Publications

Population heterogeneity in clinical cohorts affects the predictive accuracy of brain imaging
Oualid Benkarim
Casey Paquola
Bo-yong Park
Valeria Kebets
Seok-Jun Hong
Reinder Vos de Wael
Shaoshi Zhang
B. T. Thomas Yeo
Michael Eickenberg
Tian Ge
Jean-Baptiste Poline
Boris C. Bernhardt
Danilo Bzdok
Brain imaging research enjoys increasing adoption of supervised machine learning for single-participant disease classification. Yet, the suc… (see more)cess of these algorithms likely depends on population diversity, including demographic differences and other factors that may be outside of primary scientific interest. Here, we capitalize on propensity scores as a composite confound index to quantify diversity due to major sources of population variation. We delineate the impact of population heterogeneity on the predictive accuracy and pattern stability in 2 separate clinical cohorts: the Autism Brain Imaging Data Exchange (ABIDE, n = 297) and the Healthy Brain Network (HBN, n = 551). Across various analysis scenarios, our results uncover the extent to which cross-validated prediction performances are interlocked with diversity. The instability of extracted brain patterns attributable to diversity is located preferentially in regions part of the default mode network. Collectively, our findings highlight the limitations of prevailing deconfounding practices in mitigating the full consequences of population diversity.
2022-03-31
PLoS Biology (published)
doi.org
Fast-Converging Simulated Annealing for Ising Models Based on Integral Stochastic Computing
Naoya Onizawa
Kota Katsuki
Duckgyu Shin
Warren J. Gross
Takahiro Hanyu
Probabilistic bits (p-bits) have recently been presented as a spin (basic computing element) for the simulated annealing (SA) of Ising model… (see more)s. In this brief, we introduce fast-converging SA based on p-bits designed using integral stochastic computing. The stochastic implementation approximates a p-bit function, which can search for a solution to a combinatorial optimization problem at lower energy than conventional p-bits. Searching around the global minimum energy can increase the probability of finding a solution. The proposed stochastic computing-based SA method is compared with conventional SA and quantum annealing (QA) with a D-Wave Two quantum annealer on the traveling salesman, maximum cut (MAX-CUT), and graph isomorphism (GI) problems. The proposed method achieves a convergence speed a few orders of magnitude faster while dealing with an order of magnitude larger number of spins than the other methods.
2022-03-27
IEEE Transactions on Neural Networks and Learning Systems (published)
doi.org
From Points to Functions: Infinite-dimensional Representations in Diffusion Models
Sarthak Mittal
Guillaume Lajoie
Stefan Bauer
Arash Mehrjou
Diffusion-based generative models learn to iteratively transfer unstructured noise to a complex target distribution as opposed to Generative… (see more) Adversarial Networks (GANs) or the decoder of Variational Autoencoders (VAEs) which produce samples from the target distribution in a single step. Thus, in diffusion models every sample is naturally connected to a random trajectory which is a solution to a learned stochastic differential equation (SDE). Generative models are only concerned with the final state of this trajectory that delivers samples from the desired distribution. Abstreiter et. al showed that these stochastic trajectories can be seen as continuous filters that wash out information along the way. Consequently, it is reasonable to ask if there is an intermediate time step at which the preserved information is optimal for a given downstream task. In this work, we show that a combination of information content from different time steps gives a strictly better representation for the downstream task. We introduce an attention and recurrence based modules that ``learn to mix'' information content of various time-steps such that the resultant representation leads to superior performance in downstream tasks.
2022-03-27
ICLR.cc/2022/Workshop/DGM4HSD (poster)
doi.org
openreview.net
Reproducibility and Evolution of Diffusion Mri Measurements Within the Cervical Spinal Cord in Multiple Sclerosis
Haykel Snoussi
Emmanuel Caruyer
Benoit Combes
Olivier Commowick
Elise Bannier
Anne Kerbrat
Julien Cohen-Adad
Christian Barillot
In Multiple Sclerosis (MS), there is a large discrepancy between the clinical observations and how the pathology is exhibited on brain image… (see more)s, this is known as the clinical-radiological paradox. One of the hypotheses is that the clinical deficit may be more related to the spinal cord damage than the number or location of lesions in the brain. Therefore, investigating how the spinal cord is damaged becomes an acute challenge to better understand and overcome this paradox. Diffusion MRI is known to provide quantitative figures of neuronal degeneration and axonal loss, in the brain as well as in the spinal cord. In this paper, we propose to investigate how diffusion MRI metrics vary in the different cervical regions with the progression of the disease. We first study the reproducibility of diffusion MRI on healthy volunteers with a test-retest procedure using both standard diffusion tensor imaging (DTI) and multi-compartment Ball-and-Stick models. Then, based on the test re-test quantitative calibration, we provide quantitative figures of pathology evolution between M0 and M12 in the cervical spine on a set of 31 MS patients, exhibiting how the pathology damage spans in the cervical spinal cord.
2022-03-27
2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI) (published)
doi.org
arxiv.org
Inductive Biases for Relational Tasks
Giancarlo Kerg
Sarthak Mittal
David Rolnick
Yoshua Bengio
Blake Aaron Richards
Guillaume Lajoie
Current deep learning approaches have shown good in-distribution performance but struggle in out-of-distribution settings. This is especiall… (see more)y true in the case of tasks involving abstract relations like recognizing rules in sequences, as required in many intelligence tests. In contrast, our brains are remarkably flexible at such tasks, an attribute that is likely linked to anatomical constraints on computations. Inspired by this, recent work has explored how enforcing that relational representations remain distinct from sensory representations can help artificial systems. Building on this work, we further explore and formalize the advantages afforded by ``partitioned'' representations of relations and sensory details. We investigate inductive biases that ensure abstract relations are learned and represented distinctly from sensory data across several neural network architectures and show that they outperform existing architectures on out-of-distribution generalization for various relational tasks. These results show that partitioning relational representations from other information streams may be a simple way to augment existing network architectures' robustness when performing relational computations.
2022-03-24
ICLR.cc/2022/Workshop/OSC (poster)
openreview.net
openreview.net
INFERNO: Inferring Object-Centric 3D Scene Representations without Supervision
Lluis Castrejon
Nicolas Ballas
Aaron Courville
We propose INFERNO, a method to infer object-centric representations of visual scenes without annotations. Our method decomposes a scene int… (see more)o multiple objects, with each object having a structured representation that disentangles its shape, appearance and pose. Each object representation defines a localized neural radiance field used to generate 2D views of the scene through differentiable rendering. Our model is subsequently trained by minimizing a reconstruction loss between inputs and corresponding rendered scenes. We empirically show that INFERNO discovers objects in a scene without supervision. We also validate the interpretability of the learned representations by manipulating inferred scenes and showing the corresponding effect in the rendered output. Finally, we demonstrate the usefulness of our 3D object representations in a visual reasoning task using the CATER dataset.
2022-03-24
ICLR.cc/2022/Workshop/OSC (poster)
openreview.net
openreview.net
Neurobiological Correlates of Change in Adaptive Behavior in Autism.
Charlotte M. Pretzsch
Tim Schäfer
Michael V. Lombardo
Varun Warrier
Caroline Mann
Anke Bletsch
Chris H. Chatham
Dorothea L. Floris
Julian Tillmann
Afsheen Yousaf
Emily J. H. Jones
Tony Charman
Sara Ambrosino
Thomas Bourgeron
Guillaume Dumas
Eva Loth
Beth Oakley
Jan K. Buitelaar
Freddy Cliquet
Claire Leblond … (see 7 more)
Simon Baron-Cohen
Christian Beckmann
Tobias Banaschewski
Sarah Durston
Christine M. Freitag
Declan Murphy
Christine Ecker
2022-03-24
American Journal of Psychiatry (published)
doi.org
Object-centric Compositional Imagination for Visual Abstract Reasoning
Rim Assouel
Pau Rodríguez
Perouz Taslakian
David Vázquez
Yoshua Bengio
Like humans devoid of imagination, current machine learning systems lack the ability to adapt to new, unexpected situations by foreseeing th… (see more)em, which makes them unable to solve new tasks by analogical reasoning. In this work, we introduce a new compositional imagination framework that improves a model's ability to generalize. One of the key components of our framework is object-centric inductive biases that enables models to perceive the environment as a series of objects, properties, and transformations. By composing these key ingredients, it is possible to generate new unseen tasks that, when used to train the model, improve generalization. Experiments on a simplified version of the Abstraction and Reasoning Corpus (ARC) demonstrate the effectiveness of our framework.
2022-03-24
ICLR.cc/2022/Workshop/OSC (poster)
openreview.net
openreview.net
Monoallelic Heb/Tcf12 Deletion Reduces the Requirement for NOTCH1 Hyperactivation in T-Cell Acute Lymphoblastic Leukemia
Diogo F. T. Veiga
Mathieu Tremblay
Bastien Gerby
Sabine Herblot
André Haman
Patrick Gendron
Sébastien Lemieux
Juan Carlos Zúñiga-Pflücker
Josée Hébert
Joseph Paul Cohen
Trang Hoang
Early T-cell development is precisely controlled by E proteins, that indistinguishably include HEB/TCF12 and E2A/TCF3 transcription factors,… (see more) together with NOTCH1 and pre-T cell receptor (TCR) signalling. Importantly, perturbations of early T-cell regulatory networks are implicated in leukemogenesis. NOTCH1 gain of function mutations invariably lead to T-cell acute lymphoblastic leukemia (T-ALL), whereas inhibition of E proteins accelerates leukemogenesis. Thus, NOTCH1, pre-TCR, E2A and HEB functions are intertwined, but how these pathways contribute individually or synergistically to leukemogenesis remain to be documented. To directly address these questions, we leveraged Cd3e-deficient mice in which pre-TCR signaling and progression through β-selection is abrogated to dissect and decouple the roles of pre-TCR, NOTCH1, E2A and HEB in SCL/TAL1-induced T-ALL, via the use of Notch1 gain of function transgenic (Notch1ICtg) and Tcf12+/- or Tcf3+/- heterozygote mice. As a result, we now provide evidence that both HEB and E2A restrain cell proliferation at the β-selection checkpoint while the clonal expansion of SCL-LMO1-induced pre-leukemic stem cells in T-ALL is uniquely dependent on Tcf12 gene dosage. At the molecular level, HEB protein levels are decreased via proteasomal degradation at the leukemic stage, pointing to a reversible loss of function mechanism. Moreover, in SCL-LMO1-induced T-ALL, loss of one Tcf12 allele is sufficient to bypass pre-TCR signaling which is required for Notch1 gain of function mutations and for progression to T-ALL. In contrast, Tcf12 monoallelic deletion does not accelerate Notch1IC-induced T-ALL, indicating that Tcf12 and Notch1 operate in the same pathway. Finally, we identify a tumor suppressor gene set downstream of HEB, exhibiting significantly lower expression levels in pediatric T-ALL compared to B-ALL and brain cancer samples, the three most frequent pediatric cancers. In summary, our results indicate a tumor suppressor function of HEB/TCF12 in T-ALL to mitigate cell proliferation controlled by NOTCH1 in pre-leukemic stem cells and prevent NOTCH1-driven progression to T-ALL.
2022-03-23
Frontiers in Immunology (published)
doi.org
Mapping parallelism in a functional IR through constraint satisfaction: a case study on convolution for mobile GPUs
Naums Mogers
Li Li
Valentin Radu
Christophe Dubach
Graphics Processing Units (GPUs) are notoriously hard to optimize for manually. What is needed are good automatic code generators and optimi… (see more)zers. Accelerate, Futhark and Lift demonstrated that a functional approach is well suited for this challenge. Lift, for instance, uses a system of rewrite rules with a multi-stage approach. Algorithmic optimizations are first explored, followed by hardware-specific optimizations such as using shared memory and mapping parallelism. While the algorithmic exploration leads to correct transformed programs by construction, it is not necessarily true for the latter phase. Exploiting shared memory and mapping parallelism while ensuring correct synchronization is a delicate balancing act, and is hard to encode in a rewrite system. Currently, Lift relies on heuristics with ad-hoc mechanisms to check for correctness. Although this practical approach eventually produces high-performance code, it is not an ideal state of affairs. This paper proposes to extract parallelization constraints automatically from a functional IR and use a solver to identify valid rewriting. Using a convolutional neural network on a mobile GPU as a use case, this approach matches the performance of the ARM Compute Library GEMM convolution and the TVM-generated kernel consuming between 2.7x and 3.6x less memory on average. Furthermore, a speedup of 12x is achieved over the ARM Compute Library direct convolution implementation.
2022-03-17
Proceedings of the 31st ACM SIGPLAN International Conference on Compiler Construction (published)
doi.org
WOODS: Benchmarks for Out-of-Distribution Generalization in Time Series Tasks
Jean-christophe Gagnon-audet
Kartik Ahuja
Mohammad Javad Darvishi Bayazi
Guillaume Dumas
Irina Rish
2022-03-17
ArXiv (preprint)
doi.org
arxiv.org
<i>APOE</i> ɛ2 vs <i>APOE</i> ɛ4 dosage shows sex-specific links to hippocampus-default network subregion co-variation
Chloé Savignac
Sylvia Villeneuve
AmanPreet Badhwar
Karin Saltoun
Kimia Shafighi
Chris Zajner
Vaibhav Sharma
Sarah A Gagliano Taliun
Sali Farhan
Judes Poirier
Danilo Bzdok
Alzheimer’s disease and related dementias (ADRD) are marked by intracellular tau aggregates in the medial-temporal lobe (MTL) and extracel… (see more)lular amyloid aggregates in the default network (DN). Here, we sought to clarify ADRD-related co-dependencies between the MTL’s most vulnerable structure, the hippocampus (HC), and the highly associative DN at a subregion resolution. We confronted the effects of APOE ɛ2 and ɛ4, rarely investigated together, with their impact on HC-DN co-variation regimes at the population level. In a two-pronged decomposition of structural brain scans from ∼40,000 UK Biobank participants, we located co-deviating structural patterns in HC and DN subregions as a function of ADRD family risk. Across the disclosed HC-DN signatures, recurrent deviations in the CA1, CA2/3, molecular layer, fornix’s fimbria, and their cortical partners related to ADRD risk. Phenome-wide profiling of HC-DN co- variation expressions from these population signatures revealed male-specific associations with air-pollution, and female-specific associations with cardiovascular traits. We highlighted three main factors associated with brain-APOE associations across the different gene variants: happiness, and satisfaction with friendships, and with family. We further showed that APOE ɛ2/2 interacts preferentially with HC-DN co-variation patterns in estimating social lifestyle in males and physical activity in females. Our findings reinvigorate the often-neglected interplay between APOE ɛ2 dosage and sex, which we have linked to fine-grained structural divergences indicative of ADRD susceptibility.
2022-03-14
bioRxiv (preprint)
doi.org