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Deep learning models for medical image classification tasks are becoming widely implemented in AI-assisted diagnostic tools, aiming to enhance diagnostic accuracy, reduce clinician workloads, and improve patient outcomes. However, their vulnerability to adversarial attacks poses significant risks to patient safety. Current attack methodologies use general techniques such as model querying or pixel value perturbations to generate adversarial examples designed to fool a model. These approaches may not adequately address the unique characteristics of clinical errors stemming from missed or incorrectly identified clinical features. We propose the Concept-based Report Perturbation Attack (CoRPA), a clinically-focused black-box adversarial attack framework tailored to the medical imaging domain. CoRPA leverages clinical concepts to generate adversarial radiological reports and images that closely mirror realistic clinical misdiagnosis scenarios. We demonstrate the utility of CoRPA using the MIMIC-CXR-JPG dataset of chest X-rays and radiological reports. Our evaluation reveals that deep learning models exhibiting strong resilience to conventional adversarial attacks are significantly less robust when subjected to CoRPA's clinically-focused perturbations. This underscores the importance of addressing domain-specific vulnerabilities in medical AI systems. By introducing a specialized adversarial attack framework, this study provides a foundation for developing robust, real-world-ready AI models in healthcare, ensuring their safe and reliable deployment in high-stakes clinical environments., Comment: 12 pages, 5 figures

The Go programming language has gained significant traction for developing software, especially in various infrastructure systems. Nonetheless, concurrency bugs have become a prevalent issue within Go, presenting a unique challenge due to the language's dual concurrency mechanisms-communicating sequential processes and shared memory. Detecting concurrency bugs and accurately classifying program executions as pass or fail presents an immense challenge, even for domain experts. We conducted a survey with expert developers at Bytedance that confirmed this challenge. Our work seeks to address the test oracle problem for Go programs, to automatically classify test executions as pass or fail. This problem has not been investigated in the literature for Go programs owing to its distinctive programming model. Our approach involves collecting both passing and failing execution traces from various subject Go programs. We capture a comprehensive array of execution events using the native Go execution tracer. Subsequently, we preprocess and encode these traces before training a transformer-based neural network to effectively classify the traces as either passing or failing. The evaluation of our approach encompasses 8 subject programs sourced from the GoBench repository. These subject programs are routinely used as benchmarks in an industry setting. Encouragingly, our test oracle, Go-Oracle, demonstrates high accuracies even when operating with a limited dataset, showcasing the efficacy and potential of our methodology. Developers at Bytedance strongly agreed that they would use the Go-Oracle tool over the current practice of manual inspections to classify tests for Go programs as pass or fail.

This paper proposes a fully explainable approach to speaker verification (SV), a task that fundamentally relies on individual speaker characteristics. The opaque use of speaker attributes in current SV systems raises concerns of trust. Addressing this, we propose an attribute-based explainable SV system that identifies speakers by comparing personal attributes such as gender, nationality, and age extracted automatically from voice recordings. We believe this approach better aligns with human reasoning, making it more understandable than traditional methods. Evaluated on the Voxceleb1 test set, the best performance of our system is comparable with the ground truth established when using all correct attributes, proving its efficacy. Whilst our approach sacrifices some performance compared to non-explainable methods, we believe that it moves us closer to the goal of transparent, interpretable AI and lays the groundwork for future enhancements through attribute expansion.

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., Comment: 12 pages, 10 figures

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. In this paper 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 reported \nick{in code repositories and forums}) to localize potential conversion faults in the converted target model and then repair 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, comparing 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 fix $462$ out of $755$ detected conversion faults, either completely repairing or significantly improving the performance of $14$ out of the $15$ erroneous conversion cases., Comment: 12 pages, 4 figures, 3 tables, 1 algorithm

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.

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 widely 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 stages of analysis: 1) conversion tools, 2) model parameters, 3) model hyperparameters, and 4) graph representation. In addition, we propose various strategies towards fault repair of the faults detected. We implement our technique on top of the 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 a fault in a common DNN converter tool, which introduced precision errors in weights, reducing model accuracy. After our fault localization, we repaired the issue, reducing our conversion error to zero., Comment: 5 pages, 3 figures, 1 table

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 using multiple software components like deep learning frameworks, compilers, and 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 yet well understood. In this paper we present a differential testing framework, DeltaNN, that allows us to assess the impact of different computational environment parameters on the performance of image recognition models during deployment, post training. DeltaNN generates different implementations of a given image recognition model for variations in environment parameters, namely, deep learning frameworks, compiler optimizations and hardware devices and analyzes differences in model performance as a result. Using DeltaNN, we conduct an empirical study of robustness analysis of three popular image recognition models using the ImageNet dataset. We report the impact in terms of misclassifications and inference time differences across different settings. In total, we observed up to 100% output label differences across deep learning frameworks, and up to 81% unexpected performance degradation in terms of inference time, when applying compiler optimizations., Comment: 11 pages, 10 figures, 2 tables

The increased utilization of Artificial Intelligence (AI) solutions brings with it inherent risks, such as misclassification and sub-optimal execution time performance, due to errors introduced in their deployment infrastructure because of problematic configuration and software faults. On top of that, AI methods such as Deep Neural Networks (DNNs) are utilized to perform demanding, resource-intensive and even safety-critical tasks, and in order to effectively increase the performance of the DNN models deployed, a variety of Machine Learning (ML) compilers have been developed, allowing compatibility of DNNs with a variety of hardware acceleration devices, such as GPUs and TPUs. Furthermore the correctness of the compilation process should be verified. In order to allow developers and researchers to explore the robustness of DNN models deployed on different hardware accelerators via ML compilers, in this paper we propose MutateNN, a tool that provides mutation testing and model analysis features in the context of deployment on different hardware accelerators. To demonstrate the capabilities of MutateNN, we focus on the image recognition domain by applying mutation testing to 7 well-established models utilized for image classification. We instruct 21 mutations of 6 different categories, and deploy our mutants on 4 different hardware acceleration devices of varying capabilities. Our results indicate that models are proven robust to changes related to layer modifications and arithmetic operators, while presenting discrepancies of up to 90.3% in mutants related to conditional operators. We also observed unexpectedly severe performance degradation on mutations related to arithmetic types of variables, leading the mutants to produce the same classifications for all dataset inputs., Comment: 7 pages, 7 figures

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.

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.

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 .

The exponential increase of hardware-software complexity has made it impossible for compiler engineers to find the right optimization heuristics manually. Predictive models have been shown to find near optimal heuristics with little human effort but they are limited by a severe lack of diverse benchmarks to train on. Generative AI has been used by researchers to synthesize benchmarks into existing datasets. However, the synthetic programs are short, exceedingly simple and lacking diversity in their features. We develop BenchPress, the first ML compiler benchmark generator that can be directed within source code feature representations. BenchPress synthesizes executable functions by infilling code that conditions on the program's left and right context. BenchPress uses active learning to introduce new benchmarks with unseen features into the dataset of Grewe's et al. CPU vs GPU heuristic, improving its acquired performance by 50%. BenchPress targets features that has been impossible for other synthesizers to reach. In 3 feature spaces, we outperform human-written code from GitHub, CLgen, CLSmith and the SRCIROR mutator in targeting the features of Rodinia benchmarks. BenchPress steers generation with beam search over a feature-agnostic language model. We improve this with BenchDirect which utilizes a directed LM that infills programs by jointly observing source code context and the compiler features that are targeted. BenchDirect achieves up to 36% better accuracy in targeting the features of Rodinia benchmarks, it is 1.8x more likely to give an exact match and it speeds up execution time by up to 72% compared to BenchPress. Both our models produce code that is difficult to distinguish from human-written code. We conduct a Turing test which shows our models' synthetic benchmarks are labelled as 'human-written' as often as human-written code from GitHub., Comment: arXiv admin note: substantial text overlap with arXiv:2208.06555

We address quality assessment for neural network based ASR by providing explanations that help increase our understanding of the system and ultimately help build trust in the system. Compared to simple classification labels, explaining transcriptions is more challenging as judging their correctness is not straightforward and transcriptions as a variable-length sequence is not handled by existing interpretable machine learning models. We provide an explanation for an ASR transcription as a subset of audio frames that is both a minimal and sufficient cause of the transcription. To do this, we adapt existing explainable AI (XAI) techniques from image classification-Statistical Fault Localisation(SFL) and Causal. Additionally, we use an adapted version of Local Interpretable Model-Agnostic Explanations (LIME) for ASR as a baseline in our experiments. We evaluate the quality of the explanations generated by the proposed techniques over three different ASR ,Google API, the baseline model of Sphinx, Deepspeech and 100 audio samples from the Commonvoice dataset., Comment: Accepted by Speech Track, ICASSP 2023

Image recognition tasks typically use deep learning and require enormous processing power, thus relying on hardware accelerators like GPUs and FPGAs for fast, timely processing. Failure in real-time image recognition tasks can occur due to incorrect mapping on hardware accelerators, which may lead to timing uncertainty and incorrect behavior. 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 parameters like deep learning frameworks, compiler optimizations for code generation, and hardware devices are not regulated with varying impact on model performance and correctness. In this paper we conduct robustness analysis of four popular image recognition models (MobileNetV2, ResNet101V2, DenseNet121 and InceptionV3) with the ImageNet dataset, assessing the impact of the following parameters in the model's computational environment: (1) deep learning frameworks; (2) compiler optimizations; and (3) hardware devices. We report sensitivity of model performance in terms of output label and inference time for changes in each of these environment parameters. We find that output label predictions for all four models are sensitive to choice of deep learning framework (by up to 57%) and insensitive to other parameters. On the other hand, model inference time was affected by all environment parameters with changes in hardware device having the most effect. The extent of effect was not uniform across models., Comment: 9 pages, 8 figures, 1 table

We develop BenchPress, the first ML benchmark generator for compilers that is steerable within feature space representations of source code. BenchPress synthesizes compiling functions by adding new code in any part of an empty or existing sequence by jointly observing its left and right context, achieving excellent compilation rate. BenchPress steers benchmark generation towards desired target features that has been impossible for state of the art synthesizers (or indeed humans) to reach. It performs better in targeting the features of Rodinia benchmarks in 3 different feature spaces compared with (a) CLgen - a state of the art ML synthesizer, (b) CLSmith fuzzer, (c) SRCIROR mutator or even (d) human-written code from GitHub. BenchPress is the first generator to search the feature space with active learning in order to generate benchmarks that will improve a downstream task. We show how using BenchPress, Grewe's et al. CPU vs GPU heuristic model can obtain a higher speedup when trained on BenchPress's benchmarks compared to other techniques. BenchPress is a powerful code generator: Its generated samples compile at a rate of 86%, compared to CLgen's 2.33%. Starting from an empty fixed input, BenchPress produces 10x more unique, compiling OpenCL benchmarks than CLgen, which are significantly larger and more feature diverse., Comment: To appear in PACT 2022

Using large pre-trained models for image recognition tasks is becoming increasingly common owing to the well acknowledged success of recent models like vision transformers and other CNN-based models like VGG and Resnet. The high accuracy of these models on benchmark tasks has translated into their practical use across many domains including safety-critical applications like autonomous driving and medical diagnostics. Despite their widespread use, image models have been shown to be fragile to changes in the operating environment, bringing their robustness into question. There is an urgent need for methods that systematically characterise and quantify the capabilities of these models to help designers understand and provide guarantees about their safety and robustness. In this paper, we propose Vision Checklist, a framework aimed at interrogating the capabilities of a model in order to produce a report that can be used by a system designer for robustness evaluations. This framework proposes a set of perturbation operations that can be applied on the underlying data to generate test samples of different types. The perturbations reflect potential changes in operating environments, and interrogate various properties ranging from the strictly quantitative to more qualitative. Our framework is evaluated on multiple datasets like Tinyimagenet, CIFAR10, CIFAR100 and Camelyon17 and for models like ViT and Resnet. Our Vision Checklist proposes a specific set of evaluations that can be integrated into the previously proposed concept of a model card. Robustness evaluations like our checklist will be crucial in future safety evaluations of visual perception modules, and be useful for a wide range of stakeholders including designers, deployers, and regulators involved in the certification of these systems. Source code of Vision Checklist would be open for public use., Comment: 17 pages, 18 figures

Automatic speech recognition (ASR) models are prevalent, particularly in applications for voice navigation and voice control of domestic appliances. The computational core of ASRs are deep neural networks (DNNs) that have been shown to be susceptible to adversarial perturbations; easily misused by attackers to generate malicious outputs. To help test the security and robustnesss of ASRS, we propose techniques that generate blackbox (agnostic to the DNN), untargeted adversarial attacks that are portable across ASRs. This is in contrast to existing work that focuses on whitebox targeted attacks that are time consuming and lack portability. Our techniques generate adversarial attacks that have no human audible difference by manipulating the audio signal using a psychoacoustic model that maintains the audio perturbations below the thresholds of human perception. We evaluate portability and effectiveness of our techniques using three popular ASRs and two input audio datasets using the metrics - Word Error Rate (WER) of output transcription, Similarity to original audio, attack Success Rate on different ASRs and Detection score by a defense system. We found our adversarial attacks were portable across ASRs, not easily detected by a state-of-the-art defense system, and had significant difference in output transcriptions while sounding similar to original audio., Comment: 11 pages, 7 figures and 3 tables

The major histocompatibility complex (MHC) class-I pathway supports the detection of cancer and viruses by the immune system. It presents parts of proteins (peptides) from inside a cell on its membrane surface enabling visiting immune cells that detect non-self peptides to terminate the cell. The ability to predict whether a peptide will get presented on MHC Class I molecules helps in designing vaccines so they can activate the immune system to destroy the invading disease protein. We designed a prediction model using a BERT-based architecture (ImmunoBERT) that takes as input a peptide and its surrounding regions (N and C-terminals) along with a set of MHC class I (MHC-I) molecules. We present a novel application of well known interpretability techniques, SHAP and LIME, to this domain and we use these results along with 3D structure visualizations and amino acid frequencies to understand and identify the most influential parts of the input amino acid sequences contributing to the output. In particular, we find that amino acids close to the peptides' N- and C-terminals are highly relevant. Additionally, some positions within the MHC proteins (in particular in the A, B and F pockets) are often assigned a high importance ranking - which confirms biological studies and the distances in the structure visualizations., Comment: 10 pages

Android Apps are frequently updated, every couple of weeks, to keep up with changing user, hardware and business demands. Correctness of App updates is checked through extensive testing. Recent research has proposed tools for automated GUI event generation in Android Apps. These techniques, however, are not efficient at checking App updates as the generated GUI events do not prioritise updates, and instead explore other App behaviours. We address this need in this paper with CAT (Change-focused Android GUI Testing). For App updates, at the source code or GUI level, CAT performs change impact analysis to identify GUI elements affected by the update. CAT then generates length-3 GUI event sequences to interact with these GUI elements. Our empirical evaluations using 21 publicly available open source Android Apps demonstrated that CAT is able to automatically identify GUI elements affected by App updates, generate and execute length-3 GUI event sequences focusing on change-affected GUI elements. Comparison with two popular GUI event generation tools, DroidBot and DroidMate, revealed that CAT was more effective at interacting with the change-affected GUI elements. Finally, CAT was able to detect previously unknown change-related bugs in two Apps.

Library migration is a challenging problem, where most existing approaches rely on prior knowledge. This can be, for example, information derived from changelogs or statistical models of API usage. This paper addresses a different API migration scenario where there is no prior knowledge of the target library. We have no historical changelogs and no access to its internal representation. To tackle this problem, this paper proposes a novel approach (M$^3$), where probabilistic program synthesis is used to semantically model the behavior of library functions. Then, we use an SMT-based code search engine to discover similar code in user applications. These discovered instances provide potential locations for API migrations. We evaluate our approach against 7 well-known libraries from varied application domains, learning correct implementations for 94 functions. Our approach is integrated with standard compiler tooling, and we use this integration to evaluate migration opportunities in 9 existing C/C++ applications with over 1MLoC. We discover over 7,000 instances of these functions, of which more than 2,000 represent migration opportunities., Comment: Accepted to ASE 2020

The challenge of automatically determining the correctness of test executions is referred to as the test oracle problem and is one of the key remaining issues for automated testing. The goal in this paper is to solve the test oracle problem in a way that is general, scalable and accurate. To achieve this, we use supervised learning over test execution traces. We label a small fraction of the execution traces with their verdict of pass or fail. We use the labelled traces to train a neural network (NN) model to learn to distinguish runtime patterns for passing versus failing executions for a given program. Our approach for building this NN model involves the following steps, 1. Instrument the program to record execution traces as sequences of method invocations and global state, 2. Label a small fraction of the execution traces with their verdicts, 3. Designing a NN component that embeds information in execution traces to fixed length vectors, 4. Design a NN model that uses the trace information for classification, 5. Evaluate the inferred classification model on unseen execution traces from the program. We evaluate our approach using case studies from different application domains: 1. Module from Ethereum Blockchain, 2. Module from PyTorch deep learning framework, 3. Microsoft SEAL encryption library components, 4. Sed stream editor, 5. Value pointer library and 6. Nine network protocols from Linux packet identifier, L7-Filter. We found the classification models for all subject programs resulted in high precision, recall and specificity, over 95%, while only training with an average 9% of the total traces. Our experiments show that the proposed neural network model is highly effective as a test oracle and is able to learn runtime patterns to distinguish passing and failing test executions for systems and tests from different application domains.

Solidity is an object-oriented and high-level language for writing smart contracts that are used to execute, verify and enforce credible transactions on permissionless blockchains. In the last few years, analysis of smart contracts has raised considerable interest and numerous techniques have been proposed to check the presence of vulnerabilities in them. Current techniques lack traceability in source code and have widely differing work flows. There is no single unifying framework for analysis, instrumentation, optimisation and code generation of Solidity contracts. In this paper, we present SIF, a comprehensive framework for Solidity contract analysis, query, instrumentation, and code generation. SIF provides support for Solidity contract developers and testers to build source level techniques for analysis, understanding, diagnostics, optimisations and code generation. We show feasibility and applicability of the framework by building practical tools on top of it and running them on 1838 real smart contracts deployed on the Ethereum network.