection and precise treatment selection. However, the association between gene expression profiles and tumors is often limited to a small number of biomarker genes. While computational methods using nature-inspired algorithms have shown promise in selecting predictive genes, existing techniques are limited by inefficient search and poor generalization across diverse datasets. This study presents a framework termed Evolutionary Optimized Diverse Ensemble Learning (EODE) to improve ensemble learning for cancer classification from gene expression data. The EODE methodology combines an intelligent grey wolf optimization algorithm for selective feature space reduction, guided random injection modeling for ensemble diversity enhancement, and subset model optimization for synergistic classifier combinations. Extensive experiments were conducted across 35 gene expression benchmark datasets encompassing varied cancer types. Results demonstrated that EODE obtained significantly improved screening accuracy over individual and conventionally aggregated models. The integrated optimization of advanced feature selection, directed specialized modeling, and cooperative classifier ensembles helps address key challenges in current nature-inspired approaches. This provides an effective framework for robust and generalized ensemble learning with gene expression biomarkers. Specifically, we have opened EODE source code on Github at https://github.com/wangxb96/EODE.
This paper proposes an efficient system for classifying cervical cancer cells using pre-trained convolutional neural networks (CNNs). We first fine-tune five pre-trained CNNs and minimize the overall cost of misclassification by prioritizing accuracy for certain classes that have higher associated costs or importance. To further enhance the performance of the models, supervised contrastive learning is included to make the models more adept at capturing important features and patterns. Extensive experimentation are conducted to evaluate the proposed system on the SIPaKMeD dataset. The experimental results demonstrate the effectiveness of the developed system, achieving an accuracy of 97.29%. To make our system more trustworthy, we have employed several explainable AI techniques to interpret how the models reached a specific decision. The implementation of the system can be found at - https://github.com/isha-67/CervicalCancerStudy.
Traditional deep learning approaches for breast cancer classification has predominantly concentrated on single-view analysis. In clinical practice, however, radiologists concurrently examine all views within a mammography exam, leveraging the inherent correlations in these views to effectively detect tumors. Acknowledging the significance of multi-view analysis, some studies have introduced methods that independently process mammogram views, either through distinct convolutional branches or simple fusion strategies, inadvertently leading to a loss of crucial inter-view correlations. In this paper, we propose an innovative multi-view network exclusively based on transformers to address challenges in mammographic image classification. Our approach introduces a novel shifted window-based dynamic attention block, facilitating the effective integration of multi-view information and promoting the coherent transfer of this information between views at the spatial feature map level. Furthermore, we conduct a comprehensive comparative analysis of the performance and effectiveness of transformer-based models under diverse settings, employing the CBIS-DDSM and Vin-Dr Mammo datasets. Our code is publicly available at https://github.com/prithuls/MV-Swin-T
Breast Ultrasound plays a vital role in cancer diagnosis as a non-invasive approach with cost-effective. In recent years, with the development of deep learning, many CNN-based approaches have been widely researched in both tumor localization and cancer classification tasks. Even though previous single models achieved great performance in both tasks, these methods have some limitations in inference time, GPU requirement, and separate fine-tuning for each model. In this study, we aim to redesign and build end-to-end multi-task architecture to conduct both segmentation and classification. With our proposed approach, we achieved outstanding performance and time efficiency, with 79.8% and 86.4% in DeepLabV3+ architecture in the segmentation task.
Benefiting from the advancements in deep learning, various genomic analytical techniques, such as survival analysis, classification of tumors and their subtypes, and exploration of specific pathways, have significantly enhanced our understanding of the biological mechanisms driving cancer. However, the overfitting issue, arising from the limited number of patient samples, poses a challenge in improving the accuracy of genome analysis by deepening the neural network. Furthermore, it remains uncertain whether novel approaches such as the sparsely gated mixture of expert (MOE) and self-attention mechanisms can improve the accuracy of genomic analysis. In this paper, we introduce a novel sparsely gated RNA-seq analysis framework called Gene-MOE. This framework exploits the potential of the MOE layers and the proposed mixture of attention expert (MOAE) layers to enhance the analysis accuracy. Additionally, it addresses overfitting challenges by integrating pan-cancer information from 33 distinct cancer types through pre-training.We pre-trained Gene-MOE on TCGA pan-cancer RNA-seq dataset with 33 cancer types. Subsequently, we conducted experiments involving cancer classification and survival analysis based on the pre-trained Gene-MOE. According to the survival analysis results on 14 cancer types, Gene-MOE outperformed state-of-the-art models on 12 cancer types. Through detailed feature analysis, we found that the Gene-MOE model could learn rich feature representations of high-dimensional genes. According to the classification results, the total accuracy of the classification model for 33 cancer classifications reached 95.8%, representing the best performance compared to state-of-the-art models. These results indicate that Gene-MOE holds strong potential for use in cancer classification and survival analysis.
Visual explanation (attention)-guided learning uses not only labels but also explanations to guide model reasoning process. While visual attention-guided learning has shown promising results, it requires a large number of explanation annotations that are time-consuming to prepare. However, in many real-world situations, it is usually desired to prompt the model with visual attention without model retraining. For example, when doing AI-assisted cancer classification on a medical image, users (e.g., clinicians) can provide the AI model with visual attention prompt on which areas are indispensable and which are precluded. Despite its promising objectives, achieving visual attention-prompted prediction presents several major challenges: 1) How can the visual prompt be effectively integrated into the model's reasoning process? 2) How should the model handle samples that lack visual prompts? 3) What is the impact on the model's performance when a visual prompt is imperfect? This paper introduces a novel framework for attention-prompted prediction and learning, utilizing visual prompts to steer the model's reasoning process. To improve performance in non-prompted situations and align it with prompted scenarios, we propose a co-training approach for both non-prompted and prompted models, ensuring they share similar parameters and activations. Additionally, for instances where the visual prompt does not encompass the entire input image, we have developed innovative attention prompt refinement methods. These methods interpolate the incomplete prompts while maintaining alignment with the model's explanations. Extensive experiments on four datasets demonstrate the effectiveness of our proposed framework in enhancing predictions for samples both with and without prompt.
The use of artificial intelligence to enable precision medicine and decision support systems through the analysis of pathology images has the potential to revolutionize the diagnosis and treatment of cancer. Such applications will depend on models' abilities to capture the diverse patterns observed in pathology images. To address this challenge, we present Virchow, a foundation model for computational pathology. Using self-supervised learning empowered by the DINOv2 algorithm, Virchow is a vision transformer model with 632 million parameters trained on 1.5 million hematoxylin and eosin stained whole slide images from diverse tissue and specimen types, which is orders of magnitude more data than previous works. The Virchow model enables the development of a pan-cancer detection system with 0.949 overall specimen-level AUC across 17 different cancer types, while also achieving 0.937 AUC on 7 rare cancer types. The Virchow model sets the state-of-the-art on the internal and external image tile level benchmarks and slide level biomarker prediction tasks. The gains in performance highlight the importance of training on massive pathology image datasets, suggesting scaling up the data and network architecture can improve the accuracy for many high-impact computational pathology applications where limited amounts of training data are available.
Skin cancer is a treatable disease if discovered early. We provide a production-specific solution to the skin cancer classification problem that matches human performance in melanoma identification by training a vision transformer on melanoma medical images annotated by experts. Since inference cost, both time and memory wise is important in practice, we employ knowledge distillation to obtain a model that retains 98.33% of the teacher's balanced multi-class accuracy, at a fraction of the cost. Memory-wise, our model is 49.60% smaller than the teacher. Time-wise, our solution is 69.25% faster on GPU and 97.96% faster on CPU. By adding classification heads at each level of the transformer and employing a cascading distillation process, we improve the balanced multi-class accuracy of the base model by 2.1%, while creating a range of models of various sizes but comparable performance. We provide the code at https://github.com/Longman-Stan/SkinDistilVit.
Addressing fairness in lesion classification from dermatological images is crucial due to variations in how skin diseases manifest across skin tones. However, the absence of skin tone labels in public datasets hinders building a fair classifier. To date, such skin tone labels have been estimated prior to fairness analysis in independent studies using the Individual Typology Angle (ITA). Briefly, ITA calculates an angle based on pixels extracted from skin images taking into account the lightness and yellow-blue tints. These angles are then categorised into skin tones that are subsequently used to analyse fairness in skin cancer classification. In this work, we review and compare four ITA-based approaches of skin tone classification on the ISIC18 dataset, a common benchmark for assessing skin cancer classification fairness in the literature. Our analyses reveal a high disagreement among previously published studies demonstrating the risks of ITA-based skin tone estimation methods. Moreover, we investigate the causes of such large discrepancy among these approaches and find that the lack of diversity in the ISIC18 dataset limits its use as a testbed for fairness analysis. Finally, we recommend further research on robust ITA estimation and diverse dataset acquisition with skin tone annotation to facilitate conclusive fairness assessments of artificial intelligence tools in dermatology. Our code is available at https://github.com/tkalbl/RevisitingSkinToneFairness.
Cancer is a complex disease characterized by uncontrolled cell growth and proliferation. T cell receptors (TCRs) are essential proteins for the adaptive immune system, and their specific recognition of antigens plays a crucial role in the immune response against diseases, including cancer. The diversity and specificity of TCRs make them ideal for targeting cancer cells, and recent advancements in sequencing technologies have enabled the comprehensive profiling of TCR repertoires. This has led to the discovery of TCRs with potent anti-cancer activity and the development of TCR-based immunotherapies. In this study, we investigate the use of sparse coding for the multi-class classification of TCR protein sequences with cancer categories as target labels. Sparse coding is a popular technique in machine learning that enables the representation of data with a set of informative features and can capture complex relationships between amino acids and identify subtle patterns in the sequence that might be missed by low-dimensional methods. We first compute the k-mers from the TCR sequences and then apply sparse coding to capture the essential features of the data. To improve the predictive performance of the final embeddings, we integrate domain knowledge regarding different types of cancer properties. We then train different machine learning (linear and non-linear) classifiers on the embeddings of TCR sequences for the purpose of supervised analysis. Our proposed embedding method on a benchmark dataset of TCR sequences significantly outperforms the baselines in terms of predictive performance, achieving an accuracy of 99.8\%. Our study highlights the potential of sparse coding for the analysis of TCR protein sequences in cancer research and other related fields.
The recent development of high-throughput sequencing creates a large collection of multi-omics data, which enables researchers to better investigate cancer molecular profiles and cancer taxonomy based on molecular subtypes. Integrating multi-omics data has been proven to be effective for building more precise classification models. Current multi-omics integrative models mainly use early fusion by concatenation or late fusion based on deep neural networks. Due to the nature of biological systems, graphs are a better representation of bio-medical data. Although few graph neural network (GNN) based multi-omics integrative methods have been proposed, they suffer from three common disadvantages. One is most of them use only one type of connection, either inter-omics or intra-omic connection; second, they only consider one kind of GNN layer, either graph convolution network (GCN) or graph attention network (GAT); and third, most of these methods lack testing on a more complex cancer classification task. We propose a novel end-to-end multi-omics GNN framework for accurate and robust cancer subtype classification. The proposed model utilizes multi-omics data in the form of heterogeneous multi-layer graphs that combines both inter-omics and intra-omic connections from established biological knowledge. The proposed model incorporates learned graph features and global genome features for accurate classification. We test the proposed model on TCGA Pan-cancer dataset and TCGA breast cancer dataset for molecular subtype and cancer subtype classification, respectively. The proposed model outperforms four current state-of-the-art baseline models in multiple evaluation metrics. The comparative analysis of GAT-based models and GCN-based models reveals that GAT-based models are preferred for smaller graphs with less information and GCN-based models are preferred for larger graphs with extra information.
Well-annotated medical datasets enable deep neural networks (DNNs) to gain strong power in extracting lesion-related features. Building such large and well-designed medical datasets is costly due to the need for high-level expertise. Model pre-training based on ImageNet is a common practice to gain better generalization when the data amount is limited. However, it suffers from the domain gap between natural and medical images. In this work, we pre-train DNNs on ultrasound (US) domains instead of ImageNet to reduce the domain gap in medical US applications. To learn US image representations based on unlabeled US videos, we propose a novel meta-learning-based contrastive learning method, namely Meta Ultrasound Contrastive Learning (Meta-USCL). To tackle the key challenge of obtaining semantically consistent sample pairs for contrastive learning, we present a positive pair generation module along with an automatic sample weighting module based on meta-learning. Experimental results on multiple computer-aided diagnosis (CAD) problems, including pneumonia detection, breast cancer classification, and breast tumor segmentation, show that the proposed self-supervised method reaches state-of-the-art (SOTA). The codes are available at https://github.com/Schuture/Meta-USCL.
Traditionally, deep learning methods for breast cancer classification perform a single-view analysis. However, radiologists simultaneously analyze all four views that compose a mammography exam, owing to the correlations contained in mammography views, which present crucial information for identifying tumors. In light of this, some studies have started to propose multi-view methods. Nevertheless, in such existing architectures, mammogram views are processed as independent images by separate convolutional branches, thus losing correlations among them. To overcome such limitations, in this paper, we propose a methodological approach for multi-view breast cancer classification based on parameterized hypercomplex neural networks. Thanks to hypercomplex algebra properties, our networks are able to model, and thus leverage, existing correlations between the different views that comprise a mammogram, thus mimicking the reading process performed by clinicians. This happens because hypercomplex networks capture both global properties, as standard neural models, as well as local relations, i.e., inter-view correlations, which real-valued networks fail at modeling. We define architectures designed to process two-view exams, namely PHResNets, and four-view exams, i.e., PHYSEnet and PHYBOnet. Through an extensive experimental evaluation conducted with publicly available datasets, we demonstrate that our proposed models clearly outperform real-valued counterparts and state-of-the-art methods, proving that breast cancer classification benefits from the proposed multi-view architectures. We also assess the method generalizability beyond mammogram analysis by considering different benchmarks, as well as a finer-scaled task such as segmentation. Full code and pretrained models for complete reproducibility of our experiments are freely available at https://github.com/ispamm/PHBreast.
While machine learning is currently transforming the field of histopathology, the domain lacks a comprehensive evaluation of state-of-the-art models based on essential but complementary quality requirements beyond a mere classification accuracy. In order to fill this gap, we developed a new methodology to extensively evaluate a wide range of classification models, including recent vision transformers, and convolutional neural networks such as: ConvNeXt, ResNet (BiT), Inception, ViT and Swin transformer, with and without supervised or self-supervised pretraining. We thoroughly tested the models on five widely used histopathology datasets containing whole slide images of breast, gastric, and colorectal cancer and developed a novel approach using an image-to-image translation model to assess the robustness of a cancer classification model against stain variations. Further, we extended existing interpretability methods to previously unstudied models and systematically reveal insights of the models' classifications strategies that can be transferred to future model architectures.
For early breast cancer detection, regular screening with mammography imaging is recommended. Routinary examinations result in datasets with a predominant amount of negative samples. A potential solution to such class-imbalance is joining forces across multiple institutions. Developing a collaborative computer-aided diagnosis system is challenging in different ways. Patient privacy and regulations need to be carefully respected. Data across institutions may be acquired from different devices or imaging protocols, leading to heterogeneous non-IID data. Also, for learning-based methods, new optimization strategies working on distributed data are required. Recently, federated learning has emerged as an effective tool for collaborative learning. In this setting, local models perform computation on their private data to update the global model. The order and the frequency of local updates influence the final global model. Hence, the order in which samples are locally presented to the optimizers plays an important role. In this work, we define a memory-aware curriculum learning method for the federated setting. Our curriculum controls the order of the training samples paying special attention to those that are forgotten after the deployment of the global model. Our approach is combined with unsupervised domain adaptation to deal with domain shift while preserving data privacy. We evaluate our method with three clinical datasets from different vendors. Our results verify the effectiveness of federated adversarial learning for the multi-site breast cancer classification. Moreover, we show that our proposed memory-aware curriculum method is beneficial to further improve classification performance. Our code is publicly available at: https://github.com/ameliajimenez/curriculum-federated-learning.
The lack of explainability is one of the most prominent disadvantages of deep learning applications in omics. This "black box" problem can undermine the credibility and limit the practical implementation of biomedical deep learning models. Here we present XOmiVAE, a variational autoencoder (VAE) based interpretable deep learning model for cancer classification using high-dimensional omics data. XOmiVAE is capable of revealing the contribution of each gene and latent dimension for each classification prediction, and the correlation between each gene and each latent dimension. It is also demonstrated that XOmiVAE can explain not only the supervised classification but the unsupervised clustering results from the deep learning network. To the best of our knowledge, XOmiVAE is one of the first activation level-based interpretable deep learning models explaining novel clusters generated by VAE. The explainable results generated by XOmiVAE were validated by both the performance of downstream tasks and the biomedical knowledge. In our experiments, XOmiVAE explanations of deep learning based cancer classification and clustering aligned with current domain knowledge including biological annotation and academic literature, which shows great potential for novel biomedical knowledge discovery from deep learning models.
In clinical applications, neural networks must focus on and highlight the most important parts of an input image. Soft-Attention mechanism enables a neural network toachieve this goal. This paper investigates the effectiveness of Soft-Attention in deep neural architectures. The central aim of Soft-Attention is to boost the value of important features and suppress the noise-inducing features. We compare the performance of VGG, ResNet, InceptionResNetv2 and DenseNet architectures with and without the Soft-Attention mechanism, while classifying skin lesions. The original network when coupled with Soft-Attention outperforms the baseline[16] by 4.7% while achieving a precision of 93.7% on HAM10000 dataset [25]. Additionally, Soft-Attention coupling improves the sensitivity score by 3.8% compared to baseline[31] and achieves 91.6% on ISIC-2017 dataset [2]. The code is publicly available at github.
Data augmentation has proved extremely useful by increasing training data variance to alleviate overfitting and improve deep neural networks' generalization performance. In medical image analysis, a well-designed augmentation policy usually requires much expert knowledge and is difficult to generalize to multiple tasks due to the vast discrepancies among pixel intensities, image appearances, and object shapes in different medical tasks. To automate medical data augmentation, we propose a regularized adversarial training framework via two min-max objectives and three differentiable augmentation models covering affine transformation, deformation, and appearance changes. Our method is more automatic and efficient than previous automatic augmentation methods, which still rely on pre-defined operations with human-specified ranges and costly bi-level optimization. Extensive experiments demonstrated that our approach, with less training overhead, achieves superior performance over state-of-the-art auto-augmentation methods on both tasks of 2D skin cancer classification and 3D organs-at-risk segmentation.
Globally, Skin carcinoma is among the most lethal diseases. Millions of people are diagnosed with this cancer every year. Sill, early detection can decrease the medication cost and mortality rate substantially. The recent improvement in automated cancer classification using deep learning methods has reached a human-level performance requiring a large amount of annotated data assembled in one location, yet, finding such conditions usually is not feasible. Recently, federated learning (FL) has been proposed to train decentralized models in a privacy-preserved fashion depending on labeled data at the client-side, which is usually not available and costly. To address this, we propose \verb!FedPerl!, a semi-supervised federated learning method. Our method is inspired by peer learning from educational psychology and ensemble averaging from committee machines. FedPerl builds communities based on clients' similarities. Then it encourages communities members to learn from each other to generate more accurate pseudo labels for the unlabeled data. We also proposed the peer anonymization (PA) technique to anonymize clients. As a core component of our method, PA is orthogonal to other methods without additional complexity and reduces the communication cost while enhancing performance. Finally, we propose a dynamic peer-learning policy that controls the learning stream to avoid any degradation in the performance, especially for individual clients. Our experimental setup consists of 71,000 skin lesion images collected from 5 publicly available datasets. We test our method in four different scenarios in SSFL. With few annotated data, FedPerl is on par with a state-of-the-art method in skin lesion classification in the standard setup while outperforming SSFLs and the baselines by 1.8% and 15.8%, respectively. Also, it generalizes better to unseen clients while being less sensitive to noisy ones.