Purpose: To assess Generative Pre-trained Transformer version 4's (GPT-4) ability to classify articles containing functional evidence relevant to assessments of variant pathogenicity. Results: GPT-4 settings and prompts were trained on a set of 45 articles and genetic variants. A final test set of 72 manually classified articles and genetic variants were then processed using two prompts. The prompts asked GPT-4 to supply all functional evidence present in an article for a variant or indicate that no functional evidence is present. For articles with having functional evidence, a second prompt asked GPT-4 to classify the evidence into pathogenic, benign, intermediate, and inconclusive categories. The first prompt identified articles with variant-level functional evidence with 87% sensitivity and 89% positive predictive value (PPV). Five of 26 articles with no functional data were indicated as having functional evidence by GPT-4. For variants with functional assays present as determined by both manual review and GPT-4, the sensitivity and PPV of GPT-4 prompt concordance was: Pathogenic (92% sensitive and 73% PPV), Intermediate or Inconclusive (67% sensitive and 93% PPV), Benign (100% sensitive and 73% PPV). Conclusion: The GPT-4 prompts detected the presence or absence of a functional assay with high sensitivity and PPV, and articles with unambiguous evidence supporting a benign or pathogenic classification with high sensitivity and reasonable PPV. Our prompts detected papers with intermediate or inconclusive evidence with lower sensitivity but high PPV. Our results support that GPT-4 may be useful in variant classification workflows by enabling prioritization of articles for review that are likely to have functional evidence supporting or refuting pathogenicity, but not that GPT-4 is capable of fully automating the genetics literature review component of variant classification.
We propose a novel method for privacy-preserving deep neural networks (DNNs) with the Vision Transformer (ViT). The method allows us not only to train models and test with visually protected images but to also avoid the performance degradation caused from the use of encrypted images, whereas conventional methods cannot avoid the influence of image encryption. A domain adaptation method is used to efficiently fine-tune ViT with encrypted images. In experiments, the method is demonstrated to outperform conventional methods in an image classification task on the CIFAR-10 and ImageNet datasets in terms of classification accuracy.
This paper studies the use of Metropolis-Hastings sampling for training Spiking Neural Network (SNN) hardware subject to strong unknown non-idealities, and compares the proposed approach to the common use of the backpropagation of error (backprop) algorithm and surrogate gradients, widely used to train SNNs in literature. Simulations are conducted within a chip-in-the-loop training context, where an SNN subject to unknown distortion must be trained to detect cancer from measurements, within a biomedical application context. Our results show that the proposed approach strongly outperforms the use of backprop by up to $27\%$ higher accuracy when subject to strong hardware non-idealities. Furthermore, our results also show that the proposed approach outperforms backprop in terms of SNN generalization, needing $>10 \times$ less training data for achieving effective accuracy. These findings make the proposed training approach well-suited for SNN implementations in analog subthreshold circuits and other emerging technologies where unknown hardware non-idealities can jeopardize backprop.
Over the past few years, deep learning methods have been applied for a wide range of Software Engineering (SE) tasks, including in particular for the important task of automatically predicting and localizing faults in software. With the rapid adoption of increasingly complex machine learning models, it however becomes more and more difficult for scholars to reproduce the results that are reported in the literature. This is in particular the case when the applied deep learning models and the evaluation methodology are not properly documented and when code and data are not shared. Given some recent -- and very worrying -- findings regarding reproducibility and progress in other areas of applied machine learning, the goal of this work is to analyze to what extent the field of software engineering, in particular in the area of software fault prediction, is plagued by similar problems. We have therefore conducted a systematic review of the current literature and examined the level of reproducibility of 56 research articles that were published between 2019 and 2022 in top-tier software engineering conferences. Our analysis revealed that scholars are apparently largely aware of the reproducibility problem, and about two thirds of the papers provide code for their proposed deep learning models. However, it turned out that in the vast majority of cases, crucial elements for reproducibility are missing, such as the code of the compared baselines, code for data pre-processing or code for hyperparameter tuning. In these cases, it therefore remains challenging to exactly reproduce the results in the current research literature. Overall, our meta-analysis therefore calls for improved research practices to ensure the reproducibility of machine-learning based research.
Natural policy gradient (NPG) methods with entropy regularization achieve impressive empirical success in reinforcement learning problems with large state-action spaces. However, their convergence properties and the impact of entropy regularization remain elusive in the function approximation regime. In this paper, we establish finite-time convergence analyses of entropy-regularized NPG with linear function approximation under softmax parameterization. In particular, we prove that entropy-regularized NPG with averaging satisfies the \emph{persistence of excitation} condition, and achieves a fast convergence rate of $\tilde{O}(1/T)$ up to a function approximation error in regularized Markov decision processes. This convergence result does not require any a priori assumptions on the policies. Furthermore, under mild regularity conditions on the concentrability coefficient and basis vectors, we prove that entropy-regularized NPG exhibits \emph{linear convergence} up to a function approximation error.
This paper explores Physical-Layer Security (PLS) in Flexible Duplex (FlexD) networks, considering scenarios involving eavesdroppers. Our investigation revolves around the intricacies of the sum secrecy rate maximization problem, particularly when faced with coordinated and distributed eavesdroppers employing a Minimum Mean Square Error (MMSE) receiver. Our contributions include an iterative classical optimization solution and an unsupervised learning strategy based on Graph Neural Networks (GNNs). To the best of our knowledge, this work marks the initial exploration of GNNs for PLS applications. Additionally, we extend the GNN approach to address the absence of eavesdroppers' channel knowledge. Extensive numerical simulations highlight FlexD's superiority over Half-Duplex (HD) communications and the GNN approach's superiority over the classical method in both performance and time complexity.
Large Language Models (LLMs) have demonstrated remarkable performance across diverse tasks and exhibited impressive reasoning abilities by applying zero-shot Chain-of-Thought (CoT) prompting. However, due to the evolving nature of sentence prefixes during the pre-training phase, existing zero-shot CoT prompting methods that employ identical CoT prompting across all task instances may not be optimal. In this paper, we introduce a novel zero-shot prompting method that leverages evolutionary algorithms to generate diverse promptings for LLMs dynamically. Our approach involves initializing two CoT promptings, performing evolutionary operations based on LLMs to create a varied set, and utilizing the LLMs to select a suitable CoT prompting for a given problem. Additionally, a rewriting operation, guided by the selected CoT prompting, enhances the understanding of the LLMs about the problem. Extensive experiments conducted across ten reasoning datasets demonstrate the superior performance of our proposed method compared to current zero-shot CoT prompting methods on GPT-3.5-turbo and GPT-4. Moreover, in-depth analytical experiments underscore the adaptability and effectiveness of our method in various reasoning tasks.
Accurate tooth identification and segmentation in Cone Beam Computed Tomography (CBCT) dental images can significantly enhance the efficiency and precision of manual diagnoses performed by dentists. However, existing segmentation methods are mainly developed based on large data volumes training, on which their annotations are extremely time-consuming. Meanwhile, the teeth of each class in CBCT dental images being closely positioned, coupled with subtle inter-class differences, gives rise to the challenge of indistinct boundaries when training model with limited data. To address these challenges, this study aims to propose a tasked-oriented Masked Auto-Encoder paradigm to effectively utilize large amounts of unlabeled data to achieve accurate tooth segmentation with limited labeled data. Specifically, we first construct a self-supervised pre-training framework of masked auto encoder to efficiently utilize unlabeled data to enhance the network performance. Subsequently, we introduce a sparse masked prompt mechanism based on graph attention to incorporate boundary information of the teeth, aiding the network in learning the anatomical structural features of teeth. To the best of our knowledge, we are pioneering the integration of the mask pre-training paradigm into the CBCT tooth segmentation task. Extensive experiments demonstrate both the feasibility of our proposed method and the potential of the boundary prompt mechanism.
Few-shot Knowledge Graph (KG) completion is a focus of current research, where each task aims at querying unseen facts of a relation given its few-shot reference entity pairs. Recent attempts solve this problem by learning static representations of entities and references, ignoring their dynamic properties, i.e., entities may exhibit diverse roles within task relations, and references may make different contributions to queries. This work proposes an adaptive attentional network for few-shot KG completion by learning adaptive entity and reference representations. Specifically, entities are modeled by an adaptive neighbor encoder to discern their task-oriented roles, while references are modeled by an adaptive query-aware aggregator to differentiate their contributions. Through the attention mechanism, both entities and references can capture their fine-grained semantic meanings, and thus render more expressive representations. This will be more predictive for knowledge acquisition in the few-shot scenario. Evaluation in link prediction on two public datasets shows that our approach achieves new state-of-the-art results with different few-shot sizes.
This paper presents a new multi-objective deep reinforcement learning (MODRL) framework based on deep Q-networks. We propose the use of linear and non-linear methods to develop the MODRL framework that includes both single-policy and multi-policy strategies. The experimental results on two benchmark problems including the two-objective deep sea treasure environment and the three-objective mountain car problem indicate that the proposed framework is able to converge to the optimal Pareto solutions effectively. The proposed framework is generic, which allows implementation of different deep reinforcement learning algorithms in different complex environments. This therefore overcomes many difficulties involved with standard multi-objective reinforcement learning (MORL) methods existing in the current literature. The framework creates a platform as a testbed environment to develop methods for solving various problems associated with the current MORL. Details of the framework implementation can be referred to //www.deakin.edu.au/~thanhthi/drl.htm.
We propose a novel single shot object detection network named Detection with Enriched Semantics (DES). Our motivation is to enrich the semantics of object detection features within a typical deep detector, by a semantic segmentation branch and a global activation module. The segmentation branch is supervised by weak segmentation ground-truth, i.e., no extra annotation is required. In conjunction with that, we employ a global activation module which learns relationship between channels and object classes in a self-supervised manner. Comprehensive experimental results on both PASCAL VOC and MS COCO detection datasets demonstrate the effectiveness of the proposed method. In particular, with a VGG16 based DES, we achieve an mAP of 81.7 on VOC2007 test and an mAP of 32.8 on COCO test-dev with an inference speed of 31.5 milliseconds per image on a Titan Xp GPU. With a lower resolution version, we achieve an mAP of 79.7 on VOC2007 with an inference speed of 13.0 milliseconds per image.