From Fully-Supervised Single-Task to Semi-Supervised Multi-Task Deep Learning Architectures for Segmentation in Medical Imaging Applications

Medical imaging is routinely performed in clinics worldwide for the diagnosis and treatment of numerous medical conditions in children and adults. With the advent of these medical imaging modalities, radiologists can visualize both the structure of the body as well as the tissues within the body. However, analyzing these high-dimensional (2D/3D/4D) images demands a significant amount of time and effort from radiologists. Hence, there is an ever-growing need for medical image computing tools to extract relevant information from the image data to help radiologists perform efficiently. Image analysis based on machine learning has pivotal potential to improve the entire medical imaging pipeline, providing support for clinical decision-making and computer-aided diagnosis. To be effective in addressing challenging image analysis tasks such as classification, detection, registration, and segmentation, specifically for medical imaging applications, deep learning approaches have shown significant improvement in performance. While deep learning has shown its potential in a variety of medical image analysis problems including segmentation, motion estimation, etc., generalizability is still an unsolved problem and many of these successes are achieved at the cost of a large pool of datasets. For most practical applications, getting access to a copious dataset can be very difficult, often impossible. Annotation is tedious and time-consuming. This cost is further amplified when annotation must be done by a clinical expert in medical imaging applications. Additionally, the applications of deep learning in the real-world clinical setting are still limited due to the lack of reliability caused by the limited prediction capabilities of some deep learning models. Moreover, while using a CNN in an automated image analysis pipeline, it’s critical to understand which segmentation results are problematic and require further manual examination. To this extent, the estimation of uncertainty calibration in a semi-supervised setting for medical image segmentation is still rarely reported. This thesis focuses on developing and evaluating optimized machine learning models for a variety of medical imaging applications, ranging from fully-supervised, single-task learning to semi-supervised, multi-task learning that makes efficient use of annotated training data. The contributions of this dissertation are as follows: (1) developing a fully-supervised, single-task transfer learning for the surgical instrument segmentation from laparoscopic images; and (2) utilizing supervised, single-task, transfer learning for segmenting and digitally removing the surgical instruments from endoscopic/laparoscopic videos to allow the visualization of the anatomy being obscured by the tool. The tool removal algorithms use a tool segmentation mask and either instrument-free reference frames or previous instrument-containing frames to fill in (inpaint) the instrument segmentation mask; (3) developing fully-supervised, single-task learning via efficient weight pruning and learned group convolution for accurate left ventricle (LV), right ventricle (RV) blood pool and myocardium localization and segmentation from 4D cine cardiac MR images; (4) demonstrating the use of our fully-supervised memory-efficient model to generate dynamic patient-specific right ventricle (RV) models from cine cardiac MRI dataset via an unsupervised learning-based deformable registration field; and (5) integrating a Monte Carlo dropout into our fully-supervised memory-efficient model with inherent uncertainty estimation, with the overall goal to estimate the uncertainty associated with the obtained segmentation and error, as a means to flag regions that feature less than optimal segmentation results; (6) developing semi-supervised, single-task learning via self-training (through meta pseudo-labeling) in concert with a Teacher network that instructs the Student network by generating pseudo-labels given unlabeled input data; (7) proposing largely-unsupervised, multi-task learning to demonstrate the power of a simple combination of a disentanglement block, variational autoencoder (VAE), generative adversarial network (GAN), and a conditioning layer-based reconstructor for performing two of the foremost critical tasks in medical imaging — segmentation of cardiac structures and reconstruction of the cine cardiac MR images; (8) demonstrating the use of 3D semi-supervised, multi-task learning for jointly learning multiple tasks in a single backbone module – uncertainty estimation, geometric shape generation, and cardiac anatomical structure segmentation of the left atrial cavity from 3D Gadolinium-enhanced magnetic resonance (GE-MR) images. This dissertation summarizes the impact of the contributions of our work in terms of demonstrating the adaptation and use of deep learning architectures featuring different levels of supervision to build a variety of image segmentation tools and techniques that can be used across a wide spectrum of medical image computing applications centered on facilitating and promoting the wide-spread computer-integrated diagnosis and therapy data science

Impact of environmental production conditions on productivity and efficiency: a case study of wheat farmers in Bangladesh

Environmental conditions significantly affect production, but are often ignored in studies analysing productivity and efficiency leading to biased results. In this study, we examine the influence of selected environmental factors on productivity and efficiency in wheat farming in Bangladesh. Results reveal that environmental production conditions significantly affect the parameters of the production function and technical efficiency, as well as correlates of inefficiency. Controlling for environmental production conditions improves technical efficiency by 4 points (p<0.01) from 86% to 90%. Large farms are more efficient relative to small and medium sized farms (p<0.01 and 0.05), with no variation among regions. Policy implications include soil fertility improvement through soil conservation and crop rotation, improvement in managerial practices through extension services and adoption of modern technologies, promotion of education, strengthening the research-extension link, and development of new varieties that have higher yield potential and are also suitable for marginal areas

Assorted, Archetypal and Annotated Two Million (3A2M) Cooking Recipes Dataset based on Active Learning

Cooking recipes allow individuals to exchange culinary ideas and provide food preparation instructions. Due to a lack of adequate labeled data, categorizing raw recipes found online to the appropriate food genres is a challenging task in this domain. Utilizing the knowledge of domain experts to categorize recipes could be a solution. In this study, we present a novel dataset of two million culinary recipes labeled in respective categories leveraging the knowledge of food experts and an active learning technique. To construct the dataset, we collect the recipes from the RecipeNLG dataset. Then, we employ three human experts whose trustworthiness score is higher than 86.667% to categorize 300K recipe by their Named Entity Recognition (NER) and assign it to one of the nine categories: bakery, drinks, non-veg, vegetables, fast food, cereals, meals, sides and fusion. Finally, we categorize the remaining 1900K recipes using Active Learning method with a blend of Query-by-Committee and Human In The Loop (HITL) approaches. There are more than two million recipes in our dataset, each of which is categorized and has a confidence score linked with it. For the 9 genres, the Fleiss Kappa score of this massive dataset is roughly 0.56026. We believe that the research community can use this dataset to perform various machine learning tasks such as recipe genre classification, recipe generation of a specific genre, new recipe creation, etc. The dataset can also be used to train and evaluate the performance of various NLP tasks such as named entity recognition, part-of-speech tagging, semantic role labeling, and so on. The dataset will be available upon publication: https://tinyurl.com/3zu4778y

Towards Automated Recipe Genre Classification using Semi-Supervised Learning

Sharing cooking recipes is a great way to exchange culinary ideas and provide instructions for food preparation. However, categorizing raw recipes found online into appropriate food genres can be challenging due to a lack of adequate labeled data. In this study, we present a dataset named the ``Assorted, Archetypal, and Annotated Two Million Extended (3A2M+) Cooking Recipe Dataset" that contains two million culinary recipes labeled in respective categories with extended named entities extracted from recipe descriptions. This collection of data includes various features such as title, NER, directions, and extended NER, as well as nine different labels representing genres including bakery, drinks, non-veg, vegetables, fast food, cereals, meals, sides, and fusions. The proposed pipeline named 3A2M+ extends the size of the Named Entity Recognition (NER) list to address missing named entities like heat, time or process from the recipe directions using two NER extraction tools. 3A2M+ dataset provides a comprehensive solution to the various challenging recipe-related tasks, including classification, named entity recognition, and recipe generation. Furthermore, we have demonstrated traditional machine learning, deep learning and pre-trained language models to classify the recipes into their corresponding genre and achieved an overall accuracy of 98.6\%. Our investigation indicates that the title feature played a more significant role in classifying the genre

Smartphone-Based Prenatal Education for Parents with Preterm Birth Risk Factors

Objective To develop an educational mobile application (app) for expectant parents diagnosed with risk factors for premature birth. Methods Parent and medical advisory panels delineated the vision for the app. The app helps prepare for preterm birth. For pilot testing, obstetricians offered the app between 18–22 weeks gestational age to English speaking parents with risk factors for preterm birth. After 4 weeks of use, each participant completed a questionnaire. The software tracked topics accessed and duration of use. Results For pilot testing, 31 participants were recruited and 28 completed the questionnaire. After app utilization, participants reported heightened awareness of preterm birth (93%), more discussion of pregnancy or prematurity issues with partner (86%), increased questions at clinic visits (43%), and increased anxiety (21%). Participants reported receiving more prematurity information from the app than from their healthcare providers. The 15 participants for whom tracking data was available accessed the app for an average of 8 h. Conclusion Parents with increased risk for preterm birth may benefit from this mobile app educational program. Practice implications If the pregnancy results in preterm birth hospitalization, parents would have built a foundation of knowledge to make informed medical care choices