3,564 research outputs found
Computational techniques to interpret the neural code underlying complex cognitive processes
Advances in large-scale neural recording technology have significantly improved the
capacity to further elucidate the neural code underlying complex cognitive processes.
This thesis aimed to investigate two research questions in rodent models. First, what
is the role of the hippocampus in memory and specifically what is the underlying
neural code that contributes to spatial memory and navigational decision-making.
Second, how is social cognition represented in the medial prefrontal cortex at the
level of individual neurons. To start, the thesis begins by investigating memory and
social cognition in the context of healthy and diseased states that use non-invasive
methods (i.e. fMRI and animal behavioural studies). The main body of the thesis
then shifts to developing our fundamental understanding of the neural mechanisms
underpinning these cognitive processes by applying computational techniques to ana lyse stable large-scale neural recordings. To achieve this, tailored calcium imaging
and behaviour preprocessing computational pipelines were developed and optimised
for use in social interaction and spatial navigation experimental analysis. In parallel,
a review was conducted on methods for multivariate/neural population analysis. A
comparison of multiple neural manifold learning (NML) algorithms identified that non linear algorithms such as UMAP are more adaptable across datasets of varying noise
and behavioural complexity. Furthermore, the review visualises how NML can be
applied to disease states in the brain and introduces the secondary analyses that
can be used to enhance or characterise a neural manifold. Lastly, the preprocessing
and analytical pipelines were combined to investigate the neural mechanisms in volved in social cognition and spatial memory. The social cognition study explored
how neural firing in the medial Prefrontal cortex changed as a function of the social
dominance paradigm, the "Tube Test". The univariate analysis identified an ensemble
of behavioural-tuned neurons that fire preferentially during specific behaviours such
as "pushing" or "retreating" for the animalâs own behaviour and/or the competitorâs
behaviour. Furthermore, in dominant animals, the neural population exhibited greater
average firing than that of subordinate animals. Next, to investigate spatial memory,
a spatial recency task was used, where rats learnt to navigate towards one of three
reward locations and then recall the rewarded location of the session. During the
task, over 1000 neurons were recorded from the hippocampal CA1 region for five rats
over multiple sessions. Multivariate analysis revealed that the sequence of neurons encoding an animalâs spatial position leading up to a rewarded location was also active
in the decision period before the animal navigates to the rewarded location. The result
posits that prospective replay of neural sequences in the hippocampal CA1 region
could provide a mechanism by which decision-making is supported
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
Applications of Deep Learning Models in Financial Forecasting
In financial markets, deep learning techniques sparked a revolution, reshaping conventional approaches and amplifying predictive capabilities. This thesis explored the applications of deep learning models to unravel insights and methodologies aimed at advancing financial forecasting.
The crux of the research problem lies in the applications of predictive models within financial domains, characterised by high volatility and uncertainty. This thesis investigated the application of advanced deep-learning methodologies in the context of financial forecasting, addressing the challenges posed by the dynamic nature of financial markets. These challenges were tackled by exploring a range of techniques, including convolutional neural networks (CNNs), long short-term memory networks (LSTMs), autoencoders (AEs), and variational autoencoders (VAEs), along with
approaches such as encoding financial time series into images. Through analysis, methodologies such as transfer learning, convolutional neural networks, long short-term memory networks, generative modelling, and image encoding of time series data were examined. These methodologies collectively offered a comprehensive toolkit for extracting meaningful insights from financial data.
The present work investigated the practicality of a deep learning CNN-LSTM model within the Directional Change framework to predict significant DC eventsâa task crucial for timely decisionmaking in financial markets. Furthermore, the potential of autoencoders and variational autoencoders to enhance financial forecasting accuracy and remove noise from financial time series data was explored. Leveraging their capacity within financial time series, these models offered promising avenues for improved data representation and subsequent forecasting. To further contribute to
financial prediction capabilities, a deep multi-model was developed that harnessed the power of pre-trained computer vision models. This innovative approach aimed to predict the VVIX, utilising the cross-disciplinary synergy between computer vision and financial forecasting. By integrating knowledge from these domains, novel insights into the prediction of market volatility were provided
A review of differentiable digital signal processing for music and speech synthesis
The term âdifferentiable digital signal processingâ describes a family of techniques in which loss function gradients are backpropagated through digital signal processors, facilitating their integration into neural networks. This article surveys the literature on differentiable audio signal processing, focusing on its use in music and speech synthesis. We catalogue applications to tasks including music performance rendering, sound matching, and voice transformation, discussing the motivations for and implications of the use of this methodology. This is accompanied by an overview of digital signal processing operations that have been implemented differentiably, which is further supported by a web book containing practical advice on differentiable synthesiser programming (https://intro2ddsp.github.io/). Finally, we highlight open challenges, including optimisation pathologies, robustness to real-world conditions, and design trade-offs, and discuss directions for future research
UMSL Bulletin 2023-2024
The 2023-2024 Bulletin and Course Catalog for the University of Missouri St. Louis.https://irl.umsl.edu/bulletin/1088/thumbnail.jp
Order and Change in Art: Towards an Active Inference Account of Aesthetic Experience
How to account for the power that art holds over us? Why do artworks touch us deeply, consoling, transforming or invigorating us in the process? In this paper, we argue that an answer to this question might emerge from a fecund framework in cognitive science known as predictive processing (a.k.a. active inference). We unpack how this approach connects sense-making and aesthetic experiences through the idea of an âepistemic arcâ, consisting of three parts (curiosity, epistemic action and aha experiences), which we cast as aspects of active inference. We then show how epistemic arcs are built and sustained by artworks to provide us with those satisfying experiences that we tend to call âaestheticâ. Next, we defuse two key objections to this approach; namely, that it places undue emphasis on the cognitive component of our aesthetic encountersâat the expense of affective aspectsâand on closure and uncertainty minimization (order)âat the expense of openness and lingering uncertainty (change). We show that the approach offers crucial resources to account for the open-ended, free and playful behaviour inherent in aesthetic experiences. The upshot is a promising but deflationary approach, both philosophically informed and psychologically sound, that opens new empirical avenues for understanding our aesthetic encounters.
This article is part of the theme issue âArt, aesthetics and predictive processing: theoretical and empirical perspectivesâ
Rules, frequency, and predictability in morphological generalization: behavioral and computational evidence from the German plural system
Morphological generalization, or the task of mapping an unknown word (such as a novel noun Raun) to an inflected form (such as the plural Rauns), has historically proven a contested topic within computational linguistics and cognitive science, e.g. within the past tense debate (Rumelhart and McClelland, 1986; Pinker and Prince, 1988; Seidenberg and Plaut, 2014). Marcus et al. (1995) identified German plural inflection as a key challenge domain to evaluate two competing accounts of morphological generalization: a rule generation view focused on linguistic features of input words, and a type frequency view focused on the distribution of output inflected forms, thought to reflect more domain-general cognitive processes. More recent behavioral and computational research developments support a new view based on predictability, which integrates both input and output distributions. My research uses these methodological innovations to revisit a core dispute of the past tense debate: how do German speakers generalize plural inflection, and can computational learners generalize similarly?
This dissertation evaluates the rule generation, type frequency, and predictability accounts of morphological generalization in a series of behavioral and computational experiments with the stimuli developed by Marcus et al.. I assess predictions for three aspects of German plural generalization: distribution of infrequent plural classes, influence of grammatical gender, and within-item variability. Overall, I find that speaker behavior is best characterized as frequency-matching to a phonologically-conditioned lexical distribution. This result does not support the rule generation view, and qualifies the predictability view: speakers use some, but not all available information to reduce uncertainty in morphological generalization. Neural and symbolic model predictions are typically overconfident relative to speakers; simple Bayesian models show somewhat higher speaker-like variability and accuracy. All computational models are outperformed by a static phonologically-conditioned lexical baseline, suggesting these models have not learned the selective feature preferences that inform speaker generalization
LIPIcs, Volume 251, ITCS 2023, Complete Volume
LIPIcs, Volume 251, ITCS 2023, Complete Volum
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