arXiv subjects

Ajitha Rajan

Publications and source records attributed to Ajitha Rajan.

32 records · Page 2Linked to original sources

arXiv2023

Learning to Encode and Classify Test Executions

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.

cs.SE↗

arXiv2023

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.

cs.SE↗

arXiv2023

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.

cs.LG↗

arXiv2023

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.

cs.CL↗

arXiv2023

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 .

q-bio.BM↗

arXiv2023

BenchDirect: A Directed Language Model for Compiler Benchmarks

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.

cs.LG↗

arXiv2023

Exploring Effects of Computational Parameter Changes to Image Recognition Systems

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.

cs.LG↗

arXiv2022

BenchPress: A Deep Active Benchmark Generator

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.

cs.AI↗

arXiv2022

Catch Me If You Can: Blackbox Adversarial Attacks on Automatic Speech Recognition using Frequency Masking

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.

cs.SD↗

arXiv2022

Vision Checklist: Towards Testable Error Analysis of Image Models to Help System Designers Interrogate Model Capabilities

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.

cs.CV↗

arXiv2021

Interpreting BERT architecture predictions for peptide presentation by MHC class I proteins

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.

q-bio.QM↗

arXiv2020

CAT: Change-focused Android GUI Testing

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.

cs.SE↗

arXiv2020

M3: Semantic API Migrations

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.

cs.SE↗

arXiv2019

SIF: A Framework for Solidity Code Instrumentation and Analysis

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.

cs.SE↗