Survey on Leveraging Uncertainty Estimation Towards Trustworthy Deep Neural Networks: The Case of Reject Option and Post-training Processing

Although neural networks (especially deep neural networks) have achieved \textit{better-than-human} performance in many fields, their real-world deployment is still questionable due to the lack of awareness about the limitation in their knowledge. To incorporate such awareness in the machine learning model, prediction with reject option (also known as selective classification or classification with abstention) has been proposed in literature. In this paper, we present a systematic review of the prediction with the reject option in the context of various neural networks. To the best of our knowledge, this is the first study focusing on this aspect of neural networks. Moreover, we discuss different novel loss functions related to the reject option and post-training processing (if any) of network output for generating suitable measurements for knowledge awareness of the model. Finally, we address the application of the rejection option in reducing the prediction time for the real-time problems and present a comprehensive summary of the techniques related to the reject option in the context of extensive variety of neural networks. Our code is available on GitHub: \url{https://github.com/MehediHasanTutul/Reject_option

Investigating Citation Linkage Between Research Articles

In recent years, there has been a dramatic increase in scientific publications across the globe. To help navigate this overabundance of information, methods have been devised to find papers with related content, but they are lacking in the ability to provide specific information that a researcher may need without having to read hundreds of linked papers. The search and browsing capabilities of online domain specific scientific repositories are limited to finding a paper citing other papers, but do not point to the specific text that is being cited. Providing this capability to the research community will be beneficial in terms of the time required to acquire the amount of background information they need to undertake their research. In this thesis, we present our effort to develop a citation linkage framework for finding those sentences in a cited article that are the focus of a citation in a citing paper. This undertaking has involved the construction of datasets and corpora that are required to build models for focused information extraction, text classification and information retrieval. As the first part of this thesis, two preprocessing steps that are deemed to assist with the citation linkage task are explored: method mention extraction and rhetorical categorization of scientific discourse. In the second part of this thesis, two methodologies for achieving the citation linkage goal are investigated. Firstly, regression techniques have been used to predict the degree of similarity between citation sentences and their equivalent target sentences with medium Pearson correlation score between predicted and expected values. The resulting learning models are then used to rank sentences in the cited paper based on their predicted scores. Secondly, search engine-like retrieval techniques have been used to rank sentences in the cited paper based on the words contained in the citation sentence. Our experiments show that it is possible to find the set of sentences that a citation refers to in a cited paper with reasonable performance. Possible applications of this work include: creation of better science paper repository navigation tools, development of scientific argumentation across research articles, and multi-document summarization of science articles

A Computational Framework for Host-Pathogen Protein-Protein Interactions

Infectious diseases cause millions of illnesses and deaths every year, and raise great health concerns world widely. How to monitor and cure the infectious diseases has become a prevalent and intractable problem. Since the host-pathogen interactions are considered as the key infection processes at the molecular level for infectious diseases, there have been a large amount of researches focusing on the host-pathogen interactions towards the understanding of infection mechanisms and the development of novel therapeutic solutions. For years, the continuously development of technologies in biology has benefitted the wet lab-based experiments, such as small-scale biochemical, biophysical and genetic experiments and large-scale methods (for example yeast-two-hybrid analysis and cryogenic electron microscopy approach). As a result of past decades of efforts, there has been an exploded accumulation of biological data, which includes multi omics data, for example, the genomics data and proteomics data. Thus, an initiative review of omics data has been conducted in Chapter 2, which has exclusively demonstrated the recent update of ‘omics’ study, particularly focusing on proteomics and genomics. With the high-throughput technologies, the increasing amount of ‘omics’ data, including genomics and proteomics, has even further boosted. An upsurge of interest for data analytics in bioinformatics comes as no surprise to the researchers from a variety of disciplines. Specifically, the astonishing rate at which genomics and proteomics data are generated leads the researchers into the realm of ‘Big Data’ research. Chapter 2 is thus developed to providing an update of the omics background and the state-of-the-art developments in the omics area, with a focus on genomics data, from the perspective of big data analytics..

Deep Learning-Based Intrusion Detection Methods for Computer Networks and Privacy-Preserving Authentication Method for Vehicular Ad Hoc Networks

The incidence of computer network intrusions has significantly increased over the last decade, partially attributed to a thriving underground cyber-crime economy and the widespread availability of advanced tools for launching such attacks. To counter these attacks, researchers in both academia and industry have turned to machine learning (ML) techniques to develop Intrusion Detection Systems (IDSes) for computer networks. However, many of the datasets use to train ML classifiers for detecting intrusions are not balanced, with some classes having fewer samples than others. This can result in ML classifiers producing suboptimal results. In this dissertation, we address this issue and present better ML based solutions for intrusion detection. Our contributions in this direction can be summarized as follows: Balancing Data Using Synthetic Data to detect intrusions in Computer Networks: In the past, researchers addressed the issue of imbalanced data in datasets by using over-sampling and under-sampling techniques. In this study, we go beyond such traditional methods and utilize a synthetic data generation method called Con- ditional Generative Adversarial Network (CTGAN) to balance the datasets and in- vestigate its impact on the performance of widely used ML classifiers. To the best of our knowledge, no one else has used CTGAN to generate synthetic samples for balancing intrusion detection datasets. We use two widely used publicly available datasets and conduct extensive experiments and show that ML classifiers trained on these datasets balanced with synthetic samples generated by CTGAN have higher prediction accuracy and Matthew Correlation Coefficient (MCC) scores than those trained on imbalanced datasets by 8% and 13%, respectively. Deep Learning approach for intrusion detection using focal loss function: To overcome the data imbalance problem for intrusion detection, we leverage the specialized loss function, called focal loss, that automatically down-weighs easy ex- amples and focuses on the hard negatives by facilitating dynamically scaled-gradient updates for training ML models effectively. We implement our approach using two well-known Deep Learning (DL) neural network architectures. Compared to training DL models using cross-entropy loss function, our approach (training DL models using focal loss function) improved accuracy, precision, F1 score, and MCC score by 24%, 39%, 39%, and 60% respectively. Efficient Deep Learning approach to detect Intrusions using Few-shot Learning: To address the issue of imbalance the datasets and develop a highly effective IDS, we utilize the concept of few-shot learning. We present a Few-Shot and Self-Supervised learning framework, called FS3, for detecting intrusions in IoT networks. FS3 works in three phases. Our approach involves first pretraining an encoder on a large-scale external dataset in a selfsupervised manner. We then employ few-shot learning (FSL), which seeks to replicate the encoder’s ability to learn new patterns from only a few training examples. During the encoder training us- ing a small number of samples, we train them contrastively, utilizing the triplet loss function. The third phase introduces a novel K-Nearest neighbor algorithm that sub- samples the majority class instances to further reduce imbalance and improve overall performance. Our proposed framework FS3, utilizing only 20% of labeled data, out- performs fully supervised state-of-the-art models by up to 42.39% and 43.95% with respect to the metrics precision and F1 score, respectively. The rapid evolution of the automotive industry and advancements in wireless com- munication technologies will result in the widespread deployment of Vehicular ad hoc networks (VANETs). However, despite the network’s potential to enable intelligent and autonomous driving, it also introduces various attack vectors that can jeopardize its security. In this dissertation, we present efficient privacy-preserving authenticated message dissemination scheme in VANETs. Conditional Privacy-preserving Authentication and Message Dissemination Scheme using Timestamp based Pseudonyms: To authenticate a message sent by a vehicle using its pseudonym, a certificate of the pseudonym signed by the central authority is generally utilized. If a vehicle is found to be malicious, certificates associated with all the pseudonyms assigned to it must be revoked. Certificate revocation lists (CRLs) should be shared with all entities that will be corresponding with the vehicle. As each vehicle has a large pool of pseudonyms allocated to it, the CRL can quickly grow in size as the number of revoked vehicles increases. This results in high storage overheads for storing the CRL, and significant authentication overheads as the receivers must check their CRL for each message received to verify its pseudonym. To address this issue, we present a timestamp-based pseudonym allocation scheme that reduces the storage overhead and authentication overhead by streamlining the CRL management process