Automated Detection of Clinical Entities in Lung and Breast Cancer Reports Using NLP Techniques

Research projects, including those focused on cancer, rely on the manual extraction of information from clinical reports. This process is time-consuming and prone to errors, limiting the efficiency of data-driven approaches in healthcare. To address these challenges, Natural Language Processing (NLP) offers an alternative for automating the extraction of relevant data from electronic health records (EHRs). In this study, we focus on lung and breast cancer due to their high incidence and the significant impact they have on public health. Early detection and effective data management in both types of cancer are crucial for improving patient outcomes. To enhance the accuracy and efficiency of data extraction, we utilized GMV's NLP tool uQuery, which excels at identifying relevant entities in clinical texts and converting them into standardized formats such as SNOMED and OMOP. uQuery not only detects and classifies entities but also associates them with contextual information, including negated entities, temporal aspects, and patient-related details. In this work, we explore the use of NLP techniques, specifically Named Entity Recognition (NER), to automatically identify and extract key clinical information from EHRs related to these two cancers. A dataset from Health Research Institute Hospital La Fe (IIS La Fe), comprising 200 annotated breast cancer and 400 lung cancer reports, was used, with eight clinical entities manually labeled using the Doccano platform. To perform NER, we fine-tuned the bsc-bio-ehr-en3 model, a RoBERTa-based biomedical linguistic model pre-trained in Spanish. Fine-tuning was performed using the Transformers architecture, enabling accurate recognition of clinical entities in these cancer types. Our results demonstrate strong overall performance, particularly in identifying entities like MET and PAT, although challenges remain with less frequent entities like EVOL.

Lung Nodule-SSM: Self-Supervised Lung Nodule Detection and Classification in Thoracic CT Images

Lung cancer remains among the deadliest types of cancer in recent decades, and early lung nodule detection is crucial for improving patient outcomes. The limited availability of annotated medical imaging data remains a bottleneck in developing accurate computer-aided diagnosis (CAD) systems. Self-supervised learning can help leverage large amounts of unlabeled data to develop more robust CAD systems. With the recent advent of transformer-based architecture and their ability to generalize to unseen tasks, there has been an effort within the healthcare community to adapt them to various medical downstream tasks. Thus, we propose a novel "LungNodule-SSM" method, which utilizes selfsupervised learning with DINOv2 as a backbone to enhance lung nodule detection and classification without annotated data. Our methodology has two stages: firstly, the DINOv2 model is pre-trained on unlabeled CT scans to learn robust feature representations, then secondly, these features are fine-tuned using transformer-based architectures for lesionlevel detection and accurate lung nodule diagnosis. The proposed method has been evaluated on the challenging LUNA 16 dataset, consisting of 888 CT scans, and compared with SOTA methods. Our experimental results show the superiority of our proposed method with an accuracy of 98.37%, explaining its effectiveness in lung nodule detection. The source code, datasets, and pre-processed data can be accessed using the link:https://github.com/EMeRALDsNRPU/Lung-Nodule-SSM-Self-Supervised-Lung-Nodule-Detection-and-Classification/tree/main

Towards Facilitated Fairness Assessment of AI-based Skin Lesion Classifiers Through GenAI-based Image Synthesis

Recent advancements in Deep Learning and its application on the edge hold great potential for the revolution of routine screenings for skin cancers like Melanoma. Along with the anticipated benefits of this technology, potential dangers arise from unforseen and inherent biases. Thus, assessing and improving the fairness of such systems is of utmost importance. A key challenge in fairness assessment is to ensure that the evaluation dataset is sufficiently representative of different Personal Identifiable Information (PII) (sex, age, and race) and other minority groups. Against the backdrop of this challenge, this study leverages the state-of-the-art Generative AI (GenAI) LightningDiT model to assess the fairness of publicly available melanoma classifiers. The results suggest that fairness assessment using highly realistic synthetic data is a promising direction. Yet, our findings indicate that verifying fairness becomes difficult when the melanoma-detection model used for evaluation is trained on data that differ from the dataset underpinning the synthetic images. Nonetheless, we propose that our approach offers a valuable new avenue for employing synthetic data to gauge and enhance fairness in medical-imaging GenAI systems.

CLIP-IT: CLIP-based Pairing for Histology Images Classification

Multimodal learning has shown significant promise for improving medical image analysis by integrating information from complementary data sources. This is widely employed for training vision-language models (VLMs) for cancer detection based on histology images and text reports. However, one of the main limitations in training these VLMs is the requirement for large paired datasets, raising concerns over privacy, and data collection, annotation, and maintenance costs. To address this challenge, we introduce CLIP-IT method to train a vision backbone model to classify histology images by pairing them with privileged textual information from an external source. At first, the modality pairing step relies on a CLIP-based model to match histology images with semantically relevant textual report data from external sources, creating an augmented multimodal dataset without the need for manually paired samples. Then, we propose a multimodal training procedure that distills the knowledge from the paired text modality to the unimodal image classifier for enhanced performance without the need for the textual data during inference. A parameter-efficient fine-tuning method is used to efficiently address the misalignment between the main (image) and paired (text) modalities. During inference, the improved unimodal histology classifier is used, with only minimal additional computational complexity. Our experiments on challenging PCAM, CRC, and BACH histology image datasets show that CLIP-IT can provide a cost-effective approach to leverage privileged textual information and outperform unimodal classifiers for histology.

MSAD-Net: Multiscale and Spatial Attention-based Dense Network for Lung Cancer Classification

Lung cancer, a severe form of malignant tumor that originates in the tissues of the lungs, can be fatal if not detected in its early stages. It ranks among the top causes of cancer-related mortality worldwide. Detecting lung cancer manually using chest X-Ray image or Computational Tomography (CT) scans image poses significant challenges for radiologists. Hence, there is a need for automatic diagnosis system of lung cancers from radiology images. With the recent emergence of deep learning, particularly through Convolutional Neural Networks (CNNs), the automated detection of lung cancer has become a much simpler task. Nevertheless, numerous researchers have addressed that the performance of conventional CNNs may be hindered due to class imbalance issue, which is prevalent in medical images. In this research work, we have proposed a novel CNN architecture ``Multi-Scale Dense Network (MSD-Net)'' (trained-from-scratch). The novelties we bring in the proposed model are (I) We introduce novel dense modules in the 4th block and 5th block of the CNN model. We have leveraged 3 depthwise separable convolutional (DWSC) layers, and one 1x1 convolutional layer in each dense module, in order to reduce complexity of the model considerably. (II) Additionally, we have incorporated one skip connection from 3rd block to 5th block and one parallel branch connection from 4th block to Global Average Pooling (GAP) layer. We have utilized dilated convolutional layer (with dilation rate=2) in the last parallel branch in order to extract multi-scale features. Extensive experiments reveal that our proposed model has outperformed latest CNN model ConvNext-Tiny, recent trend Vision Transformer (ViT), Pooling-based ViT (PiT), and other existing models by significant margins.

Deep Learning Enabled Segmentation, Classification and Risk Assessment of Cervical Cancer

Cervical cancer, the fourth leading cause of cancer in women globally, requires early detection through Pap smear tests to identify precancerous changes and prevent disease progression. In this study, we performed a focused analysis by segmenting the cellular boundaries and drawing bounding boxes to isolate the cancer cells. A novel Deep Learning (DL) architecture, the ``Multi-Resolution Fusion Deep Convolutional Network", was proposed to effectively handle images with varying resolutions and aspect ratios, with its efficacy showcased using the SIPaKMeD dataset. The performance of this DL model was observed to be similar to the state-of-the-art models, with accuracy variations of a mere 2\% to 3\%, achieved using just 1.7 million learnable parameters, which is approximately 85 times less than the VGG-19 model. Furthermore, we introduced a multi-task learning technique that simultaneously performs segmentation and classification tasks and begets an Intersection over Union score of 0.83 and a classification accuracy of 90\%. The final stage of the workflow employs a probabilistic approach for risk assessment, extracting feature vectors to predict the likelihood of normal cells progressing to malignant states, which can be utilized for the prognosis of cervical cancer.

Efficient Parameter Adaptation for Multi-Modal Medical Image Segmentation and Prognosis

Cancer detection and prognosis relies heavily on medical imaging, particularly CT and PET scans. Deep Neural Networks (DNNs) have shown promise in tumor segmentation by fusing information from these modalities. However, a critical bottleneck exists: the dependency on CT-PET data concurrently for training and inference, posing a challenge due to the limited availability of PET scans. Hence, there is a clear need for a flexible and efficient framework that can be trained with the widely available CT scans and can be still adapted for PET scans when they become available. In this work, we propose a parameter-efficient multi-modal adaptation (PEMMA) framework for lightweight upgrading of a transformer-based segmentation model trained only on CT scans such that it can be efficiently adapted for use with PET scans when they become available. This framework is further extended to perform prognosis task maintaining the same efficient cross-modal fine-tuning approach. The proposed approach is tested with two well-known segementation backbones, namely UNETR and Swin UNETR. Our approach offers two main advantages. Firstly, we leverage the inherent modularity of the transformer architecture and perform low-rank adaptation (LoRA) as well as decomposed low-rank adaptation (DoRA) of the attention weights to achieve parameter-efficient adaptation. Secondly, by minimizing cross-modal entanglement, PEMMA allows updates using only one modality without causing catastrophic forgetting in the other. Our method achieves comparable performance to early fusion, but with only 8% of the trainable parameters, and demonstrates a significant +28% Dice score improvement on PET scans when trained with a single modality. Furthermore, in prognosis, our method improves the concordance index by +10% when adapting a CT-pretrained model to include PET scans, and by +23% when adapting for both PET and EHR data.

Learning from Anatomy: Supervised Anatomical Pretraining (SAP) for Improved Metastatic Bone Disease Segmentation in Whole-Body MRI

The segmentation of metastatic bone disease (MBD) in whole-body MRI (WB-MRI) is a challenging problem. Due to varying appearances and anatomical locations of lesions, ambiguous boundaries, and severe class imbalance, obtaining reliable segmentations requires large, well-annotated datasets capturing lesion variability. Generating such datasets requires substantial time and expertise, and is prone to error. While self-supervised learning (SSL) can leverage large unlabeled datasets, learned generic representations often fail to capture the nuanced features needed for accurate lesion detection. In this work, we propose a Supervised Anatomical Pretraining (SAP) method that learns from a limited dataset of anatomical labels. First, an MRI-based skeletal segmentation model is developed and trained on WB-MRI scans from healthy individuals for high-quality skeletal delineation. Then, we compare its downstream efficacy in segmenting MBD on a cohort of 44 patients with metastatic prostate cancer, against both a baseline random initialization and a state-of-the-art SSL method. SAP significantly outperforms both the baseline and SSL-pretrained models, achieving a normalized surface Dice of 0.76 and a Dice coefficient of 0.64. The method achieved a lesion detection F2 score of 0.44, improving on 0.24 (baseline) and 0.31 (SSL). When considering only clinically relevant lesions larger than 1~ml, SAP achieves a detection sensitivity of 100% in 28 out of 32 patients. Learning bone morphology from anatomy yields an effective and domain-relevant inductive bias that can be leveraged for the downstream segmentation task of bone lesions. All code and models are made publicly available.

The Application of Deep Learning for Lymph Node Segmentation: A Systematic Review

Automatic lymph node segmentation is the cornerstone for advances in computer vision tasks for early detection and staging of cancer. Traditional segmentation methods are constrained by manual delineation and variability in operator proficiency, limiting their ability to achieve high accuracy. The introduction of deep learning technologies offers new possibilities for improving the accuracy of lymph node image analysis. This study evaluates the application of deep learning in lymph node segmentation and discusses the methodologies of various deep learning architectures such as convolutional neural networks, encoder-decoder networks, and transformers in analyzing medical imaging data across different modalities. Despite the advancements, it still confronts challenges like the shape diversity of lymph nodes, the scarcity of accurately labeled datasets, and the inadequate development of methods that are robust and generalizable across different imaging modalities. To the best of our knowledge, this is the first study that provides a comprehensive overview of the application of deep learning techniques in lymph node segmentation task. Furthermore, this study also explores potential future research directions, including multimodal fusion techniques, transfer learning, and the use of large-scale pre-trained models to overcome current limitations while enhancing cancer diagnosis and treatment planning strategies.

Predicting Surgical Safety Margins in Osteosarcoma Knee Resections: An Unsupervised Approach

According to the Pan American Health Organization, the number of cancer cases in Latin America was estimated at 4.2 million in 2022 and is projected to rise to 6.7 million by 2045. Osteosarcoma, one of the most common and deadly bone cancers affecting young people, is difficult to detect due to its unique texture and intensity. Surgical removal of osteosarcoma requires precise safety margins to ensure complete resection while preserving healthy tissue. Therefore, this study proposes a method for estimating the confidence interval of surgical safety margins in osteosarcoma surgery around the knee. The proposed approach uses MRI and X-ray data from open-source repositories, digital processing techniques, and unsupervised learning algorithms (such as k-means clustering) to define tumor boundaries. Experimental results highlight the potential for automated, patient-specific determination of safety margins.