Breast cancer risk prediction using machine learning: a systematic review.

Background: Breast cancer is the leading cause of cancer-related fatalities among women worldwide. Conventional screening and risk prediction models primarily rely on demographic and patient clinical history to devise policies and estimate likelihood. However, recent advancements in artificial intelligence (AI) techniques, particularly deep learning (DL), have shown promise in the development of personalized risk models. These models leverage individual patient information obtained from medical imaging and associated reports. In this systematic review, we thoroughly investigated the existing literature on the application of DL to digital mammography, radiomics, genomics, and clinical information for breast cancer risk assessment. We critically analyzed these studies and discussed their findings, highlighting the promising prospects of DL techniques for breast cancer risk prediction. Additionally, we explored ongoing research initiatives and potential future applications of AI-driven approaches to further improve breast cancer risk prediction, thereby facilitating more effective screening and personalized risk management strategies. Objective and methods: This study presents a comprehensive overview of imaging and non-imaging features used in breast cancer risk prediction using traditional and AI models. The features reviewed in this study included imaging, radiomics, genomics, and clinical features. Furthermore, this survey systematically presented DL methods developed for breast cancer risk prediction, aiming to be useful for both beginners and advanced-level researchers. Results: A total of 600 articles were identified, 20 of which met the set criteria and were selected. Parallel benchmarking of DL models, along with natural language processing (NLP) applied to imaging and non-imaging features, could allow clinicians and researchers to gain greater awareness as they consider the clinical deployment or development of new models. This review provides a comprehensive guide for understanding the current status of breast cancer risk assessment using AI. Conclusion: This study offers investigators a different perspective on the use of AI for breast cancer risk prediction, incorporating numerous imaging and non-imaging features.

Multi-Level Swin Transformer Enabled Automatic Segmentation and Classification of Breast Metastases.

Detection of metastatic breast cancer lesions is a challenging task in breast cancer treatment. The recent advancements in deep learning gained attention owing to its robustness, particularly in addressing automated segmentation and classification issues in medical images. In this paper, we proposed a modified Swin Transformer model (mST) integrated with a novel Multi-Level Adaptive Feature Fusion (MLAFF) Module. We constructed a modified Swin Transformer network comprising of a Local Transferable MSA (LT-MSA) and a Global Transferable MSA (GT-MSA) in addition to a Feed Forward Network (FFN). Our novel Multi-Level Adaptive Feature Fusion (MLAFF) module iteratively combines the features throughout multiple transformers. We utilized a pre-trained deep learning model U-Net and trained it on mammography utilizing Transfer Learning for automated segmentation. The proposed method, mST-MLAFF, is used for breast cancer classification into normal, benign, and malignant classes. Our model outperformed comparison methods based on U-Net and Swin Transformer in breast metastatic lesion segmentation on the seven benchmark datasets, namely INBreast, DDSM, MIAS, CBIS-DDSM, MIMBCD-UI, KAU-BCMD, and Mammographic Masses. Our model achieved 98% Dice-Similarity coefficient (DSC) for segmentation and an average of 94.5% accuracy for classification, whereas U-Net based model achieved 92% DSC and Swin Transformer achieved 93% DSC. Extensive performance evaluation of our model on benchmark datasets shows the potential of our model for breast cancer classification.Clinical relevance- This research work is focused on assisting the radiologist in the early detection and classification of breast cancer. A single mammography image is analyzed in less than a minute for automated segmentation and classification into malignant and benign classes.

Deep learning, radiomics and radiogenomics applications in the digital breast tomosynthesis: a systematic review.

BACKGROUND: Recent advancements in computing power and state-of-the-art algorithms have helped in more accessible and accurate diagnosis of numerous diseases. In addition, the development of de novo areas in imaging science, such as radiomics and radiogenomics, have been adding more to personalize healthcare to stratify patients better. These techniques associate imaging phenotypes with the related disease genes. Various imaging modalities have been used for years to diagnose breast cancer. Nonetheless, digital breast tomosynthesis (DBT), a state-of-the-art technique, has produced promising results comparatively. DBT, a 3D mammography, is replacing conventional 2D mammography rapidly. This technological advancement is key to AI algorithms for accurately interpreting medical images. OBJECTIVE AND METHODS: This paper presents a comprehensive review of deep learning (DL), radiomics and radiogenomics in breast image analysis. This review focuses on DBT, its extracted synthetic mammography (SM), and full-field digital mammography (FFDM). Furthermore, this survey provides systematic knowledge about DL, radiomics, and radiogenomics for beginners and advanced-level researchers. RESULTS: A total of 500 articles were identified, with 30 studies included as the set criteria. Parallel benchmarking of radiomics, radiogenomics, and DL models applied to the DBT images could allow clinicians and researchers alike to have greater awareness as they consider clinical deployment or development of new models. This review provides a comprehensive guide to understanding the current state of early breast cancer detection using DBT images. CONCLUSION: Using this survey, investigators with various backgrounds can easily seek interdisciplinary science and new DL, radiomics, and radiogenomics directions towards DBT.

Multi-Resolution Wavelet Fractal Analysis and Subtask Training for Enhancing Few-Shot Noisy Brainwave Recognition.

The integration of healthcare monitoring with Internet of Things (IoT) networks radically transforms the management and monitoring of human well-being. Portable and lightweight electroencephalography (EEG) systems with fewer electrodes have improved convenience and flexibility while retaining adequate accuracy. However, challenges emerge when dealing with real-time EEG data from IoT devices due to the presence of noisy samples, which impedes improvements in brainwave detection accuracy. Moreover, high inter-subject variability and substantial variability in EEG signals present difficulties for conventional data augmentation and subtask learning techniques, leading to poor generalizability. To address these issues, we present a novel framework for enhancing EEG-based recognition through multi-resolution data analysis, capturing features at different scales using wavelet fractals. The original data can be expanded many times after continuous wavelet transform (CWT) and recombination, alleviating insufficient training samples. In the transfer stage of deep learning (DL) models, we adopt a subtask learning approach to train the recognition model to generalize efficiently. This incorporates wavelets at various scales instead of exclusively considering average prediction performance across scales and paradigms. Through extensive experiments, we demonstrate that our proposed DL-based method excels at extracting features from small-scale and noisy EEG data. This significantly improves healthcare monitoring performance by mitigating the impact of noise introduced by the external environment.

K-PathVQA: Knowledge-Aware Multimodal Representation for Pathology Visual Question Answering.

Pathology imaging is routinely used to detect the underlying effects and causes of diseases or injuries. Pathology visual question answering (PathVQA) aims to enable computers to answer questions about clinical visual findings from pathology images. Prior work on PathVQA has focused on directly analyzing the image content using conventional pretrained encoders without utilizing relevant external information when the image content is inadequate. In this paper, we present a knowledge-driven PathVQA (K-PathVQA), which uses a medical knowledge graph (KG) from a complementary external structured knowledge base to infer answers for the PathVQA task. K-PathVQA improves the question representation with external medical knowledge and then aggregates vision, language, and knowledge embeddings to learn a joint knowledge-image-question representation. Our experiments using a publicly available PathVQA dataset showed that our K-PathVQA outperformed the best baseline method with an increase of 4.15% in accuracy for the overall task, an increase of 4.40% in open-ended question type and an absolute increase of 1.03% in closed-ended question types. Ablation testing shows the impact of each of the contributions. Generalizability of the method is demonstrated with a separate medical VQA dataset.

Rumor Detection With Hierarchical Representation on Bipartite Ad Hoc Event Trees.

The rapid growth of social media has caused tremendous effects on information propagation, raising extreme challenges in detecting rumors. Existing rumor detection methods typically exploit the reposting propagation of a rumor candidate for detection by regarding all reposts to a rumor candidate as a temporal sequence and learning semantics representations of the repost sequence. However, extracting informative support from the topological structure of propagation and the influence of reposting authors for debunking rumors is crucial, which generally has not been well addressed by existing methods. In this article, we organize a claim post in circulation as an ad hoc event tree, extract event elements, and convert it into bipartite ad hoc event trees in terms of both posts and authors, i.e., author tree and post tree. Accordingly, we propose a novel rumor detection model with hierarchical representation on the bipartite ad hoc event trees called BAET. Specifically, we introduce word embedding and feature encoder for the author and post tree, respectively, and design a root-aware attention module to perform node representation. Then we adopt the tree-like RNN model to capture the structural correlations and propose a tree-aware attention module to learn tree representation for the author tree and post tree, respectively. Extensive experimental results on two public Twitter datasets demonstrate the effectiveness of BAET in exploring and exploiting the rumor propagation structure and the superior detection performance of BAET over state-of-the-art baseline methods.

Explainable hybrid word representations for sentiment analysis of financial news.

Due to the increasing interest of people in the stock and financial market, the sentiment analysis of news and texts related to the sector is of utmost importance. This helps the potential investors in deciding what company to invest in and what are their long-term benefits. However, it is challenging to analyze the sentiments of texts related to the financial domain, given the enormous amount of information available. The existing approaches are unable to capture complex attributes of language such as word usage, including semantics and syntax throughout the context, and polysemy in the context. Further, these approaches failed to interpret the models' predictability, which is obscure to humans. Models' interpretability to justify the predictions has remained largely unexplored and has become important to engender users' trust in the predictions by providing insight into the model prediction. Accordingly, in this paper, we present an explainable hybrid word representation that first augments the data to address the class imbalance issue and then integrates three embeddings to involve polysemy in context, semantics, and syntax in a context. We then fed our proposed word representation to a convolutional neural network (CNN) with attention to capture the sentiment. The experimental results show that our model outperforms several baselines of both classic classifiers and combinations of various word embedding models in the sentiment analysis of financial news. The experimental results also show that the proposed model outperforms several baselines of word embeddings and contextual embeddings when they are separately fed to a neural network model. Further, we show the explainability of the proposed method by presenting the visualization results to explain the reason for a prediction in the sentiment analysis of financial news.

Vision-Language Transformer for Interpretable Pathology Visual Question Answering.

Pathology visual question answering (PathVQA) attempts to answer a medical question posed by pathology images. Despite its great potential in healthcare, it is not widely adopted because it requires interactions on both the image (vision) and question (language) to generate an answer. Existing methods focused on treating vision and language features independently, which were unable to capture the high and low-level interactions that are required for VQA. Further, these methods failed to offer capabilities to interpret the retrieved answers, which are obscure to humans where the models' interpretability to justify the retrieved answers has remained largely unexplored. Motivated by these limitations, we introduce a vision-language transformer that embeds vision (images) and language (questions) features for an interpretable PathVQA. We present an interpretable transformer-based Path-VQA (TraP-VQA), where we embed transformers' encoder layers with vision and language features extracted using pre-trained CNN and domain-specific language model (LM), respectively. A decoder layer is then embedded to upsample the encoded features for the final prediction for PathVQA. Our experiments showed that our TraP-VQA outperformed the state-of-the-art comparative methods with public PathVQA dataset. Our experiments validated the robustness of our model on another medical VQA dataset, and the ablation study demonstrated the capability of our integrated transformer-based vision-language model for PathVQA. Finally, we present the visualization results of both text and images, which explain the reason for a retrieved answer in PathVQA.

A novel multiple kernel fuzzy topic modeling technique for biomedical data.

BACKGROUND: Text mining in the biomedical field has received much attention and regarded as the important research area since a lot of biomedical data is in text format. Topic modeling is one of the popular methods among text mining techniques used to discover hidden semantic structures, so called topics. However, discovering topics from biomedical data is a challenging task due to the sparsity, redundancy, and unstructured format. METHODS: In this paper, we proposed a novel multiple kernel fuzzy topic modeling (MKFTM) technique using fusion probabilistic inverse document frequency and multiple kernel fuzzy c-means clustering algorithm for biomedical text mining. In detail, the proposed fusion probabilistic inverse document frequency method is used to estimate the weights of global terms while MKFTM generates frequencies of local and global terms with bag-of-words. In addition, the principal component analysis is applied to eliminate higher-order negative effects for term weights. RESULTS: Extensive experiments are conducted on six biomedical datasets. MKFTM achieved the highest classification accuracy 99.04%, 99.62%, 99.69%, 99.61% in the Muchmore Springer dataset and 94.10%, 89.45%, 92.91%, 90.35% in the Ohsumed dataset. The CH index value of MKFTM is higher, which shows that its clustering performance is better than state-of-the-art topic models. CONCLUSION: We have confirmed from results that proposed MKFTM approach is very efficient to handles to sparsity and redundancy problem in biomedical text documents. MKFTM discovers semantically relevant topics with high accuracy for biomedical documents. Its gives better results for classification and clustering in biomedical documents. MKFTM is a new approach to topic modeling, which has the flexibility to work with a variety of clustering methods.

Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT.

BACKGROUND: The abundance of biomedical text data coupled with advances in natural language processing (NLP) is resulting in novel biomedical NLP (BioNLP) applications. These NLP applications, or tasks, are reliant on the availability of domain-specific language models (LMs) that are trained on a massive amount of data. Most of the existing domain-specific LMs adopted bidirectional encoder representations from transformers (BERT) architecture which has limitations, and their generalizability is unproven as there is an absence of baseline results among common BioNLP tasks. RESULTS: We present 8 variants of BioALBERT, a domain-specific adaptation of a lite bidirectional encoder representations from transformers (ALBERT), trained on biomedical (PubMed and PubMed Central) and clinical (MIMIC-III) corpora and fine-tuned for 6 different tasks across 20 benchmark datasets. Experiments show that a large variant of BioALBERT trained on PubMed outperforms the state-of-the-art on named-entity recognition (+ 11.09% BLURB score improvement), relation extraction (+ 0.80% BLURB score), sentence similarity (+ 1.05% BLURB score), document classification (+ 0.62% F1-score), and question answering (+ 2.83% BLURB score). It represents a new state-of-the-art in 5 out of 6 benchmark BioNLP tasks. CONCLUSIONS: The large variant of BioALBERT trained on PubMed achieved a higher BLURB score than previous state-of-the-art models on 5 of the 6 benchmark BioNLP tasks. Depending on the task, 5 different variants of BioALBERT outperformed previous state-of-the-art models on 17 of the 20 benchmark datasets, showing that our model is robust and generalizable in the common BioNLP tasks. We have made BioALBERT freely available which will help the BioNLP community avoid computational cost of training and establish a new set of baselines for future efforts across a broad range of BioNLP tasks.

Automatic COVID-19 Lung Infection Segmentation through Modified Unet Model.

The coronavirus (COVID-19) pandemic has had a terrible impact on human lives globally, with far-reaching consequences for the health and well-being of many people around the world. Statistically, 305.9 million people worldwide tested positive for COVID-19, and 5.48 million people died due to COVID-19 up to 10 January 2022. CT scans can be used as an alternative to time-consuming RT-PCR testing for COVID-19. This research work proposes a segmentation approach to identifying ground glass opacity or ROI in CT images developed by coronavirus, with a modified structure of the Unet model having been used to classify the region of interest at the pixel level. The problem with segmentation is that the GGO often appears indistinguishable from a healthy lung in the initial stages of COVID-19, and so, to cope with this, the increased set of weights in contracting and expanding the Unet path and an improved convolutional module is added in order to establish the connection between the encoder and decoder pipeline. This has a major capacity to segment the GGO in the case of COVID-19, with the proposed model being referred to as "convUnet." The experiment was performed on the Medseg1 dataset, and the addition of a set of weights at each layer of the model and modification in the connected module in Unet led to an improvement in overall segmentation results. The quantitative results obtained using accuracy, recall, precision, dice-coefficient, F1score, and IOU were 93.29%, 93.01%, 93.67%, 92.46%, 93.34%, 86.96%, respectively, which is better than that obtained using Unet and other state-of-the-art models. Therefore, this segmentation approach proved to be more accurate, fast, and reliable in helping doctors to diagnose COVID-19 quickly and efficiently.

Adaption of distance learning to continue the academic year amid COVID-19 lockdown.

This work investigates the use of distance learning in saving students' academic year amid COVID-19 lockdown. It assesses the adoption of distance learning using various online application tools that have gained widespread attention during the coronavirus infectious disease 2019 (COVID-19) pandemic. Distance learning thrives as a legitimate alternative to classroom instructions, as major cities around the globe are locked down amid the COVID-19 pandemic. To save the academic year, educational institutions have reacted to the situation impulsively and adopted distance learning platforms using online resources. This study surveyed random undergraduate students to identify the impact of trust in formal and informal information sources, awareness and the readiness to adopt distance learning. In this study, we have hypothesized that adopting distance learning is an outcome of situational awareness and readiness, which is achieved by the trust in the information sources related to distance learning. The findings indicate that trust in information sources such as institute and media information or interpersonal communication related to distance learning programs is correlated with awareness (ß = 0.423, t = 12.296, p = 0.000) and contribute to readiness (ß = 0.593, t = 28.762, p = 0.001). The structural model path coefficient indicates that readiness strongly influences the adoption of distance learning (ß = 0.660, t = 12.798, p = 0.000) amid the COVID-19 pandemic. Our proposed model recorded a predictive relevance (Q2) of 0.377 for awareness, 0.559 for readiness, and 0.309 for the adoption of distance learning, which explains how well the model and its parameter estimates reconstruct the values. This study concludes with implications for further research in this area.

COVIDSenti: A Large-Scale Benchmark Twitter Data Set for COVID-19 Sentiment Analysis.

Social media (and the world at large) have been awash with news of the COVID-19 pandemic. With the passage of time, news and awareness about COVID-19 spread like the pandemic itself, with an explosion of messages, updates, videos, and posts. Mass hysteria manifest as another concern in addition to the health risk that COVID-19 presented. Predictably, public panic soon followed, mostly due to misconceptions, a lack of information, or sometimes outright misinformation about COVID-19 and its impacts. It is thus timely and important to conduct an ex post facto assessment of the early information flows during the pandemic on social media, as well as a case study of evolving public opinion on social media which is of general interest. This study aims to inform policy that can be applied to social media platforms; for example, determining what degree of moderation is necessary to curtail misinformation on social media. This study also analyzes views concerning COVID-19 by focusing on people who interact and share social media on Twitter. As a platform for our experiments, we present a new large-scale sentiment data set COVIDSENTI, which consists of 90 000 COVID-19-related tweets collected in the early stages of the pandemic, from February to March 2020. The tweets have been labeled into positive, negative, and neutral sentiment classes. We analyzed the collected tweets for sentiment classification using different sets of features and classifiers. Negative opinion played an important role in conditioning public sentiment, for instance, we observed that people favored lockdown earlier in the pandemic; however, as expected, sentiment shifted by mid-March. Our study supports the view that there is a need to develop a proactive and agile public health presence to combat the spread of negative sentiment on social media following a pandemic.

Conventional to online education during COVID-19 pandemic: Do develop and underdeveloped nations cope alike.

BACKGROUND: Educational institutes around the globe are facing challenges of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Online learning is being carried out to avoid face to face contact in emergency scenarios such as coronavirus infectious disease 2019 (COVID-19) pandemic. Students need to adapt to new roles of learning through information technology to succeed in academics amid COVID-19. OBJECTIVE: However, access and use of online learning resources and its link with satisfaction of students amid COVID-19 are critical to explore. Therefore, in this paper, we aimed to assess and compare the access & use of online learning of Bruneians and Pakistanis amid enforced lockdown using a five-items satisfaction scale underlying existing literature. METHOD: For this, a cross-sectional study was done in the first half of June 2020 after the pandemic situation among 320 students' across Pakistan and Brunei with a pre-defined questionnaire. Data were analyzed with statistical software package for social sciences (SPSS) 2.0. RESULTS: The finding showed that there is a relationship between students' satisfaction and access & use of online learning. Outcomes of the survey suggest that Bruneian are more satisfied (50%) with the use of online learning amid lockdown as compared to Pakistanis (35.9%). Living in the Urban area as compared to a rural area is also a major factor contributing to satisfaction with the access and use of online learning for both Bruneian and Pakistanis. Moreover, previous experience with the use of online learning is observed prevalent among Bruneians (P = .000), while among friends and family is using online learning (P = .000) were encouraging factors contributed to satisfaction with the use of online learning among Pakistanis amid COVID-19. Correlation results suggest that access and use factors of online learning amid COVID-19 were positively associated with satisfaction among both populations amid COVID-19 pandemic. However, Bruneian is more satisfied with internet access (r = 0.437, P < .000) and affordability of gadgets (r = 0.577, P < .000) as compare to Pakistanis (r = 0.176, P < .050) and (r = 0.152, P < .050). CONCLUSION: The study suggested that it is crucial for the government and other policymakers worldwide to address access and use of online learning resources of their populace amid pandemic.