Chi-en Amy Tai

Yifan Wu, Hayden Gunraj, Chi-en Amy Tai et al.

The global ramifications of the COVID-19 pandemic remain significant, exerting persistent pressure on nations even three years after its initial outbreak. Deep learning models have shown promise in improving COVID-19 diagnostics but require diverse and larger-scale datasets to improve performance. In this paper, we introduce COVIDx CXR-4, an expanded multi-institutional open-source benchmark dataset for chest X-ray image-based computer-aided COVID-19 diagnostics. COVIDx CXR-4 expands significantly on the previous COVIDx CXR-3 dataset by increasing the total patient cohort size by greater than 2.66 times, resulting in 84,818 images from 45,342 patients across multiple institutions. We provide extensive analysis on the diversity of the patient demographic, imaging metadata, and disease distributions to highlight potential dataset biases. To the best of the authors' knowledge, COVIDx CXR-4 is the largest and most diverse open-source COVID-19 CXR dataset and is made publicly available as part of an open initiative to advance research to aid clinicians against the COVID-19 disease.

Chi-en Amy Tai, Elizabeth Janes, Chris Czarnecki et al.

Skin cancer is the most common type of cancer in the United States and is estimated to affect one in five Americans. Recent advances have demonstrated strong performance on skin cancer detection, as exemplified by state of the art performance in the SIIM-ISIC Melanoma Classification Challenge; however these solutions leverage ensembles of complex deep neural architectures requiring immense storage and compute costs, and therefore may not be tractable. A recent movement for TinyML applications is integrating Double-Condensing Attention Condensers (DC-AC) into a self-attention neural network backbone architecture to allow for faster and more efficient computation. This paper explores leveraging an efficient self-attention structure to detect skin cancer in skin lesion images and introduces a deep neural network design with DC-AC customized for skin cancer detection from skin lesion images. The final model is publicly available as a part of a global open-source initiative dedicated to accelerating advancement in machine learning to aid clinicians in the fight against cancer. Future work of this research includes iterating on the design of the selected network architecture and refining the approach to generalize to other forms of cancer.

Hayden Gunraj, Chi-en Amy Tai, Alexander Wong

The recent introduction of synthetic correlated diffusion (CDI$^s$) imaging has demonstrated significant potential in the realm of clinical decision support for prostate cancer (PCa). CDI$^s$ is a new form of magnetic resonance imaging (MRI) designed to characterize tissue characteristics through the joint correlation of diffusion signal attenuation across different Brownian motion sensitivities. Despite the performance improvement, the CDI$^s$ data for PCa has not been previously made publicly available. In our commitment to advance research efforts for PCa, we introduce Cancer-Net PCa-Data, an open-source benchmark dataset of volumetric CDI$^s$ imaging data of PCa patients. Cancer-Net PCa-Data consists of CDI$^s$ volumetric images from a patient cohort of 200 patient cases, along with full annotations (gland masks, tumor masks, and PCa diagnosis for each tumor). We also analyze the demographic and label region diversity of Cancer-Net PCa-Data for potential biases. Cancer-Net PCa-Data is the first-ever public dataset of CDI$^s$ imaging data for PCa, and is a part of the global open-source initiative dedicated to advancement in machine learning and imaging research to aid clinicians in the global fight against cancer.

Chi-en Amy Tai, Hayden Gunraj, Alexander Wong

Recently, a new form of magnetic resonance imaging (MRI) called synthetic correlated diffusion (CDI$^s$) imaging was introduced and showed considerable promise for clinical decision support for cancers such as prostate cancer when compared to current gold-standard MRI techniques. However, the efficacy for CDI$^s$ for other forms of cancers such as breast cancer has not been as well-explored nor have CDI$^s$ data been previously made publicly available. Motivated to advance efforts in the development of computer-aided clinical decision support for breast cancer using CDI$^s$, we introduce Cancer-Net BCa, a multi-institutional open-source benchmark dataset of volumetric CDI$^s$ imaging data of breast cancer patients. Cancer-Net BCa contains CDI$^s$ volumetric images from a pre-treatment cohort of 253 patients across ten institutions, along with detailed annotation metadata (the lesion type, genetic subtype, longest diameter on the MRI (MRLD), the Scarff-Bloom-Richardson (SBR) grade, and the post-treatment breast cancer pathologic complete response (pCR) to neoadjuvant chemotherapy). We further examine the demographic and tumour diversity of the Cancer-Net BCa dataset to gain deeper insights into potential biases. Cancer-Net BCa is publicly available as a part of a global open-source initiative dedicated to accelerating advancement in machine learning to aid clinicians in the fight against cancer.

Aditya Sridhar, Chi-en Amy Tai, Hayden Gunraj et al.

In Canada, prostate cancer is the most common form of cancer in men and accounted for 20% of new cancer cases for this demographic in 2022. Due to recent successes in leveraging machine learning for clinical decision support, there has been significant interest in the development of deep neural networks for prostate cancer diagnosis, prognosis, and treatment planning using diffusion weighted imaging (DWI) data. A major challenge hindering widespread adoption in clinical use is poor generalization of such networks due to scarcity of large-scale, diverse, balanced prostate imaging datasets for training such networks. In this study, we explore the efficacy of latent diffusion for generating realistic prostate DWI data through the introduction of an anatomic-conditional controlled latent diffusion strategy. To the best of the authors' knowledge, this is the first study to leverage conditioning for synthesis of prostate cancer imaging. Experimental results show that the proposed strategy, which we call Cancer-Net PCa-Gen, enhances synthesis of diverse prostate images through controllable tumour locations and better anatomical and textural fidelity. These crucial features make it well-suited for augmenting real patient data, enabling neural networks to be trained on a more diverse and comprehensive data distribution. The Cancer-Net PCa-Gen framework and sample images have been made publicly available at https://www.kaggle.com/datasets/deetsadi/cancer-net-pca-gen-dataset as a part of a global open-source initiative dedicated to accelerating advancement in machine learning to aid clinicians in the fight against cancer.

Chi-en Amy Tai, Hayden Gunraj, Alexander Wong

The prevalence of breast cancer continues to grow, affecting about 300,000 females in the United States in 2023. However, there are different levels of severity of breast cancer requiring different treatment strategies, and hence, grading breast cancer has become a vital component of breast cancer diagnosis and treatment planning. Specifically, the gold-standard Scarff-Bloom-Richardson (SBR) grade has been shown to consistently indicate a patient's response to chemotherapy. Unfortunately, the current method to determine the SBR grade requires removal of some cancer cells from the patient which can lead to stress and discomfort along with costly expenses. In this paper, we study the efficacy of deep learning for breast cancer grading based on synthetic correlated diffusion (CDI$^s$) imaging, a new magnetic resonance imaging (MRI) modality and found that it achieves better performance on SBR grade prediction compared to those learnt using gold-standard imaging modalities. Hence, we introduce Cancer-Net BCa-S, a volumetric deep radiomics approach for predicting SBR grade based on volumetric CDI$^s$ data. Given the promising results, this proposed method to identify the severity of the cancer would allow for better treatment decisions without the need for a biopsy. Cancer-Net BCa-S has been made publicly available as part of a global open-source initiative for advancing machine learning for cancer care.

Chi-en Amy Tai, Hayden Gunraj, Nedim Hodzic et al.

Breast cancer is the second most common type of cancer in women in Canada and the United States, representing over 25\% of all new female cancer cases. As such, there has been immense research and progress on improving screening and clinical support for breast cancer. In this paper, we investigate enhancing clinical support for breast cancer with deep learning models using a newly introduced magnetic resonance imaging (MRI) modality called synthetic correlated diffusion imaging (CDI$^s$). More specifically, we leverage a volumetric convolutional neural network to learn volumetric deep radiomic features from a pre-treatment cohort and construct a predictor based on the learnt features for grade and post-treatment response prediction. As the first study to learn CDI$^s$-centric radiomic sequences within a deep learning perspective for clinical decision support, we evaluated the proposed approach using the ACRIN-6698 study against those learnt using gold-standard imaging modalities. We find that the proposed approach can achieve better performance for both grade and post-treatment response prediction and thus may be a useful tool to aid oncologists in improving recommendation of treatment of patients. Subsequently, the approach to leverage volumetric deep radiomic features for breast cancer can be further extended to other applications of CDI$^s$ in the cancer domain to further improve clinical support.

Chi-en Amy Tai, Oustan Ding, Alexander Wong

In the United States, skin cancer ranks as the most commonly diagnosed cancer, presenting a significant public health issue due to its high rates of occurrence and the risk of serious complications if not caught early. Recent advancements in dataset curation and deep learning have shown promise in quick and accurate detection of skin cancer. However, current open-source datasets have significant class imbalances which impedes the effectiveness of these deep learning models. In healthcare, generative artificial intelligence (AI) models have been employed to create synthetic data, addressing data imbalance in datasets by augmenting underrepresented classes and enhancing the overall quality and performance of machine learning models. In this paper, we build on top of previous work by leveraging new advancements in generative AI, notably Stable Diffusion and DreamBooth. We introduce Cancer-Net SCa-Synth, an open access synthetically generated 2D skin lesion dataset for skin cancer classification. Further analysis on the data effectiveness by comparing the ISIC 2020 test set performance for training with and without these synthetic images for a simple model highlights the benefits of leveraging synthetic data to improve performance. Cancer-Net SCa-Synth is publicly available at https://github.com/catai9/Cancer-Net-SCa-Synth as part of a global open-source initiative for accelerating machine learning for cancer care.

Chi-en Amy Tai, Alexander Wong

In 2020, prostate cancer saw a staggering 1.4 million new cases, resulting in over 375,000 deaths. The accurate identification of clinically significant prostate cancer is crucial for delivering effective treatment to patients. Consequently, there has been a surge in research exploring the application of deep neural networks to predict clinical significance based on magnetic resonance images. However, these networks demand extensive datasets to attain optimal performance. Recently, transfer learning emerged as a technique that leverages acquired features from a domain with richer data to enhance the performance of a domain with limited data. In this paper, we investigate the improvement of clinically significant prostate cancer prediction in T2-weighted images through transfer learning from breast cancer. The results demonstrate a remarkable improvement of over 30% in leave-one-out cross-validation accuracy.

Chi-en Amy Tai, Alexander Wong

Peptide de novo sequencing is a method used to reconstruct amino acid sequences from tandem mass spectrometry data without relying on existing protein sequence databases. Traditional deep learning approaches, such as Casanovo, mainly utilize autoregressive decoders and predict amino acids sequentially. Subsequently, they encounter cascading errors and fail to leverage high-confidence regions effectively. To address these issues, this paper investigates using diffusion decoders adapted for the discrete data domain. These decoders provide a different approach, allowing sequence generation to start from any peptide segment, thereby enhancing prediction accuracy. We experiment with three different diffusion decoder designs, knapsack beam search, and various loss functions. We find knapsack beam search did not improve performance metrics and simply replacing the transformer decoder with a diffusion decoder lowered performance. Although peptide precision and recall were still 0, the best diffusion decoder design with the DINOISER loss function obtained a statistically significant improvement in amino acid recall by 0.373 compared to the baseline autoregressive decoder-based Casanovo model. These findings highlight the potential of diffusion decoders to not only enhance model sensitivity but also drive significant advancements in peptide de novo sequencing.

Benjamin Ng, Chi-en Amy Tai, E. Zhixuan Zeng et al.

In the United States, prostate cancer is the second leading cause of deaths in males with a predicted 35,250 deaths in 2024. However, most diagnoses are non-lethal and deemed clinically insignificant which means that the patient will likely not be impacted by the cancer over their lifetime. As a result, numerous research studies have explored the accuracy of predicting clinical significance of prostate cancer based on magnetic resonance imaging (MRI) modalities and deep neural networks. Despite their high performance, these models are not trusted by most clinical scientists as they are trained solely on a single modality whereas clinical scientists often use multiple magnetic resonance imaging modalities during their diagnosis. In this paper, we investigate combining multiple MRI modalities to train a deep learning model to enhance trust in the models for clinically significant prostate cancer prediction. The promising performance and proposed training pipeline showcase the benefits of incorporating multiple MRI modalities for enhanced trust and accuracy.

Chi-en Amy Tai, Alexander Wong

Breast cancer is a significant cause of death from cancer in women globally, highlighting the need for improved diagnostic imaging to enhance patient outcomes. Accurate tumour identification is essential for diagnosis, treatment, and monitoring, emphasizing the importance of advanced imaging technologies that provide detailed views of tumour characteristics and disease. Synthetic correlated diffusion imaging (CDI$^s$) is a recent method that has shown promise for prostate cancer delineation compared to current MRI images. In this paper, we explore tuning the coefficients in the computation of CDI$^s$ for breast cancer tumour delineation by maximizing the area under the receiver operating characteristic curve (AUC) using a Nelder-Mead simplex optimization strategy. We show that the best AUC is achieved by the CDI$^s$ - Optimized modality, outperforming the best gold-standard modality by 0.0044. Notably, the optimized CDI$^s$ modality also achieves AUC values over 0.02 higher than the Unoptimized CDI$^s$ value, demonstrating the importance of optimizing the CDI$^s$ exponents for the specific cancer application.

Chi-en Amy Tai, Alexander Wong

Breast cancer was diagnosed for over 7.8 million women between 2015 to 2020. Grading plays a vital role in breast cancer treatment planning. However, the current tumor grading method involves extracting tissue from patients, leading to stress, discomfort, and high medical costs. A recent paper leveraging volumetric deep radiomic features from synthetic correlated diffusion imaging (CDI$^s$) for breast cancer grade prediction showed immense promise for noninvasive methods for grading. Motivated by the impact of CDI$^s$ optimization for prostate cancer delineation, this paper examines using optimized CDI$^s$ to improve breast cancer grade prediction. We fuse the optimized CDI$^s$ signal with diffusion-weighted imaging (DWI) to create a multiparametric MRI for each patient. Using a larger patient cohort and training across all the layers of a pretrained MONAI model, we achieve a leave-one-out cross-validation accuracy of 95.79%, over 8% higher compared to that previously reported.

Chi-en Amy Tai, Alexander Wong

In 2020, 685,000 deaths across the world were attributed to breast cancer, underscoring the critical need for innovative and effective breast cancer treatment. Neoadjuvant chemotherapy has recently gained popularity as a promising treatment strategy for breast cancer, attributed to its efficacy in shrinking large tumors and leading to pathologic complete response. However, the current process to recommend neoadjuvant chemotherapy relies on the subjective evaluation of medical experts which contain inherent biases and significant uncertainty. A recent study, utilizing volumetric deep radiomic features extracted from synthetic correlated diffusion imaging (CDI$^s$), demonstrated significant potential in noninvasive breast cancer pathologic complete response prediction. Inspired by the positive outcomes of optimizing CDI$^s$ for prostate cancer delineation, this research investigates the application of optimized CDI$^s$ to enhance breast cancer pathologic complete response prediction. Using multiparametric MRI that fuses optimized CDI$^s$ with diffusion-weighted imaging (DWI), we obtain a leave-one-out cross-validation accuracy of 93.28%, over 5.5% higher than that previously reported.