Transparent and Clinically Interpretable AI for Lung Cancer Detection in Chest X-Rays

The rapidly advancing field of Explainable Artificial Intelligence (XAI) aims to tackle the issue of trust regarding the use of complex black-box deep learning models in real-world applications. Existing post-hoc XAI techniques have recently been shown to have poor performance on medical data, producing unreliable explanations which are infeasible for clinical use. To address this, we propose an ante-hoc approach based on concept bottleneck models which introduces for the first time clinical concepts into the classification pipeline, allowing the user valuable insight into the decision-making process. On a large public dataset of chest X-rays and associated medical reports, we focus on the binary classification task of lung cancer detection. Our approach yields improved classification performance in lung cancer detection when compared to baseline deep learning models (F1 > 0.9), while also generating clinically relevant and more reliable explanations than existing techniques. We evaluate our approach against post-hoc image XAI techniques LIME and SHAP, as well as CXR-LLaVA, a recent textual XAI tool which operates in the context of question answering on chest X-rays.

Fix-Con: Automatic Fault Localization and Repair of Deep Learning Model Conversions

Converting deep learning models between frameworks is a common step to maximize model compatibility across devices and leverage optimization features that may be exclusively provided in one deep learning framework. However, this conversion process may be riddled with bugs, making the converted models either undeployable or problematic, considerably degrading their prediction correctness. We propose an automated approach for fault localization and repair, Fix-Con, during model conversion between deep learning frameworks. Fix-Con is capable of detecting and fixing faults introduced in model input, parameters, hyperparameters, and the model graph during conversion. Fix-Con uses a set of fault types mined from surveying conversion issues raised to localize potential conversion faults in the converted target model, and then repairs them appropriately, e.g. replacing the parameters of the target model with those from the source model. This is done iteratively for every image in the dataset with output label differences between the source model and the converted target model until all differences are resolved. We evaluate the effectiveness of Fix-Con in fixing model conversion bugs of three widely used image recognition models converted across four different deep learning frameworks. Overall, Fix-Con was able to either completely repair, or significantly improve the performance of 14 out of the 15 erroneous conversion cases.

Hawkeye: Change-targeted Testing for Android Apps based on Deep Reinforcement Learning

Android Apps are frequently updated to keep up with changing user, hardware, and business demands. Ensuring the correctness of App updates through extensive testing is crucial to avoid potential bugs reaching the end user. Existing Android testing tools generate GUI events focussing on improving the test coverage of the entire App rather than prioritising updates and its impacted elements. Recent research has proposed change-focused testing but relies on random exploration to exercise the updates and impacted GUI elements that is ineffective and slow for large complex Apps with a huge input exploration space. We propose directed testing of App updates with Hawkeye that is able to prioritise executing GUI actions associated with code changes based on deep reinforcement learning from historical exploration data. Our empirical evaluation compares Hawkeye with state-of-the-art model-based and reinforcement learning-based testing tools FastBot2 and ARES using 10 popular open-source and 1 commercial App. We find that Hawkeye is able to generate GUI event sequences targeting changed functions more reliably than FastBot2 and ARES for the open source Apps and the large commercial App. Hawkeye achieves comparable performance on smaller open source Apps with a more tractable exploration space. The industrial deployment of Hawkeye in the development pipeline also shows that Hawkeye is ideal to perform smoke testing for merge requests of a complicated commercial App.

MutateNN: Mutation Testing of Image Recognition Models Deployed on Hardware Accelerators

With the research advancement of Artificial Intelligence in the last years, there are new opportunities to mitigate real-world problems and advance technologically. Image recognition models in particular, are assigned with perception tasks to mitigate complex real-world challenges and lead to new solutions. Furthermore, the computational complexity and demand for resources of such models has also increased. To mitigate this, model optimization and hardware acceleration has come into play, but effectively integrating such concepts is a challenging and error-prone process. In order to allow developers and researchers to explore the robustness of deep learning image recognition models deployed on different hardware acceleration devices, we propose MutateNN, a tool that provides mutation testing and analysis capabilities for that purpose. To showcase its capabilities, we utilized 21 mutations for 7 widely-known pre-trained deep neural network models. We deployed our mutants on 4 different devices of varying computational capabilities and observed discrepancies in mutants related to conditional operations, as well as some unstable behaviour with those related to arithmetic types.

Fault Localization for Framework Conversions of Image Recognition Models

When deploying Deep Neural Networks (DNNs), developers often convert models from one deep learning framework to another (e.g., TensorFlow to PyTorch). However, this process is error-prone and can impact target model accuracy. To identify the extent of such impact, we perform and briefly present a differential analysis against three DNNs used for image recognition (MobileNetV2, ResNet101, and InceptionV3), converted across four well-known deep learning frameworks (PyTorch, Keras, TensorFlow (TF), and TFLite), which revealed numerous model crashes and output label discrepancies of up to 100%. To mitigate such errors, we present a novel approach towards fault localization and repair of buggy deep learning framework conversions, focusing on pre-trained image recognition models. Our technique consists of four primary stages of analysis: 1) conversion tools, 2) model parameters, 3) model hyperparameters, and 4) graph representation. In addition, we propose a number of strategies towards fault repair of the faults detected. We implement our technique on top of Apache TVM deep learning compiler, and we test it by conducting a preliminary fault localization analysis for the conversion of InceptionV3, from TF to TFLite. Our approach detected that the tf2onnx tool used in the conversion process introduced precision errors to model weights for convolutional layers in particular, which negatively affected the model accuracy. We then repaired the target model by replacing the affected weights with those from source model.

A Differential Testing Framework to Evaluate Image Recognition Model Robustness

Image recognition tasks typically use deep learning and require enormous processing power, thus relying on hardware accelerators like GPUs and TPUs for fast, timely processing. Failure in real-time image recognition tasks can occur due to sub-optimal mapping on hardware accelerators during model deployment, which may lead to timing uncertainty and erroneous behavior. Mapping on hardware accelerators is done through multiple software components like deep learning frameworks, compilers, device libraries, that we refer to as the computational environment. Owing to the increased use of image recognition tasks in safety-critical applications like autonomous driving and medical imaging, it is imperative to assess their robustness to changes in the computational environment, as the impact of parameters like deep learning frameworks, compiler optimizations, and hardware devices on model performance and correctness is not well understood. In this paper we present a differential testing framework, which allows deep learning model variant generation, execution, differential analysis and testing for a number of computational environment parameters. Using our framework, we conduct an empirical study of robustness analysis of three popular image recognition models using the ImageNet dataset, assessing the impact of changing deep learning frameworks, compiler optimizations, and hardware devices. We report the impact in terms of misclassifications and inference time differences across different settings. In total, we observed up to 72% output label differences across deep learning frameworks, and up to 82% unexpected performance degradation in terms of inference time, when applying compiler optimizations. Using the analysis tools in our framework, we also perform fault analysis to understand the reasons for the observed differences.

Knowledge Graph Embeddings in the Biomedical Domain: Are They Useful? A Look at Link Prediction, Rule Learning, and Downstream Polypharmacy Tasks

Knowledge graphs are powerful tools for representing and organising complex biomedical data. Several knowledge graph embedding algorithms have been proposed to learn from and complete knowledge graphs. However, a recent study demonstrates the limited efficacy of these embedding algorithms when applied to biomedical knowledge graphs, raising the question of whether knowledge graph embeddings have limitations in biomedical settings. This study aims to apply state-of-the-art knowledge graph embedding models in the context of a recent biomedical knowledge graph, BioKG, and evaluate their performance and potential downstream uses. We achieve a three-fold improvement in terms of performance based on the HITS@10 score over previous work on the same biomedical knowledge graph. Additionally, we provide interpretable predictions through a rule-based method. We demonstrate that knowledge graph embedding models are applicable in practice by evaluating the best-performing model on four tasks that represent real-life polypharmacy situations. Results suggest that knowledge learnt from large biomedical knowledge graphs can be transferred to such downstream use cases. Our code is available at https://github.com/aryopg/biokge.

Can We Trust Explainable AI Methods on ASR? An Evaluation on Phoneme Recognition

Explainable AI (XAI) techniques have been widely used to help explain and understand the output of deep learning models in fields such as image classification and Natural Language Processing. Interest in using XAI techniques to explain deep learning-based automatic speech recognition (ASR) is emerging. but there is not enough evidence on whether these explanations can be trusted. To address this, we adapt a state-of-the-art XAI technique from the image classification domain, Local Interpretable Model-Agnostic Explanations (LIME), to a model trained for a TIMIT-based phoneme recognition task. This simple task provides a controlled setting for evaluation while also providing expert annotated ground truth to assess the quality of explanations. We find a variant of LIME based on time partitioned audio segments, that we propose in this paper, produces the most reliable explanations, containing the ground truth 96% of the time in its top three audio segments.

Vaxformer: Antigenicity-controlled Transformer for Vaccine Design Against SARS-CoV-2

The SARS-CoV-2 pandemic has emphasised the importance of developing a universal vaccine that can protect against current and future variants of the virus. The present study proposes a novel conditional protein Language Model architecture, called Vaxformer, which is designed to produce natural-looking antigenicity-controlled SARS-CoV-2 spike proteins. We evaluate the generated protein sequences of the Vaxformer model using DDGun protein stability measure, netMHCpan antigenicity score, and a structure fidelity score with AlphaFold to gauge its viability for vaccine development. Our results show that Vaxformer outperforms the existing state-of-the-art Conditional Variational Autoencoder model to generate antigenicity-controlled SARS-CoV-2 spike proteins. These findings suggest promising opportunities for conditional Transformer models to expand our understanding of vaccine design and their role in mitigating global health challenges. The code used in this study is available at https://github.com/aryopg/vaxformer .