Andrew Scott

Michael Tanzer, Pedro Ferreira, Andrew Scott et al.

Diffusion Tensor Cardiac Magnetic Resonance (DT-CMR) enables us to probe the microstructural arrangement of cardiomyocytes within the myocardium in vivo and non-invasively, which no other imaging modality allows. This innovative technology could revolutionise the ability to perform cardiac clinical diagnosis, risk stratification, prognosis and therapy follow-up. However, DT-CMR is currently inefficient with over six minutes needed to acquire a single 2D static image. Therefore, DT-CMR is currently confined to research but not used clinically. We propose to reduce the number of repetitions needed to produce DT-CMR datasets and subsequently de-noise them, decreasing the acquisition time by a linear factor while maintaining acceptable image quality. Our proposed approach, based on Generative Adversarial Networks, Vision Transformers, and Ensemble Learning, performs significantly and considerably better than previous proposed approaches, bringing single breath-hold DT-CMR closer to reality.

Yinzhe Wu, Jiahao Huang, Fanwen Wang et al.

Diffusion Tensor Cardiac Magnetic Resonance (DT-CMR) is the only in vivo method to non-invasively examine the microstructure of the human heart. Current research in DT-CMR aims to improve the understanding of how the cardiac microstructure relates to the macroscopic function of the healthy heart as well as how microstructural dysfunction contributes to disease. To get the final DT-CMR metrics, we need to acquire diffusion weighted images of at least 6 directions. However, due to DWI's low signal-to-noise ratio, the standard voxel size is quite big on the scale for microstructures. In this study, we explored the potential of deep-learning-based methods in improving the image quality volumetrically (x4 in all dimensions). This study proposed a novel framework to enable volumetric super-resolution, with an additional model input of high-resolution b0 DWI. We demonstrated that the additional input could offer higher super-resolved image quality. Going beyond, the model is also able to super-resolve DWIs of unseen b-values, proving the model framework's generalizability for cardiac DWI superresolution. In conclusion, we would then recommend giving the model a high-resolution reference image as an additional input to the low-resolution image for training and inference to guide all super-resolution frameworks for parametric imaging where a reference image is available.

Aishwarya Sivaraman, Rui Abreu, Andrew Scott et al.

Existing code repositories contain numerous instances of code patterns that are idiomatic ways of accomplishing a particular programming task. Sometimes, the programming language in use supports specific operators or APIs that can express the same idiomatic imperative code much more succinctly. However, those code patterns linger in repositories because the developers may be unaware of the new APIs or have not gotten around to them. Detection of idiomatic code can also point to the need for new APIs. We share our experiences in mine idiomatic patterns from the Hack repo at Facebook. We found that existing techniques either cannot identify meaningful patterns from syntax trees or require test-suite-based dynamic analysis to incorporate semantic properties to mine useful patterns. The key insight of the approach proposed in this paper -- \emph{Jezero} -- is that semantic idioms from a large codebase can be learned from \emph{canonicalized} dataflow trees. We propose a scalable, lightweight static analysis-based approach to construct such a tree that is well suited to mine semantic idioms using nonparametric Bayesian methods. Our experiments with Jezero on Hack code shows a clear advantage of adding canonicalized dataflow information to ASTs: \emph{Jezero} was significantly more effective than a baseline that did not have the dataflow augmentation in being able to effectively find refactoring opportunities from unannotated legacy code.

Moritz Beller, Chu-Pan Wong, Johannes Bader et al.

Traditionally, mutation testing generates an abundance of small deviations of a program, called mutants. At industrial systems the scale and size of Facebook's, doing this is infeasible. We should not create mutants that the test suite would likely fail on or that give no actionable signal to developers. To tackle this problem, in this paper, we semi-automatically learn error-inducing patterns from a corpus of common Java coding errors and from changes that caused operational anomalies at Facebook specifically. We combine the mutations with instrumentation that measures which tests exactly visited the mutated piece of code. Results on more than 15,000 generated mutants show that more than half of the generated mutants survive Facebook's rigorous test suite of unit, integration, and system tests. Moreover, in a case study with 26 developers, all but two found information of automatically detected test holes interesting in principle. As such, almost half of the 26 would actually act on the mutant presented to them by adapting an existing or creating a new test. The others did not for a variety of reasons often outside the scope of mutation testing. It remains a practical challenge how we can include such external information to increase the true actionability rate on mutants.

Johannes Bader, Andrew Scott, Michael Pradel et al.

Static analyzers help find bugs early by warning about recurring bug categories. While fixing these bugs still remains a mostly manual task in practice, we observe that fixes for a specific bug category often are repetitive. This paper addresses the problem of automatically fixing instances of common bugs by learning from past fixes. We present Getafix, an approach that produces human-like fixes while being fast enough to suggest fixes in time proportional to the amount of time needed to obtain static analysis results in the first place. Getafix is based on a novel hierarchical clustering algorithm that summarizes fix patterns into a hierarchy ranging from general to specific patterns. Instead of a computationally expensive exploration of a potentially large space of candidate fixes, Getafix uses a simple yet effective ranking technique that uses the context of a code change to select the most appropriate fix for a given bug. Our evaluation applies Getafix to 1,268 bug fixes for six bug categories reported by popular static analyzers for Java, including null dereferences, incorrect API calls, and misuses of particular language constructs. The approach predicts exactly the human-written fix as the top-most suggestion between 12% and 91% of the time, depending on the bug category. The top-5 suggestions contain fixes for 526 of the 1,268 bugs. Moreover, we report on deploying the approach within Facebook, where it contributes to the reliability of software used by billions of people. To the best of our knowledge, Getafix is the first industrially-deployed automated bug-fixing tool that learns fix patterns from past, human-written fixes to produce human-like fixes.

Jo Schlemper, Guang Yang, Pedro Ferreira et al.

Understanding the structure of the heart at the microscopic scale of cardiomyocytes and their aggregates provides new insights into the mechanisms of heart disease and enables the investigation of effective therapeutics. Diffusion Tensor Cardiac Magnetic Resonance (DT-CMR) is a unique non-invasive technique that can resolve the microscopic structure, organisation, and integrity of the myocardium without the need for exogenous contrast agents. However, this technique suffers from relatively low signal-to-noise ratio (SNR) and frequent signal loss due to respiratory and cardiac motion. Current DT-CMR techniques rely on acquiring and averaging multiple signal acquisitions to improve the SNR. Moreover, in order to mitigate the influence of respiratory movement, patients are required to perform many breath holds which results in prolonged acquisition durations (e.g., ~30 mins using the existing technology). In this study, we propose a novel cascaded Convolutional Neural Networks (CNN) based compressive sensing (CS) technique and explore its applicability to improve DT-CMR acquisitions. Our simulation based studies have achieved high reconstruction fidelity and good agreement between DT-CMR parameters obtained with the proposed reconstruction and fully sampled ground truth. When compared to other state-of-the-art methods, our proposed deep cascaded CNN method and its stochastic variation demonstrated significant improvements. To the best of our knowledge, this is the first study using deep CNN based CS for the DT-CMR reconstruction. In addition, with relatively straightforward modifications to the acquisition scheme, our method can easily be translated into a method for online, at-the-scanner reconstruction enabling the deployment of accelerated DT-CMR in various clinical applications.