Motivation: Machine learning methods can be used to support scientific discovery in healthcare-related research fields. However, these methods can only be reliably used if they can be trained on high-quality and curated datasets. Currently, no such dataset for the exploration of Plasmodium falciparum protein antigen candidates exists. The parasite Plasmodium falciparum causes the infectious disease malaria. Thus, identifying potential antigens is of utmost importance for the development of antimalarial drugs and vaccines. Since exploring antigen candidates experimentally is an expensive and time-consuming process, applying machine learning methods to support this process has the potential to accelerate the development of drugs and vaccines, which are needed for fighting and controlling malaria. Results: We developed PlasmoFAB, a curated benchmark that can be used to train machine learning methods for the exploration of Plasmodium falciparum protein antigen candidates. We combined an extensive literature search with domain expertise to create high-quality labels for Plasmodium falciparum specific proteins that distinguish between antigen candidates and intracellular proteins. Additionally, we used our benchmark to compare different well-known prediction models and available protein localization prediction services on the task of identifying protein antigen candidates. We show that available general-purpose services are unable to provide sufficient performance on identifying protein antigen candidates and are outperformed by our models that were trained on this tailored data. Availability: PlasmoFAB is publicly available on Zenodo with DOI 10.5281/zenodo.7433087. Furthermore, all scripts that were used in the creation of PlasmoFAB and the training and evaluation of machine learning models are open source and publicly available on GitHub here: //github.com/msmdev/PlasmoFAB.
Over the past few years, Federated Learning (FL) has become an emerging machine learning technique to tackle data privacy challenges through collaborative training. In the Federated Learning algorithm, the clients submit a locally trained model, and the server aggregates these parameters until convergence. Despite significant efforts that have been made to FL in fields like computer vision, audio, and natural language processing, the FL applications utilizing multimodal data streams remain largely unexplored. It is known that multimodal learning has broad real-world applications in emotion recognition, healthcare, multimedia, and social media, while user privacy persists as a critical concern. Specifically, there are no existing FL benchmarks targeting multimodal applications or related tasks. In order to facilitate the research in multimodal FL, we introduce FedMultimodal, the first FL benchmark for multimodal learning covering five representative multimodal applications from ten commonly used datasets with a total of eight unique modalities. FedMultimodal offers a systematic FL pipeline, enabling end-to-end modeling framework ranging from data partition and feature extraction to FL benchmark algorithms and model evaluation. Unlike existing FL benchmarks, FedMultimodal provides a standardized approach to assess the robustness of FL against three common data corruptions in real-life multimodal applications: missing modalities, missing labels, and erroneous labels. We hope that FedMultimodal can accelerate numerous future research directions, including designing multimodal FL algorithms toward extreme data heterogeneity, robustness multimodal FL, and efficient multimodal FL. The datasets and benchmark results can be accessed at: //github.com/usc-sail/fed-multimodal.
Reliable probabilistic primality tests are fundamental in public-key cryptography. In adversarial scenarios, a composite with a high probability of passing a specific primality test could be chosen. In such cases, we need worst-case error estimates for the test. However, in many scenarios the numbers are randomly chosen and thus have significantly smaller error probability. Therefore, we are interested in average case error estimates. In this paper, we establish such bounds for the strong Lucas primality test, as only worst-case, but no average case error bounds, are currently available. This allows us to use this test with more confidence. We examine an algorithm that draws odd $k$-bit integers uniformly and independently, runs $t$ independent iterations of the strong Lucas test with randomly chosen parameters, and outputs the first number that passes all $t$ consecutive rounds. We attain numerical upper bounds on the probability on returing a composite. Furthermore, we consider a modified version of this algorithm that excludes integers divisible by small primes, resulting in improved bounds. Additionally, we classify the numbers that contribute most to our estimate.
Out-of-Distribution (OOD) detection is critical for the reliable operation of open-world intelligent systems. Despite the emergence of an increasing number of OOD detection methods, the evaluation inconsistencies present challenges for tracking the progress in this field. OpenOOD v1 initiated the unification of the OOD detection evaluation but faced limitations in scalability and usability. In response, this paper presents OpenOOD v1.5, a significant improvement from its predecessor that ensures accurate, standardized, and user-friendly evaluation of OOD detection methodologies. Notably, OpenOOD v1.5 extends its evaluation capabilities to large-scale datasets such as ImageNet, investigates full-spectrum OOD detection which is important yet underexplored, and introduces new features including an online leaderboard and an easy-to-use evaluator. This work also contributes in-depth analysis and insights derived from comprehensive experimental results, thereby enriching the knowledge pool of OOD detection methodologies. With these enhancements, OpenOOD v1.5 aims to drive advancements and offer a more robust and comprehensive evaluation benchmark for OOD detection research.
Real-world software applications must constantly evolve to remain relevant. This evolution occurs when developing new applications or adapting existing ones to meet new requirements, make corrections, or incorporate future functionality. Traditional methods of software quality control involve software quality models and continuous code inspection tools. These measures focus on directly assessing the quality of the software. However, there is a strong correlation and causation between the quality of the development process and the resulting software product. Therefore, improving the development process indirectly improves the software product, too. To achieve this, effective learning from past processes is necessary, often embraced through post mortem organizational learning. While qualitative evaluation of large artifacts is common, smaller quantitative changes captured by application lifecycle management are often overlooked. In addition to software metrics, these smaller changes can reveal complex phenomena related to project culture and management. Leveraging these changes can help detect and address such complex issues. Software evolution was previously measured by the size of changes, but the lack of consensus on a reliable and versatile quantification method prevents its use as a dependable metric. Different size classifications fail to reliably describe the nature of evolution. While application lifecycle management data is rich, identifying which artifacts can model detrimental managerial practices remains uncertain. Approaches such as simulation modeling, discrete events simulation, or Bayesian networks have only limited ability to exploit continuous-time process models of such phenomena. Even worse, the accessibility and mechanistic insight into such gray- or black-box models are typically very low. To address these challenges, we suggest leveraging objectively [...]
Recent years have seen a strongly increased visibility of non-binary people in public discourse. Accordingly, considerations of gender-fair language go beyond a binary conception of male/female. However, language technology, especially machine translation (MT), still suffers from binary gender bias. Proposing a solution for gender-fair MT beyond the binary from a purely technological perspective might fall short to accommodate different target user groups and in the worst case might lead to misgendering. To address this challenge, we propose a method and case study building on participatory action research to include experiential experts, i.e., queer and non-binary people, translators, and MT experts, in the MT design process. The case study focuses on German, where central findings are the importance of context dependency to avoid identity invalidation and a desire for customizable MT solutions.
More than one hundred benchmarks have been developed to test the commonsense knowledge and commonsense reasoning abilities of artificial intelligence (AI) systems. However, these benchmarks are often flawed and many aspects of common sense remain untested. Consequently, we do not currently have any reliable way of measuring to what extent existing AI systems have achieved these abilities. This paper surveys the development and uses of AI commonsense benchmarks. We discuss the nature of common sense; the role of common sense in AI; the goals served by constructing commonsense benchmarks; and desirable features of commonsense benchmarks. We analyze the common flaws in benchmarks, and we argue that it is worthwhile to invest the work needed ensure that benchmark examples are consistently high quality. We survey the various methods of constructing commonsense benchmarks. We enumerate 139 commonsense benchmarks that have been developed: 102 text-based, 18 image-based, 12 video based, and 7 simulated physical environments. We discuss the gaps in the existing benchmarks and aspects of commonsense reasoning that are not addressed in any existing benchmark. We conclude with a number of recommendations for future development of commonsense AI benchmarks.
Deep neural networks (DNNs) have become a proven and indispensable machine learning tool. As a black-box model, it remains difficult to diagnose what aspects of the model's input drive the decisions of a DNN. In countless real-world domains, from legislation and law enforcement to healthcare, such diagnosis is essential to ensure that DNN decisions are driven by aspects appropriate in the context of its use. The development of methods and studies enabling the explanation of a DNN's decisions has thus blossomed into an active, broad area of research. A practitioner wanting to study explainable deep learning may be intimidated by the plethora of orthogonal directions the field has taken. This complexity is further exacerbated by competing definitions of what it means ``to explain'' the actions of a DNN and to evaluate an approach's ``ability to explain''. This article offers a field guide to explore the space of explainable deep learning aimed at those uninitiated in the field. The field guide: i) Introduces three simple dimensions defining the space of foundational methods that contribute to explainable deep learning, ii) discusses the evaluations for model explanations, iii) places explainability in the context of other related deep learning research areas, and iv) finally elaborates on user-oriented explanation designing and potential future directions on explainable deep learning. We hope the guide is used as an easy-to-digest starting point for those just embarking on research in this field.
Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect subgraphs, rendering subgraph prediction tasks challenging to tackle in many impactful applications. Further, subgraph prediction tasks present several unique challenges, because subgraphs can have non-trivial internal topology, but also carry a notion of position and external connectivity information relative to the underlying graph in which they exist. Here, we introduce SUB-GNN, a subgraph neural network to learn disentangled subgraph representations. In particular, we propose a novel subgraph routing mechanism that propagates neural messages between the subgraph's components and randomly sampled anchor patches from the underlying graph, yielding highly accurate subgraph representations. SUB-GNN specifies three channels, each designed to capture a distinct aspect of subgraph structure, and we provide empirical evidence that the channels encode their intended properties. We design a series of new synthetic and real-world subgraph datasets. Empirical results for subgraph classification on eight datasets show that SUB-GNN achieves considerable performance gains, outperforming strong baseline methods, including node-level and graph-level GNNs, by 12.4% over the strongest baseline. SUB-GNN performs exceptionally well on challenging biomedical datasets when subgraphs have complex topology and even comprise multiple disconnected components.
Deep learning models on graphs have achieved remarkable performance in various graph analysis tasks, e.g., node classification, link prediction and graph clustering. However, they expose uncertainty and unreliability against the well-designed inputs, i.e., adversarial examples. Accordingly, various studies have emerged for both attack and defense addressed in different graph analysis tasks, leading to the arms race in graph adversarial learning. For instance, the attacker has poisoning and evasion attack, and the defense group correspondingly has preprocessing- and adversarial- based methods. Despite the booming works, there still lacks a unified problem definition and a comprehensive review. To bridge this gap, we investigate and summarize the existing works on graph adversarial learning tasks systemically. Specifically, we survey and unify the existing works w.r.t. attack and defense in graph analysis tasks, and give proper definitions and taxonomies at the same time. Besides, we emphasize the importance of related evaluation metrics, and investigate and summarize them comprehensively. Hopefully, our works can serve as a reference for the relevant researchers, thus providing assistance for their studies. More details of our works are available at //github.com/gitgiter/Graph-Adversarial-Learning.
Time Series Classification (TSC) is an important and challenging problem in data mining. With the increase of time series data availability, hundreds of TSC algorithms have been proposed. Among these methods, only a few have considered Deep Neural Networks (DNNs) to perform this task. This is surprising as deep learning has seen very successful applications in the last years. DNNs have indeed revolutionized the field of computer vision especially with the advent of novel deeper architectures such as Residual and Convolutional Neural Networks. Apart from images, sequential data such as text and audio can also be processed with DNNs to reach state-of-the-art performance for document classification and speech recognition. In this article, we study the current state-of-the-art performance of deep learning algorithms for TSC by presenting an empirical study of the most recent DNN architectures for TSC. We give an overview of the most successful deep learning applications in various time series domains under a unified taxonomy of DNNs for TSC. We also provide an open source deep learning framework to the TSC community where we implemented each of the compared approaches and evaluated them on a univariate TSC benchmark (the UCR/UEA archive) and 12 multivariate time series datasets. By training 8,730 deep learning models on 97 time series datasets, we propose the most exhaustive study of DNNs for TSC to date.