3,298 research outputs found
Computational Analyses of Metagenomic Data
Metagenomics studies the collective microbial genomes extracted from a particular environment without requiring the culturing or isolation of individual genomes, addressing questions revolving around the composition, functionality, and dynamics of microbial communities. The intrinsic complexity of metagenomic data and the diversity of applications call for efficient and accurate computational methods in data handling. In this thesis, I present three primary projects that collectively focus on the computational analysis of metagenomic data, each addressing a distinct topic.
In the first project, I designed and implemented an algorithm named Mapbin for reference-free genomic binning of metagenomic assemblies. Binning aims to group a mixture of genomic fragments based on their genome origin. Mapbin enhances binning results by building a multilayer network that combines the initial binning, assembly graph, and read-pairing information from paired-end sequencing data. The network is further partitioned by the community-detection algorithm, Infomap, to yield a new binning result. Mapbin was tested on multiple simulated and real datasets. The results indicated an overall improvement in the common binning quality metrics.
The second and third projects are both derived from ImMiGeNe, a collaborative and multidisciplinary study investigating the interplay between gut microbiota, host genetics, and immunity in stem-cell transplantation (SCT) patients. In the second project, I conducted microbiome analyses for the metagenomic data. The workflow included the removal of contaminant reads and multiple taxonomic and functional profiling. The results revealed that the SCT recipients' samples yielded significantly fewer reads with heavy contamination of the host DNA, and their microbiomes displayed evident signs of dysbiosis. Finally, I discussed several inherent challenges posed by extremely low levels of target DNA and high levels of contamination in the recipient samples, which cannot be rectified solely through bioinformatics approaches.
The primary goal of the third project is to design a set of primers that can be used to cover bacterial flagellin genes present in the human gut microbiota. Considering the notable diversity of flagellins, I incorporated a method to select representative bacterial flagellin gene sequences, a heuristic approach based on established primer design methods to generate a degenerate primer set, and a selection method to filter genes unlikely to occur in the human gut microbiome. As a result, I successfully curated a reduced yet representative set of primers that would be practical for experimental implementation
Advances in machine learning algorithms for financial risk management
In this thesis, three novel machine learning techniques are introduced to address distinct
yet interrelated challenges involved in financial risk management tasks. These approaches
collectively offer a comprehensive strategy, beginning with the precise classification of credit
risks, advancing through the nuanced forecasting of financial asset volatility, and ending
with the strategic optimisation of financial asset portfolios.
Firstly, a Hybrid Dual-Resampling and Cost-Sensitive technique has been proposed to combat the prevalent issue of class imbalance in financial datasets, particularly in credit risk
assessment. The key process involves the creation of heuristically balanced datasets to effectively address the problem. It uses a resampling technique based on Gaussian mixture
modelling to generate a synthetic minority class from the minority class data and concurrently uses k-means clustering on the majority class. Feature selection is then performed
using the Extra Tree Ensemble technique. Subsequently, a cost-sensitive logistic regression
model is then applied to predict the probability of default using the heuristically balanced
datasets. The results underscore the effectiveness of our proposed technique, with superior
performance observed in comparison to other imbalanced preprocessing approaches. This
advancement in credit risk classification lays a solid foundation for understanding individual
financial behaviours, a crucial first step in the broader context of financial risk management.
Building on this foundation, the thesis then explores the forecasting of financial asset volatility, a critical aspect of understanding market dynamics. A novel model that combines a
Triple Discriminator Generative Adversarial Network with a continuous wavelet transform
is proposed. The proposed model has the ability to decompose volatility time series into
signal-like and noise-like frequency components, to allow the separate detection and monitoring of non-stationary volatility data. The network comprises of a wavelet transform
component consisting of continuous wavelet transforms and inverse wavelet transform components, an auto-encoder component made up of encoder and decoder networks, and a
Generative Adversarial Network consisting of triple Discriminator and Generator networks.
The proposed Generative Adversarial Network employs an ensemble of unsupervised loss derived from the Generative Adversarial Network component during training, supervised
loss and reconstruction loss as part of its framework. Data from nine financial assets are
employed to demonstrate the effectiveness of the proposed model. This approach not only
enhances our understanding of market fluctuations but also bridges the gap between individual credit risk assessment and macro-level market analysis.
Finally the thesis ends with a novel proposal of a novel technique or Portfolio optimisation. This involves the use of a model-free reinforcement learning strategy for portfolio
optimisation using historical Low, High, and Close prices of assets as input with weights of
assets as output. A deep Capsules Network is employed to simulate the investment strategy, which involves the reallocation of the different assets to maximise the expected return
on investment based on deep reinforcement learning. To provide more learning stability in
an online training process, a Markov Differential Sharpe Ratio reward function has been
proposed as the reinforcement learning objective function. Additionally, a Multi-Memory
Weight Reservoir has also been introduced to facilitate the learning process and optimisation of computed asset weights, helping to sequentially re-balance the portfolio throughout
a specified trading period. The use of the insights gained from volatility forecasting into
this strategy shows the interconnected nature of the financial markets. Comparative experiments with other models demonstrated that our proposed technique is capable of achieving
superior results based on risk-adjusted reward performance measures.
In a nut-shell, this thesis not only addresses individual challenges in financial risk management but it also incorporates them into a comprehensive framework; from enhancing the
accuracy of credit risk classification, through the improvement and understanding of market
volatility, to optimisation of investment strategies. These methodologies collectively show
the potential of the use of machine learning to improve financial risk management
Robustness, Heterogeneity and Structure Capturing for Graph Representation Learning and its Application
Graph neural networks (GNNs) are potent methods for graph representation learn- ing (GRL), which extract knowledge from complicated (graph) structured data in various real-world scenarios. However, GRL still faces many challenges. Firstly GNN-based node classification may deteriorate substantially by overlooking the pos- sibility of noisy data in graph structures, as models wrongly process the relation among nodes in the input graphs as the ground truth. Secondly, nodes and edges have different types in the real-world and it is essential to capture this heterogeneity in graph representation learning. Next, relations among nodes are not restricted to pairwise relations and it is necessary to capture the complex relations accordingly. Finally, the absence of structural encodings, such as positional information, deterio- rates the performance of GNNs. This thesis proposes novel methods to address the aforementioned problems:
1. Bayesian Graph Attention Network (BGAT): Developed for situations with scarce data, this method addresses the influence of spurious edges. Incor- porating Bayesian principles into the graph attention mechanism enhances robustness, leading to competitive performance against benchmarks (Chapter 3).
2. Neighbour Contrastive Heterogeneous Graph Attention Network (NC-HGAT): By enhancing a cutting-edge self-supervised heterogeneous graph neural net- work model (HGAT) with neighbour contrastive learning, this method ad- dresses heterogeneity and uncertainty simultaneously. Extra attention to edge relations in heterogeneous graphs also aids in subsequent classification tasks (Chapter 4).
3. A novel ensemble learning framework is introduced for predicting stock price movements. It adeptly captures both group-level and pairwise relations, lead- ing to notable advancements over the existing state-of-the-art. The integration of hypergraph and graph models, coupled with the utilisation of auxiliary data via GNNs before recurrent neural network (RNN), provides a deeper under- standing of long-term dependencies between similar entities in multivariate time series analysis (Chapter 5).
4. A novel framework for graph structure learning is introduced, segmenting graphs into distinct patches. By harnessing the capabilities of transformers and integrating other position encoding techniques, this approach robustly capture intricate structural information within a graph. This results in a more comprehensive understanding of its underlying patterns (Chapter 6)
Self-supervised learning for transferable representations
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
Classical and quantum algorithms for scaling problems
This thesis is concerned with scaling problems, which have a plethora of connections to different areas of mathematics, physics and computer science. Although many structural aspects of these problems are understood by now, we only know how to solve them efficiently in special cases.We give new algorithms for non-commutative scaling problems with complexity guarantees that match the prior state of the art. To this end, we extend the well-known (self-concordance based) interior-point method (IPM) framework to Riemannian manifolds, motivated by its success in the commutative setting. Moreover, the IPM framework does not obviously suffer from the same obstructions to efficiency as previous methods. It also yields the first high-precision algorithms for other natural geometric problems in non-positive curvature.For the (commutative) problems of matrix scaling and balancing, we show that quantum algorithms can outperform the (already very efficient) state-of-the-art classical algorithms. Their time complexity can be sublinear in the input size; in certain parameter regimes they are also optimal, whereas in others we show no quantum speedup over the classical methods is possible. Along the way, we provide improvements over the long-standing state of the art for searching for all marked elements in a list, and computing the sum of a list of numbers.We identify a new application in the context of tensor networks for quantum many-body physics. We define a computable canonical form for uniform projected entangled pair states (as the solution to a scaling problem), circumventing previously known undecidability results. We also show, by characterizing the invariant polynomials, that the canonical form is determined by evaluating the tensor network contractions on networks of bounded size
Multidisciplinary perspectives on Artificial Intelligence and the law
This open access book presents an interdisciplinary, multi-authored, edited collection of chapters on Artificial Intelligence (âAIâ) and the Law. AI technology has come to play a central role in the modern data economy. Through a combination of increased computing power, the growing availability of data and the advancement of algorithms, AI has now become an umbrella term for some of the most transformational technological breakthroughs of this age. The importance of AI stems from both the opportunities that it offers and the challenges that it entails. While AI applications hold the promise of economic growth and efficiency gains, they also create significant risks and uncertainty. The potential and perils of AI have thus come to dominate modern discussions of technology and ethics â and although AI was initially allowed to largely develop without guidelines or rules, few would deny that the law is set to play a fundamental role in shaping the future of AI. As the debate over AI is far from over, the need for rigorous analysis has never been greater. This book thus brings together contributors from different fields and backgrounds to explore how the law might provide answers to some of the most pressing questions raised by AI. An outcome of the CatĂłlica Research Centre for the Future of Law and its interdisciplinary working group on Law and Artificial Intelligence, it includes contributions by leading scholars in the fields of technology, ethics and the law.info:eu-repo/semantics/publishedVersio
Predicting Paid Certification in Massive Open Online Courses
Massive open online courses (MOOCs) have been proliferating because of the free or low-cost offering of content for learners, attracting the attention of many stakeholders across the entire educational landscape. Since 2012, coined as âthe Year of the MOOCsâ, several platforms have gathered millions of learners in just a decade. Nevertheless, the certification rate of both free and paid courses has been low, and only about 4.5â13% and 1â3%, respectively, of the total number of enrolled learners obtain a certificate at the end of their courses. Still, most research concentrates on completion, ignoring the certification problem, and especially its financial aspects. Thus, the research described in the present thesis aimed to investigate paid certification in MOOCs, for the first time, in a comprehensive way, and as early as the first week of the course, by exploring its various levels. First, the latent correlation between learner activities and their paid certification decisions was examined by (1) statistically comparing the activities of non-paying learners with course purchasers and (2) predicting paid certification using different machine learning (ML) techniques. Our temporal (weekly) analysis showed statistical significance at various levels when comparing the activities of non-paying learners with those of the certificate purchasers across the five courses analysed. Furthermore, we used the learnerâs activities (number of step accesses, attempts, correct and wrong answers, and time spent on learning steps) to build our paid certification predictor, which achieved promising balanced accuracies (BAs), ranging from 0.77 to 0.95. Having employed simple predictions based on a few clickstream variables, we then analysed more in-depth what other information can be extracted from MOOC interaction (namely discussion forums) for paid certification prediction. However, to better explore the learnersâ discussion forums, we built, as an original contribution, MOOCSent, a cross- platform review-based sentiment classifier, using over 1.2 million MOOC sentiment-labelled reviews. MOOCSent addresses various limitations of the current sentiment classifiers including (1) using one single source of data (previous literature on sentiment classification in MOOCs was based on single platforms only, and hence less generalisable, with relatively low number of instances compared to our obtained dataset;) (2) lower model outputs, where most of the current models are based on 2-polar
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classifier (positive or negative only); (3) disregarding important sentiment indicators, such as emojis and emoticons, during text embedding; and (4) reporting average performance metrics only, preventing the evaluation of model performance at the level of class (sentiment). Finally, and with the help of MOOCSent, we used the learnersâ discussion forums to predict paid certification after annotating learnersâ comments and replies with the sentiment using MOOCSent. This multi-input model contains raw data (learner textual inputs), sentiment classification generated by MOOCSent, computed features (number of likes received for each textual input), and several features extracted from the texts (character counts, word counts, and part of speech (POS) tags for each textual instance). This experiment adopted various deep predictive approaches â specifically that allow multi-input architecture - to early (i.e., weekly) investigate if data obtained from MOOC learnersâ interaction in discussion forums can predict learnersâ purchase decisions (certification). Considering the staggeringly low rate of paid certification in MOOCs, this present thesis contributes to the knowledge and field of MOOC learner analytics with predicting paid certification, for the first time, at such a comprehensive (with data from over 200 thousand learners from 5 different discipline courses), actionable (analysing learners decision from the first week of the course) and longitudinal (with 23 runs from 2013 to 2017) scale. The present thesis contributes with (1) investigating various conventional and deep ML approaches for predicting paid certification in MOOCs using learner clickstreams (Chapter 5) and course discussion forums (Chapter 7), (2) building the largest MOOC sentiment classifier (MOOCSent) based on learnersâ reviews of the courses from the leading MOOC platforms, namely Coursera, FutureLearn and Udemy, and handles emojis and emoticons using dedicated lexicons that contain over three thousand corresponding explanatory words/phrases, (3) proposing and developing, for the first time, multi-input model for predicting certification based on the data from discussion forums which synchronously processes the textual (comments and replies) and numerical (number of likes posted and received, sentiments) data from the forums, adapting the suitable classifier for each type of data as explained in detail in Chapter 7
LIPIcs, Volume 251, ITCS 2023, Complete Volume
LIPIcs, Volume 251, ITCS 2023, Complete Volum
Data-assisted modeling of complex chemical and biological systems
Complex systems are abundant in chemistry and biology; they can be multiscale, possibly high-dimensional or stochastic, with nonlinear dynamics and interacting components. It is often nontrivial (and sometimes impossible), to determine and study the macroscopic quantities of interest and the equations they obey. One can only (judiciously or randomly) probe the system, gather observations and study trends. In this thesis, Machine Learning is used as a complement to traditional modeling and numerical methods to enable data-assisted (or data-driven) dynamical systems. As case studies, three complex systems are sourced from diverse fields: The first one is a high-dimensional computational neuroscience model of the Suprachiasmatic Nucleus of the human brain, where bifurcation analysis is performed by simply probing the system. Then, manifold learning is employed to discover a latent space of neuronal heterogeneity. Second, Machine Learning surrogate models are used to optimize dynamically operated catalytic reactors. An algorithmic pipeline is presented through which it is possible to program catalysts with active learning. Third, Machine Learning is employed to extract laws of Partial Differential Equations describing bacterial Chemotaxis. It is demonstrated how Machine Learning manages to capture the rules of bacterial motility in the macroscopic level, starting from diverse data sources (including real-world experimental data). More importantly, a framework is constructed though which already existing, partial knowledge of the system can be exploited. These applications showcase how Machine Learning can be used synergistically with traditional simulations in different scenarios: (i) Equations are available but the overall system is so high-dimensional that efficiency and explainability suffer, (ii) Equations are available but lead to highly nonlinear black-box responses, (iii) Only data are available (of varying source and quality) and equations need to be discovered. For such data-assisted dynamical systems, we can perform fundamental tasks, such as integration, steady-state location, continuation and optimization. This work aims to unify traditional scientific computing and Machine Learning, in an efficient, data-economical, generalizable way, where both the physical system and the algorithm matter
Multi-class Categorization of Reasons behind Mental Disturbance in Long Texts
Motivated with recent advances in inferring users' mental state in social
media posts, we identify and formulate the problem of finding causal indicators
behind mental illness in self-reported text. In the past, we witness the
presence of rule-based studies for causal explanation analysis on curated
Facebook data. The investigation on transformer-based model for multi-class
causal categorization in Reddit posts point to a problem of using long-text
which contains as many as 4000 words. Developing end-to-end transformer-based
models subject to the limitation of maximum-length in a given instance. To
handle this problem, we use Longformer and deploy its encoding on
transformer-based classifier. The experimental results show that Longformer
achieves new state-of-the-art results on M-CAMS, a publicly available dataset
with 62\% F1-score. Cause-specific analysis and ablation study prove the
effectiveness of Longformer. We believe our work facilitates causal analysis of
depression and suicide risk on social media data, and shows potential for
application on other mental health conditions
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