NCube/papyrus huggingface dataset:
Towards computationally efficient neural networks with adaptive and dynamic computations

Over the past few years, artificial intelligence has been greatly advanced, and deep learning, where deep neural networks are used to attempt to loosely emulate the human brain, has significantly contributed to it. Deep neural networks are now able to achieve great success based on a large amount of data and sufficient computational resources. Despite their success, their ability to quickly adapt to new concepts, tasks, and environments is quite limited or even non-existent. In this thesis, we are interested in how deep neural networks can become adaptive to continually changing or totally new circumstances, similarly to human intelligence, and further introduce adaptive and dynamic architectural modules or meta-learning frameworks to make it happen in computationally efficient ways. This thesis consists of a series of studies proposing methods to utilize adaptive and dynamic computations to tackle adaptation problems that are investigated from different perspectives such as task-level, temporal-level, and context-level adaptations.     In the first article, we focus on task-level fast adaptation based on a meta-learning framework.   More specifically, we investigate the inherent model uncertainty that is induced from quickly adapting to a new task with a few examples. This problem is alleviated by combining the efficient gradient-based meta-learning with nonparametric variational inference in a principled probabilistic framework. It is an important step towards robust meta-learning that we develop a Bayesian few-shot learning method to prevent task-level overfitting.    In the second article, we attempt to improve the performance of sequence (i.e. future) prediction by introducing a jumpy future prediction that is based on the adaptive step size. It is a critical ability for an intelligent agent to explore an environment that enables efficient option-learning and jumpy future imagination. We make this possible by introducing the Hierarchical Recurrent State Space Model (HRSSM) that can discover the latent temporal structure (e.g. subsequences) while also modeling its stochastic state transitions hierarchically.    Finally, in the last article, we investigate a framework that can capture the global context in image data in an adaptive way and further process the data based on that information. We implement this framework by extracting high-level visual concepts through attention modules and using graph-based reasoning to capture the global context from them. In addition, feature-wise transformations are used to propagate the global context to all local descriptors in an adaptive way.

Keyphrases: deep learning, deep neural networks, adaptive neural networks, adaptive computation, dynamic computation, few-shot learning, learn-to-learn, attention mechanism, feature modulation, concept reasoning, temporal abstraction, artificial intelligence, machine learning, meta-learning, modulation de feature, abstraction temporelle
Efficient frequency-space methods for light transport caching

Light transport is the method of physically simulating the movement of photons in an environment. Applied to rendering, light travels one last time to a virtual sensor that captures it as an image displayed to an observer. As it travels, light is analysable frequentially to understand how it varies spatially and angularly to accelerate rendering. Recent advances in physically-based realistic rendering have been closing the gap between reality and simulation but the memory and performance costs still preclude the inclusion of the more computationally expensive effects in interactive and real-time applications. Because of this, modern production renderers rely on the ahead-of-time precomputation of data for efficient reuse in the form of offline computational processes and asynchronously distributed procedures. This thesis by publication investigates with two papers the simulation of light transport from a frequency-based perspective for interactive and precomputed real-time applications. We first propose a method for efficiently reusing light path computations over time in interactive Monte Carlo path-traced animation sequences. We leverage to this end the frequency analysis of light transport introduced in previous works, extended to spatial, angular and temporal sampling and reconstruction. Our second method investigates the precomputation of participating volume-to-surface light transport as impulse responses, a compact and efficient frequency-based transport operator. In turn, these operators accelerate by orders of magnitude the computation of multi-scattered volume-to-surface transport in arbitrary, potentially heterogeneous media conditions.

Keyphrases: Rendering, Light Transport, Frequency Analysis, Participating Media, Adaptive Sampling, Filtering, Spherical Harmonics
Des désirs qui orientent : une analyse phénoménologique des identifications et désidentifications lezbiqueer dans l’espace montréalais

Through a critical phenomenological perspective using walking interviews (Ahmed 2006, Lee 2015, Weiss et al., 2019), this thesis explores different meanings associated with the sexual orientations of lesbian, bisexual, queer, fluid and pansexual women in the Montreal context. This approach is based on the experiential sharing of 21 lezbiqueer women with various positionnalities, co-constructing meaning through the trajectories we followed and the photographs submitted by the participants. Sexual identifications questions are linked to spatial questions (Jones and Garde-Hansen 2012, Longhurst and Johnston 2010, Collie 2013, Browne and Ferreira 2015, Podmore 2006 and 2019) through an analysis of both the content of the interviews and the way we walked during these interviews. The three parts of the thesis address migratory trajectories (the experience of arriving in Montreal as a lezbiqueer person), the spaces and identifications of lezbiqueer communities in Montreal from 1980 to today, and the visibilities and sensitivities perceived by lezbiqueer women in public spaces.

Keyphrases: LGBTQ, lesbian, bisexual, space, identity, space, Montreal, phenomenology, orientation, identification, queer
How does fatigue contribute to cognitive dysfunction in childhood acute lymphoblastic leukemia survivors

Objectives: The present study aims to (1) describe neurocognitive difficulties and fatigue in a well-characterized cohort of long-term acute lymphoblastic leukemia (ALL) survivors and (2) explore the contribution of self-reported fatigue to objective neurocognitive difficulties typically studied in this population. Method: Pediatric ALL survivors (N = 285) from the PETALE PSY-ALL cohort completed the DIVERGT battery of cognitive tests, the Pediatric Quality of Life Inventory Multidimensional Fatigue Scale (PedsQL MFS) and the Distress Thermometer (DT). We conducted frequency and comparison analyses for factors of interest. We performed multiple regression models to assess the contribution of fatigue in explaining cognitive deficits beyond known risk factors (age, age at diagnosis, sex, ALL risk status, emotional distress). Results: At least one cognitive difficulty (one DIVERGT scale <1.5 SD) occurred in 66% of participants. Domains primarily affected were verbal fluency, working memory and fine motor skills. Participants had normal levels of fatigue except for the subscale Sleep/rest fatigue showing 7% higher fatigue in those <18 years than in comparison samples across ages. Sleep/rest fatigue was associated with working memory (Digit Span Total score, r = 0.117; p = 0.049). Fatigue did not explain neurocognitive dysfunction beyond known risk factors from the clinical history. Conclusions: Pediatric ALL survivors have many cognitive difficulties and experience fatigue due to sleep/rest issues. The contribution of fatigue to cognitive dysfunction is lower than expected, which may be due to specificities of cognitive dysfunctions, the impact of normalization processes on the measure of fatigue or the lack of sensibility of our fatigue measure.

Keyphrases: Fatigue, Neurocognitive, Oncology, Pediatric acte lymphoblastic leukemia, Survivors
Décrochage scolaire au secondaire : synergie entre l’adversité familiale perdurant depuis l’enfance et l’exposition aux évènements stressants à l’adolescence

High school dropout is a major issue due to its individual and social costs. Recent studies suggest that dropping out results not only from exposure to long-term risk factors, but also from proximal exposure to stressful life events. According to the stress sensitization model, this apparent precipitating role of stressor exposure should be exacerbated among those exposed to family adversity during childhood. The goal of this study was to test this hypothesis, by examining (1) whether exposure to stressful events and the presence of family adversity during childhood were directly associated with high school dropout, and (2) whether this kind of adversity exacerbated the association between exposure to recent stressful events and high school dropout. These associations were tested within a sample (n = 545) of youths aged 16 years old on average (M = 16.5; SD = 0.9) recruited in 12 public high schools located in and around Montreal and overrepresenting early school leavers. After accounting for potential confounders, adolescents who had recently experienced severe stressful life events were found to be more at risk of dropping out, as were those with a history of follow-up with child protection services. However, dropping out was not more frequent among adolescents exposed to other forms of family adversity, namely the presence of family crises and parental chronic mental health problems. Also, the expected sensitization effects were not observed in moderation analyzes. These results partially aligned with hypotheses are discussed in terms of theoretical and practical implications.

Keyphrases: Adolescents, Childhood adversity, Stressful life events, High school dropout
Contribution du récepteur GPR55 à la synaptogenèse

Functional connections between nerve cells (called synapses) are essential to establish the architecture of the nervous system. The modification of synapses is thought to be one of the mechanisms by which learning and memory occur. It has been known for decades that cannabis consumption has a profound influence on learning and memory, and that maternal marijuana smoking during perinatal period causes cognitive deficits that last in the adulthood of the offspring. For the moment, we do not know if these effects are mediated by the classic CB1 and CB2 cannabinoid receptors or by other receptors such as GPR55. Recent studies by Pr. Bouchard have demonstrated an important role for the endocannabinoid system in the development of the nervous system, including the presence of GPR55 and its involvement in axon growth and target innervation during the fetal and early postnatal periods. As certain molecules and cellular mechanisms involved in these processes may also regulate synapse formation (synaptogenesis), the objective of the present study is to determine the contribution of GPR55 in the formation of new synaptic contacts. Primary cortical neurons isolated from embryonic mice were cultivated and then treated either with a selective agonist of GPR55 (O-1602) or his selective antagonist (ML-193), or with a phytocannabinoid (cannabidiol) for 24h at the ninth day in vitro (DIV9). In immunocytochemistry, neurons treated with ML-193 have shown a decrease in synaptic density, while the treatment with O-1602 or cannabidiol increased it. These anatomical changes were correlated with changes in the expression of synaptic proteins GluR1 and synaptophysin. Results from this study provide important insight on the development of the nervous system and contribute to improving our knowledge on developmental abnormalities induced by perinatal cannabis use.

Keyphrases: GPR55, Synaptogenesis, Cannabinoids, Development of the central nervous system
Effet neuroprotecteur de Lacticaseibacillus rhamnosus HA-114 chez divers modèles de la maladie d’Alzheimer

Alzheimer’s disease (AD) often presents itself as a progressive decline of behavioral and cognitive functions such as memory impairment. On a biological level, this disease presents extracellular accumulation of amyloid-beta (Aß), intracellular accumulation of tau, alteration of synaptic function and neuronal loss. Recent data showed that a supplementation with a specific probiotic strain of bacteria, Lacticaseibacillus rhamnosus HA-114 (HA-114), had a neuroprotective effect in several neurodegenerative disease models. This project aimed to characterize the neurophysiological aspects of a specific nematode strain expressing the Aß1-42 fragment and to validate the neuroprotective effect of HA-114 in this nematode strain as well as in the APP/PS1 murin model of AD. Following biochemical and behavioral experiments, data showed that this strain recapitulates key traits of AD: an age-dependent alteration of neuronal health and memory impairment. It was also observed that administrating HA-114 probiotic strain could attenuate age-related phenotypes of neurodegeneration and paralysis. This transgenic strain is therefore a new tool for drug screening and investigating AD’s pathogenesis. The neuroprotective effect of HA-114 observed in this strain shows potential towards an amelioration of the patient’s quality of life. Studying the effects of HA-114 in a murin model could reveal new investigation opportunities for AD’s pathogenesis and mechanisms that could one day cure this disease.

Keyphrases: Memory, Microbiome, Aging, Nematode, Neurodegeneration, C. elegans, Alzheimer's Disease, Amyloid-beta, Worm
L’amygdale et la réponse aux stimuli associés aux récompenses : rôle des récepteurs glutamatergiques métabotropes du groupe II

Conditioned stimuli (CS) guide animals towards rewards needed for survival, such as food and water. In parallel, they can also promote maladaptive reward seeking, as in addiction. Glutamate signaling within the basolateral amygdala (BLA) modulates the effects of cues. However, the role of metabotropic group II glutamate (mGlu2/3) receptors in the BLA is unknown. mGlu2/3 are localized predominantly extrasynaptically on presynaptic terminals. The activation of these receptors suppresses synaptic glutamate release. Thus, we hypothesized that activating BLA mGlu2/3 receptors would attenuate cue-triggered increases in incentive motivation for reward, via reduced glutamate release. The Pavlovian-to-Instrumental transfer (PIT) method was used to test this hypothesis. We first confirmed a PIT effect in a cohort of male rats. Rats initially learned to press a lever to obtain a water reward. Then, they learned that one auditory cue predicts noncontingent delivery of water (CS+), while a second different auditory cue does not (CS-). On PIT test day, the rats could lever press under extinction (water deliveries omitted), and we assessed changes in lever pressing in response to CS+ and CS-. The rats pressed more on the lever during CS+ versus CS-, indicating cue-triggered potentiation of incentive motivation. In a separate cohort of male rats, the methods were repeated with the mGlu2/3 agonist LY379268 (0, 3 or 6 μg/hemisphere) infused into the BLA prior to PIT testing. LY379268 abolished CS+ potentiated pressing on the water-associated lever. In a last study, we examined the influence of systemic administration of LY379268 (0, 0.3 or 1 mg/kg, subcutaneous) on PIT, in a cohort of female and male rats. We found that cue-triggered increases in incentive motivation was similar across sexes, and that systemic injection of LY379268 decreased this effect in both sexes. These results indicate that mGlu2/3 receptors mediate the motivational effects of cues in both sexes.

Keyphrases: Glutamate, Instrumental conditioning, Pavlovian conditioning, Pavlovian-to-instrumental transfer, Basolateral amygdala, mGlu2/3 receptors, Sex differences
The relationship between co-rumination and different forms of normative anxiety in Quebec youth

Friends can rely on each other when faced with problems, though these discussions may lead to co-rumination. Co-rumination occurs early in life and has been associated with various forms of anxiety symptoms and/or clinical anxiety disorders. However, a scarcity of literature has explored the association between co-rumination and forms of normative anxiety, including state anxiety, trait anxiety, test anxiety, and anxiety sensitivity. This thesis examined the relationship between co-rumination and these forms of normative anxiety while considering sex and age. In total, 1204 children (ages 11 to 12) and adolescents (ages 16 to 17) were recruited from elementary and high schools in Quebec. Participants completed questionnaires measuring co-rumination and the four forms of normative anxiety in their classrooms. The results revealed that co-rumination was associated with one form of normative anxiety (anxiety sensitivity) in children and three forms (trait anxiety, test anxiety, and anxiety sensitivity) in adolescents. Thus, co-rumination may be differentially associated with various forms of normative anxiety due to certain developmental factors. Future longitudinal confirmatory studies should test the hypotheses generated from the findings of this exploratory study. Beyond the implications discussed in the article, this thesis features potential research avenues and considerations for future studies investigating the relationship between co-rumination and different forms of normative anxiety.

Keyphrases: Co-rumination, Adolescents, State anxiety, Trait anxiety, Test anxiety, Anxiety sensitivity, Children
Le réflexe photomoteur pour évaluer l’état analgésique des patients traumatisés crâniens sédationnés et incapables de communiquer à l’unité des soins intensifs

Background: Analgesia monitoring is essential to preserve comfort in critically ill sedated patients with traumatic brain injury (TBI). While pupil dilation (PD) and pain behaviors can be used to assess analgesia, these indicators require application of noxious stimulations. Recently, the pupillary light reflex (PLR) has emerged as a non-noxious parameter that may be used to predict analgesia requirements in non-brain-injured patients. Here, we investigated whether PLR can be used for the purpose of analgesia monitoring in critically ill sedated TBI patients. Methods: Fifteen mechanically ventilated TBI patients (11 men; 54±20 years) under perfusions of analgesia and sedation were assessed at predefined time within 72 hours of intensive care unit admission. Data collection was performed using video-pupillometry and the Behavioral Pain Scale (BPS). At each assessment, pupil size and PLR at rest were recorded followed immediately by the documentation of PD and pain behaviors elicited by a calibrated noxious stimulation. Blood concentrations of analgesics/sedatives were monitored. Results: 103 assessments were completed. PLR resulted in an average decrease of -19% in pupil diameter and PD resulted in average increase of +10%. Variations in PLR and PD were more pronounced in participants who showed a BPS score > 3 (a recognized sign of sub analgesia) compared to those with no behavioral reaction. Multiple regression analyzes showed a significant overlap between fluctuations in pupillary reflexes and blood levels of fentanyl, not propofol. Conclusions: PLR may be useful to assess analgesia requirements before a nociceptive procedure in critically ill sedated patients with TBI.

Keyphrases: Pupillometry, Analgesia, Pain, Traumatic brain injury
Étude observationnelle des effets associés à divers agents de sédation et d'analgésie administrés en période périopératoire chez les nourrissons atteints d’une cardiopathie congénitale complexe sur l’EEG et le neurodéveloppement

Congenital heart disease (CHD) is one of the most common congenital defects. Almost half of neonates affected require heart surgery during their first month of life, which exposes them to an increased risk of brain damage and has been associated with impaired neurodevelopment. It is therefore important to identify effective neuroprotective strategies to improve their neurological outcomes. This thesis describes the influence of the administration of pharmacological agents during the perioperative period on postoperative EEG recovery and neurodevelopmental outcomes at 12 and 24 months. We hypothesized that the administration of certain pharmacological agents for sedation, anesthesia and analgesia given during the intra- and post-operative period could have a beneficial effect on cerebral recovery, by decreasing the postoperative EEG discontinuity and/or improving neurodevelopmental outcomes. Our results suggest that the administration of higher doses of opioids during the perioperative period could reduce the pain and stress induced by cardiac surgery and are thus associated with improved neurodevelopmental outcomes. The administration of higher doses of dexmedetomidine and midazolam was marked by a delayed recovery of brain activity after cardiac surgery without any noticeable impact on neurodevelopmental outcomes in our cohort. Similarly, the doses of ketamine had no impact on postoperative brain recovery and on their long-term development.

Keyphrases: Congenital heart disease, Quantitative EEG analysis, Neurodevelopment, Pharmacological agents, Cardiac surgery, Pediatric critical care
Caractérisation de deux familles de pharmacogènes, les gènes CYP3A et CYP4F

Cytochromes P450 (CYP450) are hemoproteins generally involved in the detoxification of the body of xenobiotic molecules and participate in the metabolism of many drugs. Genetic polymorphisms have been found to impact drugs responses and metabolic functions.  However, genes encoding CYP450 proteins are often under-analyzed in large-scale genomic studies because the difficulty of analysis due to of their high rate of polymorphism. In this study, we investigate the genetic diversity for CYP450 genes. We found that two clusters, CYP3A and CYP4F, are notably differentiated across human populations with evidence for selective pressures acting on both clusters. The CYP3A subfamily metabolizes approximately 50\% of drugs while CYP4F enzymes are involved in the metabolism of endogenous compounds, nutrients and drugs. Indeed, we found signals of recent positive selection in CYP3A and CYP4F genes and signals of balancing selection in CYP4F genes. Futhermore, unusual linkage disequilibrium is detected in both cluster, suggesting co-evolution. eQTLs were also found in both clusters which indicate co-regulation and epistasis.

Keyphrases: Cytochromes P450, CYP3A, CYP4F, Population genetics, Bioinformatics, Genomics, Transcriptomics