Pre-text Representation Transfer for Deep Learning with Limited Imbalanced Data : Application to CT-based COVID-19 Detection

Annotating medical images for disease detection is often tedious and expensive. Moreover, the available training samples for a given task are generally scarce and imbalanced. These conditions are not conducive for learning effective deep neural models. Hence, it is common to 'transfer' neural networks trained on natural images to the medical image domain. However, this paradigm lacks in performance due to the large domain gap between the natural and medical image data. To address that, we propose a novel concept of Pre-text Representation Transfer (PRT). In contrast to the conventional transfer learning, which fine-tunes a source model after replacing its classification layers, PRT retains the original classification layers and updates the representation layers through an unsupervised pre-text task. The task is performed with (original, not synthetic) medical images, without utilizing any annotations. This enables representation transfer with a large amount of training data. This high-fidelity representation transfer allows us to use the resulting model as a more effective feature extractor. Moreover, we can also subsequently perform the traditional transfer learning with this model. We devise a collaborative representation based classification layer for the case when we leverage the model as a feature extractor. We fuse the output of this layer with the predictions of a model induced with the traditional transfer learning performed over our pre-text transferred model. The utility of our technique for limited and imbalanced data classification problem is demonstrated with an extensive five-fold evaluation for three large-scale models, tested for five different class-imbalance ratios for CT based COVID-19 detection. Our results show a consistent gain over the conventional transfer learning with the proposed method.

Resetting the baseline: CT-based COVID-19 diagnosis with Deep Transfer Learning is not as accurate as widely thought

Deep learning is gaining instant popularity in computer aided diagnosis of COVID-19. Due to the high sensitivity of Computed Tomography (CT) to this disease, CT-based COVID-19 detection with visual models is currently at the forefront of medical imaging research. Outcomes published in this direction are frequently claiming highly accurate detection under deep transfer learning. This is leading medical technologists to believe that deep transfer learning is the mainstream solution for the problem. However, our critical analysis of the literature reveals an alarming performance disparity between different published results. Hence, we conduct a systematic thorough investigation to analyze the effectiveness of deep transfer learning for COVID-19 detection with CT images. Exploring 14 state-of-the-art visual models with over 200 model training sessions, we conclusively establish that the published literature is frequently overestimating transfer learning performance for the problem, even in the prestigious scientific sources. The roots of overestimation trace back to inappropriate data curation. We also provide case studies that consider more realistic scenarios, and establish transparent baselines for the problem. We hope that our reproducible investigation will help in curbing hype-driven claims for the critical problem of COVID-19 diagnosis, and pave the way for a more transparent performance evaluation of techniques for CT-based COVID-19 detection.

Boosting Deep Transfer Learning for COVID-19 Classification

COVID-19 classification using chest Computed Tomography (CT) has been found pragmatically useful by several studies. Due to the lack of annotated samples, these studies recommend transfer learning and explore the choices of pre-trained models and data augmentation. However, it is still unknown if there are better strategies than vanilla transfer learning for more accurate COVID-19 classification with limited CT data. This paper provides an affirmative answer, devising a novel `model' augmentation technique that allows a considerable performance boost to transfer learning for the task. Our method systematically reduces the distributional shift between the source and target domains and considers augmenting deep learning with complementary representation learning techniques. We establish the efficacy of our method with publicly available datasets and models, along with identifying contrasting observations in the previous studies.

Going Deep in Medical Image Analysis: Concepts, Methods, Challenges and Future Directions

Medical Image Analysis is currently experiencing a paradigm shift due to Deep Learning. This technology has recently attracted so much interest of the Medical Imaging community that it led to a specialized conference in `Medical Imaging with Deep Learning' in the year 2018. This article surveys the recent developments in this direction, and provides a critical review of the related major aspects. We organize the reviewed literature according to the underlying Pattern Recognition tasks, and further sub-categorize it following a taxonomy based on human anatomy. This article does not assume prior knowledge of Deep Learning and makes a significant contribution in explaining the core Deep Learning concepts to the non-experts in the Medical community. Unique to this study is the Computer Vision/Machine Learning perspective taken on the advances of Deep Learning in Medical Imaging. This enables us to single out `lack of appropriately annotated large-scale datasets' as the core challenge (among other challenges) in this research direction. We draw on the insights from the sister research fields of Computer Vision, Pattern Recognition and Machine Learning etc.; where the techniques of dealing with such challenges have already matured, to provide promising directions for the Medical Imaging community to fully harness Deep Learning in the future.