Publications

Active learning meets fractal decision boundaries: a cautionary tale from the Sitnikov three-body problem
Mario Pasquato
Alessandro A. Trani
Chaotic systems such as the gravitational N-body problem are ubiquitous in astronomy. Machine learning (ML) is increasingly deployed to pred… (see more)ict the evolution of such systems, e.g. with the goal of speeding up simulations. Strategies such as active Learning (AL) are a natural choice to optimize ML training. Here we showcase an AL failure when predicting the stability of the Sitnikov three-body problem, the simplest case of N-body problem displaying chaotic behavior. We link this failure to the fractal nature of our classification problem's decision boundary. This is a potential pitfall in optimizing large sets of N-body simulations via AL in the context of star cluster physics, galactic dynamics, or cosmology.
Bayesian Imaging for Radio Interferometry with Score-Based Priors
No'e Dia
M. J. Yantovski-Barth
Micah Bowles
A. Scaife
U. Montŕeal
Ciela Institute
Flatiron Institute
Learning an Effective Evolution Equation for Particle-Mesh Simulations Across Cosmologies
Silent Bugs in Deep Learning Frameworks: An Empirical Study of Keras and TensorFlow
Florian Tambon
Amin Nikanjam
Le An
Giuliano Antoniol
Deep Learning (DL) frameworks are now widely used, simplifying the creation of complex models as well as their integration to various applic… (see more)ations even to non DL experts. However, like any other programs, they are prone to bugs. This paper deals with the subcategory of bugs named silent bugs: they lead to wrong behavior but they do not cause system crashes or hangs, nor show an error message to the user. Such bugs are even more dangerous in DL applications and frameworks due to the "black-box" and stochastic nature of the systems (the end user can not understand how the model makes decisions). This paper presents the first empirical study of Keras and TensorFlow silent bugs, and their impact on users' programs. We extracted closed issues related to Keras from the TensorFlow GitHub repository. Out of the 1,168 issues that we gathered, 77 were reproducible silent bugs affecting users' programs. We categorized the bugs based on the effects on the users' programs and the components where the issues occurred, using information from the issue reports. We then derived a threat level for each of the issues, based on the impact they had on the users' programs. To assess the relevance of identified categories and the impact scale, we conducted an online survey with 103 DL developers. The participants generally agreed with the significant impact of silent bugs in DL libraries and acknowledged our findings (i.e., categories of silent bugs and the proposed impact scale). Finally, leveraging our analysis, we provide a set of guidelines to facilitate safeguarding against such bugs in DL frameworks.
Unraveling the Mysteries of Galaxy Clusters: Recurrent Inference Deconvolution of X-ray Spectra
C. L. Rhea
J. Hlavacek-Larrondo
Ralph P. Kraft
Ákos Bogdán
H3K27me3 spreading organizes canonical PRC1 chromatin architecture to
regulate developmental programs
Brian Krug
Bo Hu
Haifen Chen
Adam Ptack
Xiao Chen
Kristjan H. Gretarsson
Shriya Deshmukh
Nisha Kabir
Augusto Faria Andrade
Elias Jabbour
Ashot S. Harutyunyan
John J. Y. Lee
Maud Hulswit
Damien Faury
Caterina Russo
Xinjing Xu
Michael J. Johnston
Audrey Baguette
Nathan A. Dahl
Alexander G. Weil … (see 12 more)
Benjamin Ellezam
Rola Dali
Khadija Wilson
Benjamin A. Garcia
Rajesh Kumar Soni
Marco Gallo
Michael D. Taylor
Claudia L. Kleinman
Jacek Majewski
Nada Jabado
Chao Lu
Polycomb Repressive Complex 2 (PRC2)-mediated histone H3K27 tri-methylation (H3K27me3) recruits canonical PRC1 (cPRC1) to maintain heterochr… (see more)omatin. In early development, polycomb-regulated genes are connected through long-range 3D interactions which resolve upon differentiation. Here, we report that polycomb looping is controlled by H3K27me3 spreading and regulates target gene silencing and cell fate specification. Using glioma-derived H3 Lys-27-Met (H3K27M) mutations as tools to restrict H3K27me3 deposition, we show that H3K27me3 confinement concentrates the chromatin pool of cPRC1, resulting in heightened 3D interactions mirroring chromatin architecture of pluripotency, and stringent gene repression that maintains cells in progenitor states to facilitate tumor development. Conversely, H3K27me3 spread in pluripotent stem cells, following neural differentiation or loss of the H3K36 methyltransferase NSD1, dilutes cPRC1 concentration and dissolves polycomb loops. These results identify the regulatory principles and disease implications of polycomb looping and nominate histone modification-guided distribution of reader complexes as an important mechanism for nuclear compartment organization. The confinement of H3K27me3 at PRC2 nucleation sites without its spreading correlates with increased 3D chromatin interactions. The H3K27M oncohistone concentrates canonical PRC1 that anchors chromatin loop interactions in gliomas, silencing developmental programs. Stem and progenitor cells require factors promoting H3K27me3 confinement, including H3K36me2, to maintain cPRC1 loop architecture. The cPRC1-H3K27me3 interaction is a targetable driver of aberrant self-renewal in tumor cells.
Harnessing TCR/CAR Antagonism to Enhance Immunotherapeutic Precision
Taisuke Kondo
François X. P. Bourassa
Sooraj R. Achar
Justyn DuSold
Pablo Cespedes
Madison Wahlsten
Audun Kvalvaag
Guillaume Gaud
Paul E. Love
Michael Dustin
Grégoire Altan-Bonnet
Naomi Taylor
Learning few-shot imitation as cultural transmission
Avishkar Bhoopchand
Bethanie Brownfield
Adrian Collister
Agustin Dal Lago
Ashley Edwards
Richard Everett
Alexandre Fréchette
Yanko Gitahy Oliveira
Edward Hughes
Kory Mathewson
Piermaria Mendolicchio
Julia Pawar
Miruna Pȋslar
Alex Platonov
Evan Senter
Sukhdeep Singh
Alexander Zacherl
Lei M Zhang
Room-temperature correlated states in twisted bilayer MoS$_2$
Fanfan Wu
Qiaoling Xu
Qinqin Wang
Yanbang Chu
Li Li
Jieying Liu
Jinpeng Tian
Yiru Ji
Le Liu
Yalong Yuan
Zhiheng Huang
Jiaojiao Zhao
Xiaozhou Zan
Kenji Watanabe
Takashi Taniguchi
Dongxia Shi
Gangxu Gu
Yang Xu
Lede Xian … (see 3 more)
Wei Yang
Luojun Du
Guangyu Zhang
Symmetry Breaking and Equivariant Neural Networks
Sékou-Oumar Kaba
Using symmetry as an inductive bias in deep learning has been proven to be a principled approach for sample-efficient model design. However,… (see more) the relationship between symmetry and the imperative for equivariance in neural networks is not always obvious. Here, we analyze a key limitation that arises in equivariant functions: their incapacity to break symmetry at the level of individual data samples. In response, we introduce a novel notion of 'relaxed equivariance' that circumvents this limitation. We further demonstrate how to incorporate this relaxation into equivariant multilayer perceptrons (E-MLPs), offering an alternative to the noise-injection method. The relevance of symmetry breaking is then discussed in various application domains: physics, graph representation learning, combinatorial optimization and equivariant decoding.
On the Information Geometry of Vision Transformers
On the Varied Faces of Overparameterization in Supervised and Self-Supervised Learning
Matteo Gamba
Blake Aaron Richards
Agrawal
Hossein Azizpour
Mårten Björkman
The quality of the representations learned by neural networks depends on several factors, including the loss function, learning algorithm, a… (see more)nd model architecture. In this work, we use information geometric measures to assess the representation quality in a principled manner. We demonstrate that the sensitivity of learned representations to input perturbations, measured by the spectral norm of the feature Jacobian, provides valuable information about downstream generalization. On the other hand, measuring the coefficient of spectral decay observed in the eigenspectrum of feature covariance provides insights into the global representation geometry. First, we empirically establish an equivalence between these notions of representation quality and show that they are inversely correlated. Second, our analysis reveals the varying roles that overparameterization plays in improving generalization. Unlike supervised learning, we observe that increasing model width leads to higher discriminability and less smoothness in the self-supervised regime. Furthermore, we report that there is no observable double descent phenomenon in SSL with non-contrastive objectives for commonly used parameterization regimes, which opens up new opportunities for tight asymptotic analysis. Taken together, our results provide a loss-aware characterization of the different role of overparameterization in supervised and self-supervised learning.