Computational Neuroscience Commons^™

Perceptograms And Cortical Models For Amblyopic Form Distortions, Akihito Maruya, Farzaneh Olianezhad, Jingyun Wang, Jose-Manuel Alonso, Qasim Zaidi

MODVIS Workshop

No abstract provided.

Influence Of Task On The Geometry Of A Perceptual Space, Jonathan D. Victor, Mary M. Conte

MODVIS Workshop

Perceptual spaces are representations of a sensory or cognitive domain in which the domain’s elements correspond to points, and distances between these points are perceptual differences. Proximity relationships within a perceptual space can support a variety of functions, including discrimination, grouping, learning, and generalization. These diverse functions may use the features of the domain in different ways, resulting in task-dependent influences on the geometry of the space.

To identify and characterize these influences, we focused on a domain of visual textures. These textures varied across many dimensions, including mean luminance and low- and high-order spatial correlations, which formed the axes …

Using Neural Networks To Better Understand Static And Dynamic Components Of Facial Expression Recognition, Yi-Fan Li, Anne Bibiana Sereno

MODVIS Workshop

Facial expressions are crucial social information for human communication. In the real world, facial expressions are dynamic; however, much of existing research in facial expressions relies on static stimuli. This static approach may limit the ecological validity of our understanding of the emotional information on faces. Our study aims to investigate the dynamic and static information contained in different emotional categories of facial expressions (e.g., happy, sad). Four convolutional neural networks are introduced as models to be trained with a large-scale dynamic facial expression dataset (short videoclips of 16 frames of 7 different emotional categories) in four different ways: ordered …

Modeling Effects Of Edge Classification And Perceptual Organization On The Appearance Of Disk/Annulus Stimuli, Michael E. Rudd

MODVIS Workshop

In classical theories of sensory psychophysics, appearance matches conducted with simple stimuli consisting of disks surrounded by annuli were posited to probe low-level contrast mechanisms in the visual pathways that computed the approximate luminance ratio between the disk and annulus for the purpose of achieving lightness constancy (Wallach, 1948). Subsequent models have explained such matches on the basis of neural edge integration (Shapley & Reid, 1985; Rudd & Zemach, 2004). Here, I demonstrate that appearances matches made in the disk/annulus paradigm are influenced by at least two types of top-down effects involving edge classification and perceptual organization. I present a …

Fixational Eye Movements Shake Up The Stationary View On Pattern Vision, Lynn Schmittwilken, Marianne Maertens

MODVIS Workshop

No abstract provided.

A Computational Perspective On Segregated Processing And The Privileged Role Of Space In Binding, Anne Sereno, Zhixian Han, Elizabeth M. Frazier

MODVIS Workshop

No abstract provided.

Sliding Window Method For Simulating Action Potentials In Axons, Hayden Reed

Honors Theses

ABSTRACT Hodgkin and Huxley’s nonlinear partial differential equations model the excitation and propagation of action potentials in neurons, and there have been numerous attempts at finding the best numerical solution method. This thesis proposes a novel approach to solving these equations: the Sliding Window method, in which a fixed sub-interval is found through capturing the signal’s head and tail. The system is then solved on the sub-interval instead of the entire interval. Using the Sliding Window technique also involves implementing the backward and forward Euler methods and the finite difference method. It will be demonstrated that, in utilizing the Sliding …

Deep Jansen-Rit Parameter Inference For Model-Driven Analysis Of Brain Activity, Deepa Tilwani, Christian O'Reilly

Faculty Publications

Accurately modeling effective connectivity (EC) is critical for understanding how the brain processes and integrates sensory information. Yet, it remains a formidable challenge due to complex neural dynamics and noisy measurements such as those obtained from the electroencephalogram (EEG). Model-driven EC infers local (within a brain region) and global (between brain regions) EC parameters by fitting a generative model of neural activity onto experimental data. This approach offers a promising route for various applications, including investigating neurodevel- opmental disorders. However, current approaches fail to scale to whole-brain analyses and are highly noise-sensitive. In this work, we employ three deep-learning architectures—a …

Web Application For Simulation Of An Agent-Based Model In Netlogo3d, Chris Davis Perumal, Abraham Nofal, Benedict J. Kolber, Rachael Miller Neilan

Spora: A Journal of Biomathematics

Agent-based models (ABMs) are computer simulation models for studying systems of autonomous agents. Modelers often use specialized software like NetLogo to develop ABMs, but this software poses barriers to researchers in other disciplines with no prior programming experience. To address this issue, we developed a web application that allows users to simulate our ABM via a web browser, eliminating the need for the user to download and use specialized software. While presented in the context of a specific ABM, our approach can be applied to other ABMs to enhance accessibility. The ABM presented here was developed in NetLogo3D. The model …

Designing Accessible Ui/Ux For Epileptic Patients: A Scalable Solution For Music Therapy Delivery, Amethyst G.H. Mckenzie

Computer Science Senior Theses

How can we design an accessible, scalable UI/UX system tailored to the cognitive, visual, and motor impairments of epileptic patients, that ensures safe and effective interactions with music therapy applications? This research explores the intersection of accessibility, user-centred design, and digital health, using an iterative design process to develop and refine the SONATA app—a clinically deployable music therapy platform.

Through two prototype iterations, usability testing, and quantitative event logging, this study compares the effectiveness of structured versus flexible navigation in improving user experience. Key findings reveal that structured navigation reduces unintended detours, while progressive disclosure techniques enhance instructional clarity. Additionally, …

Constructing A Parameterized Stimuli Space Suitable To Induce Controlled Changes In Human And Machine Perceptual Systems, Andrew Frankel

Dissertations, Theses, and Capstone Projects

Traditional computer vision applications focus on objective tasks, such as object detection, classification, or segmentation. Much of human experience is inherently subjective, such as our personal response to artwork. Individualized experiences are challenging to replicate in a controlled laboratory environment, as those experiences depend on the unique history and internal models of the observer. This work presents a technique to construct a 2-dimensional parameterized stimuli space suitable to induce controlled changes in the perceptual systems of both human and machine observers. Our contributions are threefold:

1. Using a balanced dataset of 8,800 fine art images spanning 11 art movements and 88 …

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Vertex-Based Analysis Of Cerebral Blood Flow And Fractional Amplitude Of Low-Frequency Fluctuations (Cbf-Falff) Coupling In Moderate-To-Severe Traumatic Brain Injury During The First Year Post-Injury, Vaidehi Hemkumar Patel

Dissertations, Theses, and Capstone Projects

Traumatic brain injury (TBI) is known to involve damage in the neurovascular unit. TBI may disrupt the brain’s neurovascular coupling–the relationship between cerebral blood flow and neural activity–that can lead to cognitive and functional impairments. This study attempted to non-invasively investigate neurovascular coupling in patients with moderate to severe TBI (msTBI) during the first year post-injury using a combined metric of cerebral blood flow (CBF) and fractional amplitude of low-frequency fluctuations (fALFF), a proxy for spontaneous neural activity. Using arterial spin labeling (ASL) and functional MRI sequences, CBF and fALFF were measured in 29 msTBI patients 3-, 6- and 12-months …

A Framework For Biomimetic Robot Design Applied To The Development Of A Robotic Model Of Drosophila Melanogaster, Clarissa A. Goldsmith

Graduate Theses, Dissertations, and Problem Reports (ETD)

For decades, the field of biologically inspired robotics has leveraged insights from animal locomotion to improve the walking ability of legged robots. Recently, “biomimetic” robots have been developed to model how specific animals walk. By prioritizing biological accuracy to the target organism rather than the application of general principles from biology, these robots can be used to develop detailed biological hypotheses for animal experiments, ultimately improving our understanding of the biological control of legs while improving technical solutions. Much of this work involves biologically inspired walking controllers informed by the morphology and dynamics of the insect nervous system, which necessitate …

Theoretical Analysis Of Cnns For Automatic Seizure Detection In Eeg Signals, Jackson T. Small

Honors Undergraduate Theses

Epilepsy is a common brain disorder where neurons in the brain rapidly fire, causing recurring seizures. The brain activity during a seizure can be detected by electroencephalogram (EEG) signals; however, this process is not only labor-intensive and time-consuming but is also subject to inter-rater variability, with a study showing only moderate agreement when diagnosing patients, even among experts. Convolutional Neural Networks (CNNs) are often proposed to detect seizures automatically, achieving high performance. The focus on performance comes at a cost of losing interpretability, leaving the model as effective but seen as a ’black box’. This thesis confronts the interpretability knowledge …

Cgrp Modulation Of Intracellular Calcium Levels In Trigeminal Ganglion Neurons And Glia, Nicole M. Nalley

Graduate Theses/Dissertations

Elevated levels of calcitonin gene-related peptide (CGRP) are implicated in migraine and TMD pathology, but its effects on the excitability state of Aδ and C-fiber neurons and glia have not been investigated. The goal of this study was to determine changes mediated by CGRP on intracellular calcium levels in trigeminal ganglion neurons and glia in response to depolarizing stimulation. Intracellular calcium levels were determined in Aδ and C-fiber neurons of primary trigeminal ganglion cultures obtained from neonatal Sprague Dawley rats using Fura-2 and fluorescent microscopy. Cells were left untreated or preincubated for 2 hours with CGRP, then incubated with the …

The Effect Of Cerebellar Feedback On The Spatial Processing Of Conspecific Signals In The Electrosensory System, Dakota Ray Miller

Graduate Theses, Dissertations, and Problem Reports (ETD)

Animals have evolved sensory systems to help decipher important environmental signals that are vital for their survival. Feedback pathways are necessary to allow these signals to stand out in a noisy background, enabling the animal to focus on them more effectively. The electrosensory system of Apteronotus leptorhynchus allows the fish to sense the modulations caused by other conspecifics to allow for proper responses during social interactions. Electroreceptors detect these EODs, and afferent nerves project these signals to the ELL, where electrosensory information is projected to other parts of the brain. Cerebellar feedback to the ELL allows the suppression of lower …

Individual And Collective Properties Of Tunable Photochemical Belousov-Zhabotinsky Micro-Reactors, Kudakwashe Benedict Shumba

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cell-like model chemical systems are powerful tools that can be used to explore the role of intercellular coupling on population level behaviors in communities of biological cells. Firstly, we present a new method for fabricating such micro-reactors using the photosensitive Belousov–Zhabotinsky (BZ) reaction system employed in silica microparticles. These BZ micro-reactors have a tunable response to photochemical coupling, varying from a fully excitatory response to a fully inhibitory response. Their response can be tuned through variations in either the reactive mixture or, on an individual micro-reactor level, by changes in the synthesis temperature used during the fabrication of the silica …

Computational Approaches For Diagnosing Neurological Impairments And Restoring Functional Movement, Serhii Bahdasariants

Graduate Theses, Dissertations, and Problem Reports (ETD)

Movement is the primary means by which the nervous system converts intention into interaction with the environment. Voluntary limb motion enables standing, walking, reaching, and grasping—actions that underpin self‑care, communication, and economic participation. When diseases or injuries disrupt the pathways that couple neural commands to muscle forces—whether through cortical stroke, spinal cord injury, or peripheral nerve damage—mechanical outcomes such as weakness, loss of coordination, and ultimately reduced mobility emerge. These impairments cascade into secondary complications, increased dependence on caregivers, and diminished quality of life. Quantifying how the lesion alters the mechanics of movement is therefore essential for designing targeted interventions …

Robust And Generalizable Representations In The Hippocampus, Hung-Tu Chen

Dartmouth College Ph.D Dissertations

An intelligent system must balance generalizing across similar experiences with maintaining the distinctiveness of each experience. This thesis explores how the hippocampus manages this balance through its neural representations to support adaptive behavior. In Chapter 1, I provide an overview of key hippocampal phenomena that contribute to this process, including remapping, splitter signal, and replay. In Chapter 2, I challenge the concept of random remapping by showing that it is possible to predict, better than chance, how a given experience will be encoded in the hippocampus across different subjects. This suggests that encoding of related experiences, which was previously thought …

Genomic Data Science Approaches For Understanding Human Diseases, Snehal Shah

All Dissertations

The intricate interplay of genetic predisposition, environmental influences, and lifestyle acts as the multifactorial landscape of diseases. Understanding this complexity presents a significant challenge. Molecular insights into disease mechanisms, particularly the interactions of DNA, RNA, and proteins with environmental and lifestyle factors, have revolutionized disease diagnosis, prognosis, and treatment. High-throughput technologies, such as next-generation sequencing, generate large amounts of molecular data, holding a wealth of knowledge. These datasets unveil the roles of genes and their interactions with various factors through analysis, shedding light on previously unknown molecular mechanisms underlying disease pathogenesis. Furthermore, they facilitate the discovery of biomarkers crucial for …