Publications

A neurodynamic model of inter-brain coupling in the gamma band
Quentin Moreau
Lena Adel
Caitriona Douglas
Ranjbaran Ghazaleh
Guillaume Dumas
2022-04-10
bioRxiv (prépublication)
doi.org
Can neurogenesis act as a neural regularizer?
Lina M. Tran
Adam Santoro
Lulu Liu
Sheena A. Josselyn
Blake A. Richards
Paul W. Frankland
New neurons are continuously generated in the subgranular zone of the dentate gyrus throughout adulthood. These new neurons gradually integr… (voir plus)ate into hippocampal circuits, forming new naïve synapses. Viewed from this perspective, these new neurons may represent a significant source of ‘wiring’ noise in hippocampal networks. In machine learning, such noise injection is commonly used as a regularization technique. Regularization techniques help prevent overfitting training data, and allow models to generalize learning to new, unseen data. Using a computational modeling approach, here we ask whether a neurogenesis-like process similarly acts as a regularizer, facilitating generalization in a category learning task. In a convolutional neural network (CNN) trained on the CIFAR-10 object recognition dataset, we modeled neurogenesis as a replacement/turnover mechanism, where weights for a randomly chosen small subset of neurons in a chosen hidden layer were re-initialized to new values as the model learned to categorize 10 different classes of objects. We found that neurogenesis enhanced generalization on unseen test data compared to networks with no neurogenesis. Moreover, neurogenic networks either outperformed or performed similarly to networks with conventional noise injection (i.e., dropout, weight decay, and neural noise). These results suggest that neurogenesis can enhance generalization in hippocampal learning through noise-injection, expanding on the roles that neurogenesis may have in cognition. In deep neural networks, various forms of noise injection are used as regularization techniques to prevent overfitting and promote generalization on unseen test data. Here, we were interested in whether adult neurogenesis– the lifelong production of new neurons in the hippocampus– might similarly function as a regularizer in the brain. We explored this question computationally, assessing whether implementing a neurogenesis-like process in a hidden layer within a convolutional neural network trained in a category learning task would prevent overfitting and promote generalization. We found that neurogenesis regularization was as least as effective as, or more effective than, conventional regularizers (i.e., dropout, weight decay and neural noise) in improving model performance. These results suggest that optimal levels of hippocampal neurogenesis may improve memory-guided decision making by preventing overfitting, thereby promoting the formation of more generalized memories that can be applied in a broader range of circumstances. We outline how these predictions may be evaluated behaviorally in rodents with altered hippocampal neurogenesis.
2022-04-09
bioRxiv (prépublication)
doi.org
GCNFusion: An efficient graph convolutional network based model for information diffusion
Bahareh Fatemi
Soheila Molaei
Shirui Pan
Samira Abbasgholizadeh Rahimi
2022-04-08
Expert Systems with Applications (inconnu)
doi.org
Clones in Deep Learning Code: What, Where, and Why?
Hadhemi Jebnoun
Md Saidur Rahman
Foutse Khomh
Biruk Asmare Muse
Deep Learning applications are becoming increasingly popular. Developers of deep learning systems strive to write more efficient code. Deep … (voir plus)learning systems are constantly evolving, imposing tighter development timelines and increasing complexity, which may lead to bad design decisions. A copy-paste approach is widely used among deep learning developers because they rely on common frameworks and duplicate similar tasks. Developers often fail to properly propagate changes to all clones fragments during a maintenance activity. To our knowledge, no study has examined code cloning practices in deep learning development. Given the negative impacts of clones on software quality reported in the studies on traditional systems, it is very important to understand the characteristics and potential impacts of code clones on deep learning systems. To this end, we use the NiCad tool to detect clones from 59 Python, 14 C# and 6 Java-based deep learning systems and an equal number of traditional software systems. We then analyze the frequency and distribution of code clones in deep learning and traditional systems. We do further analysis of the distribution of code clones using location-based taxonomy. We also study the correlation between bugs and code clones to assess the impacts of clones on the quality of the studied systems. Finally, we introduce a code clone taxonomy related to deep learning programs and identify the deep learning system development phases in which cloning has the highest risk of faults. Our results show that code cloning is a frequent practice in deep learning systems and that deep learning developers often clone code from files in distant repositories in the system. In addition, we found that code cloning occurs more frequently during DL model construction. And that hyperparameters setting is the phase during which cloning is the riskiest, since it often leads to faults.
2022-04-07
Empirical Software Engineering (publié)
doi.org
arxiv.org
Rapid, automated nerve histomorphometry through open-source artificial intelligence
Simeon Christian Daeschler
Marie-Hélène Bourget
Dorsa Derakhshan
Vasudev Sharma
Stoyan Ivaylov Asenov
Tessa Gordon
Julien Cohen-Adad
Gregory Howard Borschel
We aimed to develop and validate a deep learning model for automated segmentation and histomorphometry of myelinated peripheral nerve fibers… (voir plus) from light microscopic images. A convolutional neural network integrated in the AxonDeepSeg framework was trained for automated axon/myelin segmentation using a dataset of light-microscopic cross-sectional images of osmium tetroxide-stained rat nerves including various axonal regeneration stages. In a second dataset, accuracy of automated segmentation was determined against manual axon/myelin labels. Automated morphometry results, including axon diameter, myelin sheath thickness and g-ratio were compared against manual straight-line measurements and morphometrics extracted from manual labels with AxonDeepSeg as a reference standard. The neural network achieved high pixel-wise accuracy for nerve fiber segmentations with a mean (± standard deviation) ground truth overlap of 0.93 (± 0.03) for axons and 0.99 (± 0.01) for myelin sheaths, respectively. Nerve fibers were identified with a sensitivity of 0.99 and a precision of 0.97. For each nerve fiber, the myelin thickness, axon diameter, g-ratio, solidity, eccentricity, orientation, and individual x -and y-coordinates were determined automatically. Compared to manual morphometry, automated histomorphometry showed superior agreement with the reference standard while reducing the analysis time to below 2.5% of the time needed for manual morphometry. This open-source convolutional neural network provides rapid and accurate morphometry of entire peripheral nerve cross-sections. Given its easy applicability, it could contribute to significant time savings in biomedical research while extracting unprecedented amounts of objective morphologic information from large image datasets.
2022-04-07
Scientific Reports (publié)
doi.org
Predicting Visual Improvement After Macular Hole Surgery: A Combined Model Using Deep Learning and Clinical Features
Alexandre Lachance
Mathieu Godbout
Fares Antaki
Mélanie Hébert
Serge Bourgault
Mathieu Caissie
Éric Tourville
Audrey Durand
Ali Dirani
2022-04-05
Translational Vision Science & Technology (publié)
doi.org
Comparison of multi-center MRI protocols for visualizing the spinal cord gray matter
Julien Cohen-Adad
Eva Alonso-Ortiz
Stephanie Alley
Maria Marcella Laganà
Francesca Baglio
Signe Johanna Vannesjo
Haleh Karbasforoushan
Maryam Seif
Alan C. Seifert
Junqian Xu
Joo-Won Kim
René Labounek
Lubomír Vojtíšek
Marek Dostál
Jan Valosek
Rebecca S. Samson
Francesco Grussu
Marco Battiston
Claudia A. M. Gandini Wheeler-Kingshott
Marios C. Yiannakas … (voir 4 de plus)
Guillaume Gilbert
Torben Schneider
Brian Johnson
Ferran Prados
We propose quality assessment criteria and metrics for gray‐matter visualization and apply them to different protocols. The proposed crite… (voir plus)ria and metrics, the analyzed protocols, and our open‐source code can serve as a benchmark for future optimization of spinal cord gray‐matter imaging protocols.
2022-04-04
Magnetic Resonance in Medicine (inconnu)
doi.org
E VALUATING G ENERALIZATION IN GF LOW N ETS FOR M OLECULE D ESIGN
Andrei Cristian Nica
Moksh J. Jain
Emmanuel Bengio
Cheng-Hao Liu
Maksym Korablyov
Michael M. Bronstein
Yoshua Bengio
Deep learning bears promise for drug discovery problems such as de novo molecular design. Generating data to train such models is a costly a… (voir plus)nd time-consuming process, given the need for wet-lab experiments or expensive simulations. This problem is compounded by the notorious data-hungriness of machine learning algorithms. In small molecule generation the recently proposed GFlowNet method has shown good performance in generating diverse high-scoring candidates, and has the interesting advantage of being an off-policy offline method. Finding an appropriate generalization evaluation metric for such models, one predictive of the desired search performance (i.e. finding high-scoring diverse candidates), will help guide online data collection for such an algorithm. In this work, we develop techniques for evaluating GFlowNet performance on a test set, and identify the most promising metric for predicting generalization. We present empirical results on several small-molecule design tasks in drug discovery, for several GFlowNet training setups, and we find a metric strongly correlated with diverse high-scoring batch generation. This metric should be used to identify the best generative model from which to sample batches of molecules to be evaluated.
2022-04-04
ICLR.cc/2022/Workshop/MLDD (poster)
openreview.net
openreview.net
TRACKING AND PREDICTING COVID-19 RADIOLOGICAL TRAJECTORY USING DEEP LEARNING ON CHEST X-RAYS: INITIAL ACCURACY TESTING
N. Duchesne
O. Potvin
D. Gourdeau
P. Archambault
C. Chartrand-Lefebvre
L. Dieumegarde
R. Forghani
C. Gagné
A. Hains
D. Hornstein
H. Le
S. Lemieux
M.H. Lévesque
D. Martin
L. Rosenbloom
A. Tang
F. Vecchio
A. Tang
N. Duchesne
Decision scores and ethically mindful algorithms are being established to adjudicate mechanical ventilation in the context of potential reso… (voir plus)urces shortage due to the current onslaught of COVID-19 cases. There is a need for a reproducible and objective method to provide quantitative information for those scores. Towards this goal, we present a retrospective study testing the ability of a deep learning algorithm at extracting features from chest x-rays (CXR) to track and predict radiological evolution. We trained a repurposed deep learning algorithm on the CheXnet open dataset (224,316 chest X-ray images of 65,240 unique patients) to extract features that mapped to radiological labels. We collected CXRs of COVID-19-positive patients from two open-source datasets (last accessed on April 9, 2020)(Italian Society for Medical and Interventional Radiology and MILA). Data collected form 60 pairs of sequential CXRs from 40 COVID patients (mean age ± standard deviation: 56 ± 13 years; 23 men, 10 women, seven not reported) and were categorized in three categories: “Worse”, “Stable”, or “Improved” on the basis of radiological evolution ascertained from images and reports. Receiver operating characteristic analyses, Mann-Whitney tests were performed. On patients from the CheXnet dataset, the area under ROC curves ranged from 0.71 to 0.93 for seven imaging features and one diagnosis. Deep learning features between “Worse” and “Improved” outcome categories were significantly different for three radiological signs and one diagnostic (“Consolidation”, “Lung Lesion”, “Pleural effusion” and “Pneumonia”; all P 0.05). Features from the first CXR of each pair could correctly predict the outcome category between “Worse” and “Improved” cases with 82.7% accuracy. CXR deep learning features show promise for classifying the disease trajectory. Once validated in studies incorporating clinical data and with larger sample sizes, this information may be considered to inform triage decisions.
2022-04-03
Scientific Reports (publié)
doi.org
Why Exposure Bias Matters: An Imitation Learning Perspective of Error Accumulation in Language Generation
Kushal Arora
Layla El Asri
Hareesh Bahuleyan
Jackie CK Cheung
Current language generation models suffer from issues such as repetition, incoherence, and hallucinations. An often-repeated hypothesis for … (voir plus)this brittleness of generation models is that it is caused by the training and the generation procedure mismatch, also referred to as exposure bias. In this paper, we verify this hypothesis by analyzing exposure bias from an imitation learning perspective. We show that exposure bias leads to an accumulation of errors during generation, analyze why perplexity fails to capture this accumulation of errors, and empirically show that this accumulation results in poor generation quality.
2022-04-02
ArXiv (prépublication)
doi.org
arxiv.org
Multivariate, Transgenerational Associations of the COVID-19 Pandemic Across Minoritized and Marginalized Communities.
Sarah W. Yip
Ayana Jordan
Robert J. Kohler
Avram J. Holmes
Danilo Bzdok
Importance The experienced consequences of the COVID-19 pandemic have diverged across individuals, families, and communities, resulting in i… (voir plus)nequity within a host of factors. There is a gap of quantitative evidence about the transgenerational impacts of these experiences and factors. Objective To identify baseline predictors of COVID-19 experiences, as defined by child and parent report, using a multivariate pattern-learning framework from the Adolescent Brain and Cognitive Development (ABCD) cohort. Design, Setting, and Participants ABCD is an ongoing prospective longitudinal study of child and adolescent development in the United States including 11 875 youths, enrolled at age 9 to 10 years. Using nationally collected longitudinal profiling data from 9267 families, a multivariate pattern-learning strategy was developed to identify factor combinations associated with transgenerational costs of the ongoing COVID-19 pandemic. ABCD data (release 3.0) collected from 2016 to 2020 and released between 2019 and 2021 were analyzed in combination with ABCD COVID-19 rapid response data from the first 3 collection points (May-August 2020). Exposures Social distancing and other response measures imposed by COVID-19, including school closures and shutdown of many childhood recreational activities. Main Outcomes and Measures Mid-COVID-19 experiences as defined by the ABCD's parent and child COVID-19 assessments. Results Deep profiles from 9267 youth (5681 female [47.8%]; mean [SD] age, 119.0 [7.5] months) and their caregivers were quantitatively examined. Enabled by a pattern-learning analysis, social determinants of inequity, including family structure, socioeconomic status, and the experience of racism, were found to be primarily associated with transgenerational impacts of COVID-19, above and beyond other candidate predictors such as preexisting medical or psychiatric conditions. Pooling information across more than 17 000 baseline pre-COVID-19 family indicators and more than 280 measures of day-to-day COVID-19 experiences, non-White (ie, families who reported being Asian, Black, Hispanic, other, or a combination of those choices) and/or Spanish-speaking families were found to have decreased resources (mode 1, canonical vector weight [CVW] = 0.19; rank 5 of 281), escalated likelihoods of financial worry (mode 1, CVW = -0.20; rank 4), and food insecurity (mode 1, CVW = 0.21; rank 2), yet were more likely to have parent-child discussions regarding COVID-19-associated health and prevention issues, such as handwashing (mode 1, CVW = 0.14; rank 9), conserving food or other items (mode 1, CVW = 0.21; rank 1), protecting elderly individuals (mode 1, CVW = 0.11; rank 21), and isolating from others (mode 1, CVW = 0.11; rank 23). In contrast, White families (mode 1, CVW = -0.07; rank 3), those with higher pre-COVID-19 income (mode 1, CVW = -0.07; rank 5), and presence of a parent with a postgraduate degree (mode 1, CVW = -0.06; rank 14) experienced reduced COVID-19-associated impact. In turn, children from families experiencing reduced COVID-19 impacts reported longer nighttime sleep durations (mode 1, CVW = 0.13; rank 14), less difficulties with remote learning (mode 2, CVW = 0.14; rank 7), and decreased worry about the impact of COVID-19 on their family's financial stability (mode 1, CVW = 0.134; rank 13). Conclusions and Relevance The findings of this study indicate that community-level, transgenerational intervention strategies may be needed to combat the disproportionate burden of pandemics on minoritized and marginalized racial and ethnic populations.
2022-03-31
JAMA Psychiatry (publié)
doi.org
Pattern learning reveals brain asymmetry to be linked to socioeconomic status
Timm B. Poeppl
Emile Dimas
Katrin Sakreida
Julius M. Kernbach
Ross D. Markello
Oliver Schöffski
Alain Dagher
Philipp Koellinger
Gideon Nave
Martha J. Farah
Bratislav Misic
Danilo Bzdok
Socioeconomic status (SES) anchors individuals in their social network layers. Our embedding in the societal fabric resonates with habitus, … (voir plus)world view, opportunity, and health disparity. It remains obscure how distinct facets of SES are reflected in the architecture of the central nervous system. Here, we capitalized on multivariate multi-output learning algorithms to explore possible imprints of SES in gray and white matter structure in the wider population (n ≈ 10,000 UK Biobank participants). Individuals with higher SES, compared with those with lower SES, showed a pattern of increased region volumes in the left brain and decreased region volumes in the right brain. The analogous lateralization pattern emerged for the fiber structure of anatomical white matter tracts. Our multimodal findings suggest hemispheric asymmetry as an SES-related brain signature, which was consistent across six different indicators of SES: degree, education, income, job, neighborhood and vehicle count. Hence, hemispheric specialization may have evolved in human primates in a way that reveals crucial links to SES.
2022-03-31
Cerebral Cortex Communications (publié)
doi.org