1,536 research outputs found

    Multivariate Modeling of Quasar Variability with an Attention-based Variational Autoencoder

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    This thesis applied HeTVAE, an attention-based VAE neural network capable of multivariate modeling of time series, to a dataset of several thousand multi-band AGN light curves from ZTF and was one of the first attempts to use a neural network to harness the stochastic light curves in their multivariate form. Whereas standard models of AGN variability make prior assumptions, HeTVAE uses no prior knowledge and is able to learn the data distribution in a regularized latent space, reading semantic information via its up-to-date self-supervised training regimen. We have successfully created a dataset class for preprocessing the irregular multivariate time series and in order to interface with the quasi-off-the-shelf network more conveniently. Also, we have trained several different model iterations using one, two or all three of the filter dimensions from ZTF on Durham’s NCC compute cluster, while configuring useful hyper parameter choices to work robustly for the astronomical dataset. In the network's training, we employed the Adam optimizer with a reduce-on-plateau learning rate schedule and a KL-annealing schedule optimize the VAE’s performance. In experimenting, we show how the VAE has learned the data distribution of the light curves by generating simulated light curves and its interpretability by visualizing attention scores and by visualizing the way the light curves are distributed along the continuous latent space using PCA. We show it orders the light curves across a smooth gradient from those those that have both low amplitude short-term variation and high amplitude long-term variation, to those with little variability, to those with both short-term and long-term high-amplitude variation in the condensed space. We also use PCA to display a potential filtering algorithm that enables parsing through large datasets in an intuitive way and present some of the pitfalls of algorithmic bias in anomaly detection. Finally, we fine-tuned the structurally correct but imprecise multivariate interpolations output by HeTVAE to three objects to show how they could improve constraints on time-delay estimates in the context of reverberation mapping for the relatively poor-cadenced ZTF data. In short, HeTVAE's use cases are ranged and it is a step in the right direction as far as being able to help organize and process the millions of AGN light curves incoming from Vera C. Rubin Observatory’s Legacy Survey of Space and Time in their full 6 optical broadband filter multivariate form

    4mCPred-GSIMP: Predicting DNA N4-methylcytosine sites in the mouse genome with multi-Scale adaptive features extraction and fusion

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    The epigenetic modification of DNA N4-methylcytosine (4mC) is vital for controlling DNA replication and expression. It is crucial to pinpoint 4mC's location to comprehend its role in physiological and pathological processes. However, accurate 4mC detection is difficult to achieve due to technical constraints. In this paper, we propose a deep learning-based approach 4mCPred-GSIMP for predicting 4mC sites in the mouse genome. The approach encodes DNA sequences using four feature encoding methods and combines multi-scale convolution and improved selective kernel convolution to adaptively extract and fuse features from different scales, thereby improving feature representation and optimization effect. In addition, we also use convolutional residual connections, global response normalization and pointwise convolution techniques to optimize the model. On the independent test dataset, 4mCPred-GSIMP shows high sensitivity, specificity, accuracy, Matthews correlation coefficient and area under the curve, which are 0.7812, 0.9312, 0.8562, 0.7207 and 0.9233, respectively. Various experiments demonstrate that 4mCPred-GSIMP outperforms existing prediction tools

    Towards Integration of Artificial Intelligence into Medical Devices as a Real-Time Recommender System for Personalised Healthcare:State-of-the-Art and Future Prospects

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    In the era of big data, artificial intelligence (AI) algorithms have the potential to revolutionize healthcare by improving patient outcomes and reducing healthcare costs. AI algorithms have frequently been used in health care for predictive modelling, image analysis and drug discovery. Moreover, as a recommender system, these algorithms have shown promising impacts on personalized healthcare provision. A recommender system learns the behaviour of the user and predicts their current preferences (recommends) based on their previous preferences. Implementing AI as a recommender system improves this prediction accuracy and solves cold start and data sparsity problems. However, most of the methods and algorithms are tested in a simulated setting which cannot recapitulate the influencing factors of the real world. This review article systematically reviews prevailing methodologies in recommender systems and discusses the AI algorithms as recommender systems specifically in the field of healthcare. It also provides discussion around the most cutting-edge academic and practical contributions present in the literature, identifies performance evaluation matrices, challenges in the implementation of AI as a recommender system, and acceptance of AI-based recommender systems by clinicians. The findings of this article direct researchers and professionals to comprehend currently developed recommender systems and the future of medical devices integrated with real-time recommender systems for personalized healthcare

    Self-supervised learning for transferable representations

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    Machine learning has undeniably achieved remarkable advances thanks to large labelled datasets and supervised learning. However, this progress is constrained by the labour-intensive annotation process. It is not feasible to generate extensive labelled datasets for every problem we aim to address. Consequently, there has been a notable shift in recent times toward approaches that solely leverage raw data. Among these, self-supervised learning has emerged as a particularly powerful approach, offering scalability to massive datasets and showcasing considerable potential for effective knowledge transfer. This thesis investigates self-supervised representation learning with a strong focus on computer vision applications. We provide a comprehensive survey of self-supervised methods across various modalities, introducing a taxonomy that categorises them into four distinct families while also highlighting practical considerations for real-world implementation. Our focus thenceforth is on the computer vision modality, where we perform a comprehensive benchmark evaluation of state-of-the-art self supervised models against many diverse downstream transfer tasks. Our findings reveal that self-supervised models often outperform supervised learning across a spectrum of tasks, albeit with correlations weakening as tasks transition beyond classification, particularly for datasets with distribution shifts. Digging deeper, we investigate the influence of data augmentation on the transferability of contrastive learners, uncovering a trade-off between spatial and appearance-based invariances that generalise to real-world transformations. This begins to explain the differing empirical performances achieved by self-supervised learners on different downstream tasks, and it showcases the advantages of specialised representations produced with tailored augmentation. Finally, we introduce a novel self-supervised pre-training algorithm for object detection, aligning pre-training with downstream architecture and objectives, leading to reduced localisation errors and improved label efficiency. In conclusion, this thesis contributes a comprehensive understanding of self-supervised representation learning and its role in enabling effective transfer across computer vision tasks

    Computational and experimental studies on the reaction mechanism of bio-oil components with additives for increased stability and fuel quality

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    As one of the world’s largest palm oil producers, Malaysia encountered a major disposal problem as vast amount of oil palm biomass wastes are produced. To overcome this problem, these biomass wastes can be liquefied into biofuel with fast pyrolysis technology. However, further upgradation of fast pyrolysis bio-oil via direct solvent addition was required to overcome it’s undesirable attributes. In addition, the high production cost of biofuels often hinders its commercialisation. Thus, the designed solvent-oil blend needs to achieve both fuel functionality and economic targets to be competitive with the conventional diesel fuel. In this thesis, a multi-stage computer-aided molecular design (CAMD) framework was employed for bio-oil solvent design. In the design problem, molecular signature descriptors were applied to accommodate different classes of property prediction models. However, the complexity of the CAMD problem increases as the height of signature increases due to the combinatorial nature of higher order signature. Thus, a consistency rule was developed reduce the size of the CAMD problem. The CAMD problem was then further extended to address the economic aspects via fuzzy multi-objective optimisation approach. Next, a rough-set based machine learning (RSML) model has been proposed to correlate the feedstock characterisation and pyrolysis condition with the pyrolysis bio-oil properties by generating decision rules. The generated decision rules were analysed from a scientific standpoint to identify the underlying patterns, while ensuring the rules were logical. The decision rules generated can be used to select optimal feedstock composition and pyrolysis condition to produce pyrolysis bio-oil of targeted fuel properties. Next, the results obtained from the computational approaches were verified through experimental study. The generated pyrolysis bio-oils were blended with the identified solvents at various mixing ratio. In addition, emulsification of the solvent-oil blend in diesel was also conducted with the help of surfactants. Lastly, potential extensions and prospective work for this study have been discuss in the later part of this thesis. To conclude, this thesis presented the combination of computational and experimental approaches in upgrading the fuel properties of pyrolysis bio-oil. As a result, high quality biofuel can be generated as a cleaner burning replacement for conventional diesel fuel

    LabelVizier: Interactive Validation and Relabeling for Technical Text Annotations

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    With the rapid accumulation of text data produced by data-driven techniques, the task of extracting "data annotations"--concise, high-quality data summaries from unstructured raw text--has become increasingly important. The recent advances in weak supervision and crowd-sourcing techniques provide promising solutions to efficiently create annotations (labels) for large-scale technical text data. However, such annotations may fail in practice because of the change in annotation requirements, application scenarios, and modeling goals, where label validation and relabeling by domain experts are required. To approach this issue, we present LabelVizier, a human-in-the-loop workflow that incorporates domain knowledge and user-specific requirements to reveal actionable insights into annotation flaws, then produce better-quality labels for large-scale multi-label datasets. We implement our workflow as an interactive notebook to facilitate flexible error profiling, in-depth annotation validation for three error types, and efficient annotation relabeling on different data scales. We evaluated the efficiency and generalizability of our workflow with two use cases and four expert reviews. The results indicate that LabelVizier is applicable in various application scenarios and assist domain experts with different knowledge backgrounds to efficiently improve technical text annotation quality.Comment: 10 pages, 5 figure

    Less is More: Restricted Representations for Better Interpretability and Generalizability

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    Deep neural networks are prevalent in supervised learning for large amounts of tasks such as image classification, machine translation and even scientific discovery. Their success is often at the sacrifice of interpretability and generalizability. The increasing complexity of models and involvement of the pre-training process make the inexplicability more imminent. The outstanding performance when labeled data are abundant while prone to overfit when labeled data are limited demonstrates the difficulty of deep neural networks' generalizability to different datasets. This thesis aims to improve interpretability and generalizability by restricting representations. We choose to approach interpretability by focusing on attribution analysis to understand which features contribute to prediction on BERT, and to approach generalizability by focusing on effective methods in a low-data regime. We consider two strategies of restricting representations: (1) adding bottleneck, and (2) introducing compression. Given input x, suppose we want to learn y with the latent representation z (i.e. x→z→y), adding bottleneck means adding function R such that L(R(z)) < L(z) and introducing compression means adding function R so that L(R(y)) < L(y) where L refers to the number of bits. In other words, the restriction is added either in the middle of the pipeline or at the end of it. We first introduce how adding information bottleneck can help attribution analysis and apply it to investigate BERT's behavior on text classification in Chapter 3. We then extend this attribution method to analyze passage reranking in Chapter 4, where we conduct a detailed analysis to understand cross-layer and cross-passage behavior. Adding bottleneck can not only provide insight to understand deep neural networks but can also be used to increase generalizability. In Chapter 5, we demonstrate the equivalence between adding bottleneck and doing neural compression. We then leverage this finding with a framework called Non-Parametric learning by Compression with Latent Variables (NPC-LV), and show how optimizing neural compressors can be used in the non-parametric image classification with few labeled data. To further investigate how compression alone helps non-parametric learning without latent variables (NPC), we carry out experiments with a universal compressor gzip on text classification in Chapter 6. In Chapter 7, we elucidate methods of adopting the perspective of doing compression but without the actual process of compression using T5. Using experimental results in passage reranking, we show that our method is highly effective in a low-data regime when only one thousand query-passage pairs are available. In addition to the weakly supervised scenario, we also extend our method to large language models like GPT under almost no supervision --- in one-shot and zero-shot settings. The experiments show that without extra parameters or in-context learning, GPT can be used for semantic similarity, text classification, and text ranking and outperform strong baselines, which is presented in Chapter 8. The thesis proposes to tackle two big challenges in machine learning --- "interpretability" and "generalizability" through restricting representation. We provide both theoretical derivation and empirical results to show the effectiveness of using information-theoretic approaches. We not only design new algorithms but also provide numerous insights on why and how "compression" is so important in understanding deep neural networks and improving generalizability

    Video Summarization Using Unsupervised Deep Learning

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    In this thesis, we address the task of video summarization using unsupervised deep-learning architectures. Video summarization aims to generate a short summary by selecting the most informative and important frames (key-frames) or fragments (key-fragments) of the full-length video, and presenting them in temporally-ordered fashion. Our objective is to overcome observed weaknesses of existing video summarization approaches that utilize RNNs for modeling the temporal dependence of frames, related to: i) the small influence of the estimated frame-level importance scores in the created video summary, ii) the insufficiency of RNNs to model long-range frames' dependence, and iii) the small amount of parallelizable operations during the training of RNNs. To address the first weakness, we propose a new unsupervised network architecture, called AC-SUM-GAN, which formulates the selection of important video fragments as a sequence generation task and learns this task by embedding an Actor-Critic model in a Generative Adversarial Network. The feedback of a trainable Discriminator is used as a reward by the Actor-Critic model in order to explore a space of actions and learn a value function (Critic) and a policy (Actor) for video fragment selection. To tackle the remaining weaknesses, we investigate the use of attention mechanisms for video summarization and propose a new supervised network architecture, called PGL-SUM, that combines global and local multi-head attention mechanisms which take into account the temporal position of the video frames, in order to discover different modelings of the frames' dependencies at different levels of granularity. Based on the acquired experience, we then propose a new unsupervised network architecture, called CA-SUM, which estimates the frames' importance using a novel concentrated attention mechanism that focuses on non-overlapping blocks in the main diagonal of the attention matrix and takes into account the attentive uniqueness and diversity of the associated frames of the video. All the proposed architectures have been extensively evaluated on the most commonly-used benchmark datasets, demonstrating their competitiveness against other approaches and documenting the contribution of our proposals on advancing the current state-of-the-art on video summarization. Finally, we make a first attempt on producing explanations for the video summarization results. Inspired by relevant works in the Natural Language Processing domain, we propose an attention-based method for explainable video summarization and we evaluate the performance of various explanation signals using our CA-SUM architecture and two benchmark datasets for video summarization. The experimental results indicate the advanced performance of explanation signals formed using the inherent attention weights, and demonstrate the ability of the proposed method to explain the video summarization results using clues about the focus of the attention mechanism

    Semi-Supervised Learning in the Few-Shot Zero-Shot Scenario

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    Semi-Supervised Learning (SSL) is a framework that utilizes both labeled and unlabeled data to enhance model performance. Conventional SSL methods operate under the assumption that labeled and unlabeled data share the same label space. However, in practical real-world scenarios, especially when the labeled training dataset is limited in size, some classes may be totally absent from the labeled set. To address this broader context, we propose a general approach to augment existing SSL methods, enabling them to effectively handle situations where certain classes are missing. This is achieved by introducing an additional term into their objective function, which penalizes the KL-divergence between the probability vectors of the true class frequencies and the inferred class frequencies. Our experimental results reveal significant improvements in accuracy when compared to state-of-the-art SSL, open-set SSL, and open-world SSL methods. We conducted these experiments on two benchmark image classification datasets, CIFAR-100 and STL-10, with the most remarkable improvements observed when the labeled data is severely limited, with only a few labeled examples per clas

    Computational Approaches to Drug Profiling and Drug-Protein Interactions

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    Despite substantial increases in R&D spending within the pharmaceutical industry, denovo drug design has become a time-consuming endeavour. High attrition rates led to a long period of stagnation in drug approvals. Due to the extreme costs associated with introducing a drug to the market, locating and understanding the reasons for clinical failure is key to future productivity. As part of this PhD, three main contributions were made in this respect. First, the web platform, LigNFam enables users to interactively explore similarity relationships between ‘drug like’ molecules and the proteins they bind. Secondly, two deep-learning-based binding site comparison tools were developed, competing with the state-of-the-art over benchmark datasets. The models have the ability to predict offtarget interactions and potential candidates for target-based drug repurposing. Finally, the open-source ScaffoldGraph software was presented for the analysis of hierarchical scaffold relationships and has already been used in multiple projects, including integration into a virtual screening pipeline to increase the tractability of ultra-large screening experiments. Together, and with existing tools, the contributions made will aid in the understanding of drug-protein relationships, particularly in the fields of off-target prediction and drug repurposing, helping to design better drugs faster
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