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Background, enhancing interoperability of bioinformatics knowledge bases is a high priority requirement to maximize data reusability, and thus increase their utility such as the return on investment for biomedical research. A knowledge base may provide useful information for life scientists and other knowledge bases, but it only acquires exchange value once the knowledge base is (re)used, and without interoperability the utility lies dormant. Results, in this article, we discuss several approaches to boost interoperability depending on the interoperable parts. The findings are driven by several real-world scenario examples that were mostly implemented by Bgee, a well-established gene expression database. Moreover, we discuss ten general main lessons learnt. These lessons can be applied in the context of any bioinformatics knowledge base to foster data reusability. Conclusions, this work provides pragmatic methods and transferable skills to promote reusability of bioinformatics knowledge bases by focusing on interoperability.

Generalized linear mixed models are powerful tools for analyzing clustered data, where the unknown parameters are classically (and most commonly) estimated by the maximum likelihood and restricted maximum likelihood procedures. However, since the likelihood based procedures are known to be highly sensitive to outliers, M-estimators have become popular as a means to obtain robust estimates under possible data contamination. In this paper, we prove that, for sufficiently smooth general loss functions defining the M-estimators in generalized linear mixed models, the tail probability of the deviation between the estimated and the true regression coefficients have an exponential bound. This implies an exponential rate of consistency of these M-estimators under appropriate assumptions, generalizing the existing exponential consistency results from univariate to multivariate responses. We have illustrated this theoretical result further for the special examples of the maximum likelihood estimator and the robust minimum density power divergence estimator, a popular example of model-based M-estimators, in the settings of linear and logistic mixed models, comparing it with the empirical rate of convergence through simulation studies.

Both long-tailed and noisily labeled data frequently appear in real-world applications and impose significant challenges for learning. Most prior works treat either problem in an isolated way and do not explicitly consider the coupling effects of the two. Our empirical observation reveals that such solutions fail to consistently improve the learning when the dataset is long-tailed with label noise. Moreover, with the presence of label noise, existing methods do not observe universal improvements across different sub-populations; in other words, some sub-populations enjoyed the benefits of improved accuracy at the cost of hurting others. Based on these observations, we introduce the Fairness Regularizer (FR), inspired by regularizing the performance gap between any two sub-populations. We show that the introduced fairness regularizer improves the performances of sub-populations on the tail and the overall learning performance. Extensive experiments demonstrate the effectiveness of the proposed solution when complemented with certain existing popular robust or class-balanced methods.

Controller Area Network (CAN) is an essential networking protocol that connects multiple electronic control units (ECUs) in a vehicle. However, CAN-based in-vehicle networks (IVNs) face security risks owing to the CAN mechanisms. An adversary can sabotage a vehicle by leveraging the security risks if they can access the CAN bus. Thus, recent actions and cybersecurity regulations (e.g., UNR 155) require carmakers to implement intrusion detection systems (IDSs) in their vehicles. An IDS should detect cyberattacks and provide a forensic capability to analyze attacks. Although many IDSs have been proposed, considerations regarding their feasibility and explainability remain lacking. This study proposes X-CANIDS, which is a novel IDS for CAN-based IVNs. X-CANIDS dissects the payloads in CAN messages into human-understandable signals using a CAN database. The signals improve the intrusion detection performance compared with the use of bit representations of raw payloads. These signals also enable an understanding of which signal or ECU is under attack. X-CANIDS can detect zero-day attacks because it does not require any labeled dataset in the training phase. We confirmed the feasibility of the proposed method through a benchmark test on an automotive-grade embedded device with a GPU. The results of this work will be valuable to carmakers and researchers considering the installation of in-vehicle IDSs for their vehicles.

The rising performance of deep neural networks is often empirically attributed to an increase in the available computational power, which allows complex models to be trained upon large amounts of annotated data. However, increased model complexity leads to costly deployment of modern neural networks, while gathering such amounts of data requires huge costs to avoid label noise. In this work, we study the ability of compression methods to tackle both of these problems at once. We hypothesize that quantization-aware training, by restricting the expressivity of neural networks, behaves as a regularization. Thus, it may help fighting overfitting on noisy data while also allowing for the compression of the model at inference. We first validate this claim on a controlled test with manually introduced label noise. Furthermore, we also test the proposed method on Facial Action Unit detection, where labels are typically noisy due to the subtlety of the task. In all cases, our results suggests that quantization significantly improve the results compared with existing baselines, regularization as well as other compression methods.

This paper proposes an assessor-guided learning strategy for continual learning where an assessor guides the learning process of a base learner by controlling the direction and pace of the learning process thus allowing an efficient learning of new environments while protecting against the catastrophic interference problem. The assessor is trained in a meta-learning manner with a meta-objective to boost the learning process of the base learner. It performs a soft-weighting mechanism of every sample accepting positive samples while rejecting negative samples. The training objective of a base learner is to minimize a meta-weighted combination of the cross entropy loss function, the dark experience replay (DER) loss function and the knowledge distillation loss function whose interactions are controlled in such a way to attain an improved performance. A compensated over-sampling (COS) strategy is developed to overcome the class imbalanced problem of the episodic memory due to limited memory budgets. Our approach, Assessor-Guided Learning Approach (AGLA), has been evaluated in the class-incremental and task-incremental learning problems. AGLA achieves improved performances compared to its competitors while the theoretical analysis of the COS strategy is offered. Source codes of AGLA, baseline algorithms and experimental logs are shared publicly in \url{//github.com/anwarmaxsum/AGLA} for further study.

Instrumental variable (IV) strategies are widely used in political science to establish causal relationships. However, the identifying assumptions required by an IV design are demanding, and it remains challenging for researchers to assess their validity. In this paper, we replicate 67 papers published in three top journals in political science during 2010-2022 and identify several troubling patterns. First, researchers often overestimate the strength of their IVs due to non-i.i.d. errors, such as a clustering structure. Second, the most commonly used t-test for the two-stage-least-squares (2SLS) estimates often severely underestimates uncertainty. Using more robust inferential methods, we find that around 19-30% of the 2SLS estimates in our sample are underpowered. Third, in the majority of the replicated studies, the 2SLS estimates are much larger than the ordinary-least-squares estimates, and their ratio is negatively correlated with the strength of the IVs in studies where the IVs are not experimentally generated, suggesting potential violations of unconfoundedness or the exclusion restriction. To help researchers avoid these pitfalls, we provide a checklist for better practice.

Money laundering is a profound global problem. Nonetheless, there is little scientific literature on statistical and machine learning methods for anti-money laundering. In this paper, we focus on anti-money laundering in banks and provide an introduction and review of the literature. We propose a unifying terminology with two central elements: (i) client risk profiling and (ii) suspicious behavior flagging. We find that client risk profiling is characterized by diagnostics, i.e., efforts to find and explain risk factors. On the other hand, suspicious behavior flagging is characterized by non-disclosed features and hand-crafted risk indices. Finally, we discuss directions for future research. One major challenge is the need for more public data sets. This may potentially be addressed by synthetic data generation. Other possible research directions include semi-supervised and deep learning, interpretability, and fairness of the results.

In the present academic landscape, the process of collecting data is slow, and the lax infrastructures for data collaborations lead to significant delays in coming up with and disseminating conclusive findings. Therefore, there is an increasing need for a secure, scalable, and trustworthy data-sharing ecosystem that promotes and rewards collaborative data-sharing efforts among researchers, and a robust incentive mechanism is required to achieve this objective. Reputation-based incentives, such as the h-index, have historically played a pivotal role in the academic community. However, the h-index suffers from several limitations. This paper introduces the SCIENCE-index, a blockchain-based metric measuring a researcher's scientific contributions. Utilizing the Microsoft Academic Graph and machine learning techniques, the SCIENCE-index predicts the progress made by a researcher over their career and provides a soft incentive for sharing their datasets with peer researchers. To incentivize researchers to share their data, the SCIENCE-index is augmented to include a data-sharing parameter. DataCite, a database of openly available datasets, proxies this parameter, which is further enhanced by including a researcher's data-sharing activity. Our model is evaluated by comparing the distribution of its output for geographically diverse researchers to that of the h-index. We observe that it results in a much more even spread of evaluations. The SCIENCE-index is a crucial component in constructing a decentralized protocol that promotes trust-based data sharing, addressing the current inequity in dataset sharing. The work outlined in this paper provides the foundation for assessing scientific contributions in future data-sharing spaces powered by decentralized applications.

Graph property prediction tasks are important and numerous. While each task offers a small size of labeled examples, unlabeled graphs have been collected from various sources and at a large scale. A conventional approach is training a model with the unlabeled graphs on self-supervised tasks and then fine-tuning the model on the prediction tasks. However, the self-supervised task knowledge could not be aligned or sometimes conflicted with what the predictions needed. In this paper, we propose to extract the knowledge underlying the large set of unlabeled graphs as a specific set of useful data points to augment each property prediction model. We use a diffusion model to fully utilize the unlabeled graphs and design two new objectives to guide the model's denoising process with each task's labeled data to generate task-specific graph examples and their labels. Experiments demonstrate that our data-centric approach performs significantly better than fourteen existing various methods on fifteen tasks. The performance improvement brought by unlabeled data is visible as the generated labeled examples unlike self-supervised learning.