VictorJuiz/thesis huggingface dataset:
Novel Approaches to Register Transfer Level Debugging and Embedding Representations for Knowledge Base Completion

Register Transfer Level (RTL) debugging has become one of the main bottlenecks of the VLSI design cycle, as current automated debugging tools struggle to handle to the scale of modern designs. Furthermore, automated techniques for knowledge base completion are rapidly approaching the limits of their predictive ability. This thesis addresses some of the barriers to further automating these tasks. First, a new SAT-based debugging algorithm is described which can accelerate the bug search by guiding the SAT solver to prioritize locations that are more likely to be solutions. Two different techniques are proposed to determine a good prioritization. Empirical evaluation shows that the algorithm can find 83% more suspect bug locations in a given amount of time. This thesis also presents two methods to augment knowledge graph embeddings by incorporating supplementary textual data. Experiments show that both methods lead to improved performance on standard knowledge completion tasks in the majority ofcases.

Advisor: Veneris, Andreas
Effective and Efficient Hand Detection in Egocentric Videos

Background. Individuals with spinal cord injury (SCI) report upper limb function as their top recovery priority. To accurately represent the true impact of new interventions on patient function, evaluation should occur from home. Recent work has used wearable cameras to monitor hand function of individuals with SCI in a home environment, and these egocentric videos were automatically analyzed using computer vision. A key step of this process, hand detection, is difficult to accomplish robustly and reliably, hindering the deployment of a complete monitoring system in the home. Objective. Generate an algorithm for fast and reliable hand detection in egocentric videos by combining object detection and tracking algorithms. Methods. We generated an egocentric hand detection dataset (167,622 frames) using videos of 17 individuals with SCI performing activities of daily living in a home simulation laboratory. Using existing detection and tracking algorithms, we introduced two novel combination methods: 1) using detectors to reset trackers and 2) using trackers to generate hand proposals for classification. Results. Method 1 resulted in an algorithm that was twice as fast as the fastest detector alone while being twice as accurate as the best tracker alone. Method 2 resulted in the fastest proposal generation method for hand detection with competitive recall on 1 public dataset. Conclusion. Robust and reliable hand detection that is efficient on portable CPUs will help clinicians directly measure hand function in a patient’s daily life at home.

Keywords: computer vision
egocentric
machine learning
object detection
spinal cord injury
upper limb rehabilitation
Advisor: Zariffa, Jose
Cold-fluid Modeling of Slag Air-blast Atomization

Air blast atomization is a rapidly growing process of handling metallurgical slags with significant advantages over the traditional methods. Experiments were conducted to explore the effects of various operational and material properties on the shape and size of droplets produced during air atomization. Experiments were conducted to understand the effects of the gas flow rate, liquid flow rate, distance between the gas and liquid streams, viscosity and the air velocity on the characteristics of droplets. The mechanisms behind droplet formation and aspect ratio were also investigated. Shadow imaging was employed to observe droplets in-flight; subsequent analysis of the collected images allowed quantification of droplet size and shape. It was found that the kinetic energy provided to the system influences the size of droplets and that the mean droplet size can be predicted based on the gas and liquid flow rates, air velocity and the viscosity of the liquid being atomized. .

Keywords: Atomization
Granulation
Slag
Advisor: Barati, Mansoor
Medical Imaging Semantic Segmentation with Ising Conditional Random Field Post-processing and Lesion Localization

As a scene understanding problem, image semantic segmentation is one of the most fundamental tasks in computer vision. Medical data is characterized for its imbalanced label distribution due to the infrequent occurrences of lesions and their limited size, which causes difficulties in segmenting them with high accuracy. One of the popular semantic segmentation frameworks involves convolutional neural networks (CNNs) and conditional random fields (CRFs) postprocessing. In this thesis, we propose a novel CRF model formulated using the Ising model, which is solved by applying the Digital Annealer (DA) to refine the outputs for binary segmentation problems. We also extend our method to solve multi-class problems by integrating a lesion localization step into the framework, so as to reduce the problems to binary. Our comprehensive experimental results show that the proposed method can effectively enhance the segmentation performance in comparison with traditional methods.

Advisor: Valaee, Shahrokh
On-street Parking Choice Models Based on a Stated Preference Game Simulation Survey

This study develops a stated preference survey, named iCity Park, as a parking simulation game to collect drivers’ on-street parking choices when legal and illegal parking spots are available, and parking enforcement is present. The gamification incentive and simulated hypothetical scenarios in the survey are proven to be effective for high-quality data. iCity Park also simulates parking activities with and without ITS assistance. This study develops three types of logit models for the two assistance levels. The estimated mixed logit models have the best goodness of fit and demonstrate the significance of respondents’ parking preference heterogeneity. Then models for the two assistance levels are compared, and the influential power of the explanatory variables are analyzed. This thesis contributes to innovative data collection methods and provides a better understanding of parking choice process and parking behavioural changes with the assistance of parking information systems.

Keywords: on-street parking choice
parking choice model
parking guidance and information system
parking ITS
simulation survey
stated preference survey
Advisor: Roorda, Matthew J
Investigation into the Effect of Metal Doping on the Photocurrent Response of g-C3N4

To meet the world’s rising energy demands, new materials need to be developed as renewable sources of fuel. One such material is graphitic carbon nitride whose photoelectrochemical behaviour in the visible range of light and facile synthesis makes it a promising semiconductor photocatalyst. To improve the photocatalytic efficiency of graphitic carbon nitride, we doped it with metal cations to inhibit its recombination rate. To test the effect of metal cation doping on its photoelectrochemical behaviour, an open-source potentiostat was designed and built using inexpensive microchips to perform transient photocurrent response measurements. It was found that there were large errors that affected the consistency and reproducibility of the results, which can be attributed to lack of consistency in fabrication of electrode surfaces.

Keywords: carbon nitride
instrument design
metal doping
photocatalyst
potentiostat
semiconductors
Advisor: Goh, Cynthia M
Long Ago There was a Book: Exploring the Digital Sagabon Ise Monogatari through Analytical Bibliography

This masters thesis uses bibliographical analysis to explore digital copies of the Sagabon Ise Monogatari. The digital copies are analysed both as facsimiles for the books they were created from and as digital objects in their own right. Through a combination of description, page collation, and type collation, I explore the origins of the physical and digital artifacts which comprise the Sagabon printings. Wooden movable type, early Japanese printing, Edo period aesthetics, and print variations are all examined. Upon completion of the typographical analysis, I undertake the printing and binding of a physical facsimile from the digital image files. This act of making explores the allowances and constraints digital objects and their metadata have on users and illustrates how making serves as a powerful tool for deepening bibliographic understanding of a book, be it digital or physical.

Keywords: Analytical Bibliography
Bookbinding
Book History
Digital artifacts
Digital collation
Sagabon
Advisor: Galey, Alan
Effect of RB1 Loss on Breast Cancer Cell Invasion and Response to Experimental Therapy

Breast cancer is a heterogeneous disease with triple negative breast cancer (TNBC) exhibiting the worst prognosis. Novel therapies are urgently needed. RB1 and TP53 tumor suppressors are known drivers of metastasis and are disrupted together in ~30% of TNBCs. RB1-loss is not directly druggable, and the mechanism by which it promotes TNBC metastasis is largely unknown. I found that RB knockdown enhanced migration of TNBC cells through a process potentially involving an E2F1-induced increase in mitochondrial protein translation. The CDC25 phosphatase inhibitor BN82008 killed RB1+ TNBC cells and their derivatives with RB1-knockdown, equally well, and without inhibiting cell cycle progression. I also found that RB1 knockdown modulated the expression of glycosylated PD-L1, suggesting RB1-deficient TNBC may benefit from anti-PD-L1 immunotherapy. These studies directly demonstrate that RB1-deficiency promotes migration and suggests downstream pathways that can be targeted to combat aggressive RB1-deficient TNBC and other cancers.

Keywords: Breast Cancer
Retinoblastoma
Advisor: Zacksenhaus, Eldad
Pathway-based Lineage Analysis of Time-course Single-cell RNA Sequencing Data

Time-series single-cell RNA sequencing (scRNAseq) can capture heterogeneity in cell states and transitions during dynamic biological processes, such as development and differentiation. Many trajectory inference methods have been developed to order cells by their progression through a dynamic process and infer the cells’ movement trajectory. These methods, however, do not consider time information when ordering cells. In this thesis, I present a novel method, called Tempora, that uses pathway expression profiles and experiment timepoint information to infer the lineage relationships among different cell populations captured in time-series scRNAseq experiments. Tempora accurately inferred developmental lineages and important time-dependent signaling pathways in human skeletal myoblast differentiation and murine cerebral cortex development time-series scRNAseq data. These results demonstrate the power of using time information, when available, to supervise trajectory inference, as well as suggests that pathway expression profiles are an informative alternative to gene expression profiles in representing individual cells for scRNAseq analysis.

Advisor: Bader, Gary D
A Comparison of Pre- and Post-permanent Canine Emergence Secondary Alveolar Bone Grafting on Dental Survival and Maxillary Growth in Patients with Non-syndromic Complete Unilateral Cleft Lip and Palate

Introduction: Secondary alveolar bone grafting (SABG) in complete unilateral cleft lip and palate completed before (pre-CE) or after the cleft-side permanent canine emergence (post-CE) may differentially alter dental outcomes and maxillary growth. Methods: Cleft-adjacent teeth of 21 pre-CE and 23 post-CE subjects were retrospectively analyzed at T1 (7y), T2 (SABG), and T3 (mean 4y post-SABG) for dental survival, exposures, prosthetic replacements, root development (RD), and root resorption (RR). T1 and T3 cephalograms of 12 pre-CE and 11 post-CE subjects were analyzed for maxillary growth. Results: Dental survival was similar between groups. Most teeth completed RD and pre-CE cleft-side canine RD appeared to accelerate following SABG. Pre-CE SABG required more canine exposures (33.3%; post-CE: 4.6%), but fewer prostheses (14.3%; post-CE: 26.1%) and less tendency for RR (16.3%; post-CE: 22.7%). ANB reduction at T3 was greater in post-CE SABG by 4.75o. Conclusion: Pre-CE SABG suggested a positive trend of better outcomes.

Keywords: Alveolar Bone Grafting
Cleft Lip and Palate
Orthodontics
Plastic Surgery
Advisor: Suri, Sunjay
Porphyrin Molecular Beacons – a New Approach to Osteoarthritis

Despite the substantial burden imposed by osteoarthritis (OA) upon patients and healthcare systems across the world, there are still no effective disease-modifying treatments. A recent shift to view OA as a “whole joint disease” has generated opportunities for therapeutic innovations. Photodynamic therapy (PDT), a clinically approved and minimally invasive treatment modality, holds great potential for application in OA. Herein, we describe the development of a porphyrin molecular beacon, PPMMP13B, as a new approach to OA. Upon target protease-triggered activation, PPMMP13B demonstrates a near 12-fold increase in porphyrin fluorescence as well as the restoration of PDT capabilities through generation of reactive singlet oxygen. Selective activation in vitro occurs only in the presence of human-derived OA synovial fibroblasts. Additionally, a unique intra-articular biodistribution of this porphyrin construct is observed. These results provide the foundation for future studies investigating the therapeutic efficacy of porphyrin molecular beacons to treat OA.

Keywords: fluorescence
matrix metalloproteinase
osteoarthritis
photodynamic therapy
photosensitizer
porphyrin
Advisor: Zheng, Gang
Effect of Autophagy Induction via TRPML1 Activation on Hepatic Steatosis

Discrepancies between the number of liver transplant candidates and available organs has led to an increased use of marginal grafts, including steatotic liver grafts. Steatotic grafts are frequently discarded as their use has been associated with poor transplant outcomes; further exacerbating the organ shortage. Recent studies have demonstrated that autophagy regulates lipid metabolism in hepatocytes, leading to the idea that autophagic function might regulate the development of steatotic liver diseases. A lysosomal calcium channel, TRPML1, has been implicated in the regulation of autophagy through downstream TFEB activation and successive upregulation of autophagic and lysosomal gene expression. The objective of the present study is to explore the link between the induction of autophagy via TRPML1 activation and hepatic steatosis. If an interplay between these factors is elucidated, this may delineate a mechanism by which steatotic livers may be improved during the ex vivo preservation period prior to transplantation.

Keywords: autophagy
fatty liver
hepatic steatosis
mucolipin 1
transplant
TRPML1
Advisor: Jones, Nicola L
Contrasts in Safety Management: Safety-critical Industries vs. Healthcare

Healthcare, as a safety-critical industry, has often been contrasted with aviation and nuclear energy. Though safety tactics learned from aviation and nuclear energy have proven effective, healthcare continues to have higher number of preventable serious adverse events in comparison to aviation and nuclear energy. A mixed-method study was conducted and revealed that aviation and nuclear energy have international organizations which develop standards to harmonize operations globally. According to these standards, there are explicit regulatory requirements within aviation and nuclear energy, to implement safety management systems at the organizational level. Application of safety management systems to the extent implemented in aviation and nuclear energy has not been fully investigated or applied in healthcare practice. Recommendations include but are not limited to the development and implementation of a safety management system standard which includes process control, management of change, proactive hazard identification and risk management, fatigue management, and reliability analysis of safety-critical tasks.

Keywords: Healthcare
Safety-Critical Industries
Safety Management
Standards
Advisor: Cafazzo, Joeseph
Valence Mapping or Order Effects: Comparing Two Accounts of Spatial Influences on Judgments

We noticed positional influences on ratings in a previous study: items were rated more positively when displayed at the top left of the screen (vs. elsewhere). We propose two possible explanations: valence mapping (items are rated more positively at the top and right) and order effects (items are rated more positively when seen first – the top and left for English readers). Nine total studies using behavioural items and items from the Moral Foundations Questionnaire are proposed to experimentally test and disentangle the two accounts; six were completed for this thesis. Results were inconsistent, possibly suggesting that neither account influences more complex evaluations. Implications and limitations of our findings are discussed.

Keywords: Moral judgments
Order effects
Primacy
Spatial influence
Spatial position
Valence mapping
Advisor: Lee, Spike W.S.
Development of a Functional Electrical Stimulation Rowing System and Coaching Application

Functional electrical stimulation (FES) involves electrically stimulating paralyzed muscle to contract and has been integrated into rehabilitation exercises for individuals with spinal cord injury (SCI). Unlike other exercises, FES-rowing requires many training sessions for beginners to learn the appropriate timing of administering FES to their legs through a manual push button, required for performing the exercise with correct technique. Therefore, the purpose of this study was to develop a coaching system to instruct new rowers on the optimal timing for administering FES. We analyzed the temporal and spatial differences between leg muscle activation onset in relation to seat and handle position peaks in 10 able-bodied individuals on a custom-modified FES-rowing ergometer. We identified a target range of seat positions at which to administer FES. Based on this result, we developed and validated a coaching app in 7 individuals, which was shown to improve relative timing of manual button press.

Keywords: Audiovisual Feedback
Coaching System
Functional Electrical Stimulation
Rehabilitation
Rowing
Spinal Cord Injury
Advisor: Masani, Kei
Mapping of the Akt and Beta-arrestin Interface for Drug Development

G-protein-coupled receptors (GPCRs) are well-known therapeutic targets, and it has been demonstrated that they can signal both via guanine nucleotide-binding proteins (G proteins) signaling and arrestin signaling. Dopamine (DA) and dopamine receptors, which are GPCRs, are involved in numerous neuropsychiatric disorders. Notably, dopamine D2 receptor (D2R) signaling is targeted by drugs used for mental illnesses like bipolar disorder (BP) and schizophrenia (SZ). Indeed, a signaling pathway involving arrestin signaling is targeted by both lithium and antipsychotic medications. This pathway involves a modulation of glycogen synthase kinase 3 (GSK-3) by D2Rs via a complex formed of Akt (also called protein kinase B or PKB), β-arrestin 2 (βArr2) and protein phosphatase 2A (PP2A). The aim of this project is to further elucidate this signaling pathway by studying the direct interaction between two of its components, the proteins Akt and βArr2, in view of possible drug development.

Keywords: Akt
Beta-arrestin
D2R
GPCR
Mental illness
Advisor: Beaulieu, Jean-Martin
Co-Registration of Intracardiac Echocardiography (ICE) and Computed Tomography (CT) for the Purpose of Guiding Structural Heart Disease Intervention

We demonstrate in this work a system for tracking the position and orientation of an intracardiac echocardiography (ICE) image within a CT volume for the purpose of improving imaging guidance for cardiac interventions. The method begins with a user-defined registration step, followed by subsequent automated local searches within the CT volume. The local searches are performed by a series of individual 2D-2D co-registration steps over various positions and orientations within the 3D space using an edge-sensitive algorithm. A stepwise sampling method is used to reduce the total number of processing steps. Validation testing using a silicone cardiac phantom over 10 pullback positions demonstrated average position and orientation localization errors of 4.1 mm and 8.1 degrees respectively. A high degree of rotation symmetry in the model likely contributed significantly to the orientation accuracy results. Further work is required to reduce computation time for the algorithm, including the use of parallel processing.

Keywords: Aortic Valve Disease
Computed Tomography
Echocardiography
Image Registration
Intracardiac Echocardiography
TAVI
Advisor: Wright, Graham A
Courtney, Brian K
An Efficient Hardware Architecture for Exploiting Sparsity in Neural Networks

Sparsity – the presence of many zero values – is a pervasive property of modern deep neural networks, as it is inherently induced by state-of-the-art algorithmic optimizations. Recent eﬀorts in hardware design for acceleration of neural networks have targeted the structure of computation of these workloads. However, when run on these value-agnostic accelerators, value sparsity is not exploited to provide performance or eﬃciency beneﬁts, and instead results in wasted computation. In this thesis, we present architectural optimizations that eﬃciently leverage value sparsity in network weights in order to achieve signiﬁcant performance beneﬁts, with minimal hardware overhead. The culmination of this work is a hardware front-end (data fetching and staging unit) which, when paired with our novel, co-designed software scheduling algorithm, achieves more than a 2× speedup on average for the networks studied, with just an 8.2% overhead in compute area.

Keywords: Artificial Intelligence
Computer Architecture
Hardware Acceleration
Machine Learning
Neural Networks
Sparsity
Advisor: Moshovos, Andreas
Perceptions on the Behavioural Management of Dental Patients with Developmental Disabilities: A Qualitative Study

Background: Dental patients with developmental disabilities (PDD) are complex and require various behaviour management techniques. Objective: 1. To gather behaviour management approaches of Mount Sinai Hospital’s (MSH) Dental Program for PDD and similar programs for background information. 2. To describe the experiences of special care dentists and caregivers regarding behaviour management used at MSH. Methods: 1. A questionnaire was sent to the institutions regarding behaviour management approaches. 2. Telephone interviews were conducted with 5 special care dentists and 7 caregivers. Interviews were analyzed using thematic analysis. Results: Behaviour complexities were a perceived barrier to care. Four themes emerged: 1) No two patients are the same, 2) They (patients) are more than just their teeth, 3) Who knows the patient best 4) Stop and appreciate the environment. Conclusions: PDD are heterogeneous and respond to an array of behaviour management techniques; this underscores the need to involve the caregivers in treatment decisions.

Keywords: Behaviour Management
Developmental Disabilities
General Anaesthesia
Non-Pharmacological
Pharmacological
Advisor: Azarpazhooh, Amir