Sacha Morin

Kevin R. Moon

Dimensionality reduction-based data visualization is pivotal in comprehending complex biological data. The most common methods, such as PHAT… (voir plus)E, t-SNE, and UMAP, are unsupervised and therefore reflect the dominant structure in the data, which may be independent of expert-provided labels. Here we introduce a supervised data visualization method called RF-PHATE, which integrates expert knowledge for further exploration of the data. RF-PHATE leverages random forests to capture intricate featurelabel relationships. Extracting information from the forest, RF-PHATE generates low-dimensional visualizations that highlight relevant data relationships while disregarding extraneous features. This approach scales to large datasets and applies to classification and regression. We illustrate RF-PHATE’s prowess through three case studies. In a multiple sclerosis study using longitudinal clinical and imaging data, RF-PHATE unveils a sub-group of patients with non-benign relapsingremitting Multiple Sclerosis, demonstrating its aptitude for time-series data. In the context of Raman spectral data, RF-PHATE effectively showcases the impact of antioxidants on diesel exhaust-exposed lung cells, highlighting its proficiency in noisy environments. Furthermore, RF-PHATE aligns established geometric structures with COVID-19 patient outcomes, enriching interpretability in a hierarchical manner. RF-PHATE bridges expert insights and visualizations, promising knowledge generation. Its adaptability, scalability, and noise tolerance underscore its potential for widespread adoption.

2024-01-21

bioRxiv (prépublication)

Spectral Temporal Contrastive Learning

Sacha Morin

Somjit Nath

Samira Ebrahimi Kahou

Learning useful data representations without requiring labels is a cornerstone of modern deep learning. Self-supervised learning methods, pa… (voir plus)rticularly contrastive learning (CL), have proven successful by leveraging data augmentations to define positive pairs. This success has prompted a number of theoretical studies to better understand CL and investigate theoretical bounds for downstream linear probing tasks. This work is concerned with the temporal contrastive learning (TCL) setting where the sequential structure of the data is used instead to define positive pairs, which is more commonly used in RL and robotics contexts. In this paper, we adapt recent work on Spectral CL to formulate Spectral Temporal Contrastive Learning (STCL). We discuss a population loss based on a state graph derived from a time-homogeneous reversible Markov chain with uniform stationary distribution. The STCL loss enables to connect the linear probing performance to the spectral properties of the graph, and can be estimated by considering previously observed data sequences as an ensemble of MCMC chains.

2023-12-01

ArXiv (prépublication)

ConceptGraphs: Open-Vocabulary 3D Scene Graphs for Perception and Planning

Qiao Gu

Alihusein Kuwajerwala

Sacha Morin

Krishna Murthy

Bipasha Sen

Aditya Agarwal

Corban Rivera

William Paul

Kirsty Ellis

Rama Chellappa

Chuang Gan

Celso M de Melo

Joshua B. Tenenbaum

Antonio Torralba

Florian Shkurti

For robots to perform a wide variety of tasks, they require a 3D representation of the world that is semantically rich, yet compact and effi… (voir plus)cient for task-driven perception and planning. Recent approaches have attempted to leverage features from large vision-language models to encode semantics in 3D representations. However, these approaches tend to produce maps with per-point feature vectors, which do not scale well in larger environments, nor do they contain semantic spatial relationships between entities in the environment, which are useful for downstream planning. In this work, we propose ConceptGraphs, an open-vocabulary graph-structured representation for 3D scenes. ConceptGraphs is built by leveraging 2D foundation models and fusing their output to 3D by multi-view association. The resulting representations generalize to novel semantic classes, without the need to collect large 3D datasets or finetune models. We demonstrate the utility of this representation through a number of downstream planning tasks that are specified through abstract (language) prompts and require complex reasoning over spatial and semantic concepts. (Project page: https://concept-graphs.github.io/ Explainer video: https://youtu.be/mRhNkQwRYnc )

2023-10-20

robot-learning.org/CoRL/2023/Workshop/LangRob (poster)

openreview.net

One-4-All: Neural Potential Fields for Embodied Navigation

Sacha Morin

Miguel Saavedra-Ruiz

A fundamental task in robotics is to navigate between two locations. In particular, real-world navigation can require long-horizon planning … (voir plus)using high-dimensional RGB images, which poses a substantial challenge for end-to-end learning-based approaches. Current semi-parametric methods instead achieve long-horizon navigation by combining learned modules with a topological memory of the environment, often represented as a graph over previously collected images. However, using these graphs in practice requires tuning a number of pruning heuristics. These heuristics are necessary to avoid spurious edges, limit runtime memory usage and maintain reasonably fast graph queries in large environments. In this work, we present One-4-All (O4A), a method leveraging self-supervised and manifold learning to obtain a graph-free, end-to-end navigation pipeline in which the goal is specified as an image. Navigation is achieved by greedily minimizing a potential function defined continuously over image embeddings. Our system is trained offline on non-expert exploration sequences of RGB data and controls, and does not require any depth or pose measurements. We show that 04A can reach long-range goals in 8 simulated Gibson indoor environments and that resulting embeddings are topologically similar to ground truth maps, even if no pose is observed. We further demonstrate successful real-world navigation using a Jackal UGV platform.aaProject page https://montrealrobotics.ca/o4a/.

2023-10-01

2023 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS) (publié)

Geometry Regularized Autoencoders

Andres F. Duque Correa

Sacha Morin

Kevin R. Moon

A fundamental task in data exploration is to extract low dimensional representations that capture intrinsic geometry in data, especially for… (voir plus) faithfully visualizing data in two or three dimensions. Common approaches use kernel methods for manifold learning. However, these methods typically only provide an embedding of the input data and cannot extend naturally to new data points. Autoencoders have also become popular for representation learning. While they naturally compute feature extractors that are extendable to new data and invertible (i.e., reconstructing original features from latent representation), they often fail at representing the intrinsic data geometry compared to kernel-based manifold learning. We present a new method for integrating both approaches by incorporating a geometric regularization term in the bottleneck of the autoencoder. This regularization encourages the learned latent representation to follow the intrinsic data geometry, similar to manifold learning algorithms, while still enabling faithful extension to new data and preserving invertibility. We compare our approach to autoencoder models for manifold learning to provide qualitative and quantitative evidence of our advantages in preserving intrinsic structure, out of sample extension, and reconstruction. Our method is easily implemented for big-data applications, whereas other methods are limited in this regard.

2023-06-01

IEEE Transactions on Pattern Analysis and Machine Intelligence (publié)

Monocular Robot Navigation with Self-Supervised Pretrained Vision Transformers

Miguel Saavedra-Ruiz

Sacha Morin

In this work, we consider the problem of learning a perception model for monocular robot navigation using few annotated images. Using a Visi… (voir plus)on Transformer (ViT) pretrained with a label-free self-supervised method, we successfully train a coarse image segmentation model for the Duckietown environment using 70 training images. Our model performs coarse image segmentation at the

2022-06-02

2022 19th Conference on Robots and Vision (CRV) (publié)

Monocular Robot Navigation with Self-Supervised Pretrained Vision Transformers

Miguel Saavedra-Ruiz

Sacha Morin

In this work, we consider the problem of learning a perception model for monocular robot navigation using few annotated images. Using a Visi… (voir plus)on Transformer (ViT) pretrained with a label-free self-supervised method, we successfully train a coarse image segmentation model for the Duckietown environment using 70 training images. Our model performs coarse image segmentation at the

2022-03-07

ArXiv (preprint)

Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec

Bastien Paré

Marieke Rozendaal

Sacha Morin

Raphael Poujol

Fatima Mostefai

Shawn M. Simpson

Jean-Christophe Grenier

Léa Kaufmann

Henry Xing

Miguelle Sanchez

Ariane Yechouron

Ronald Racette

Julie Hussin

Ivan Pavlov

Martin Smith

2021-12-02

PLoS ONE (publié)

Patient health records and whole viral genomes from an early SARS-CoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes

Bastien Paré

Marieke Rozendaal

Sacha Morin

Léa Kaufmann

Shawn M. Simpson

Raphael Poujol

Fatima Mostefai

Jean-Christophe Grenier

Henry Xing

Miguelle Sanchez

Ariane Yechouron

Ronald Racette

Julie Hussin

Ivan Pavlov

Martin Smith

2021-12-02

PLoS ONE (publié)

Extendable and invertible manifold learning with geometry regularized autoencoders

Andres F. Duque Correa

Sacha Morin

Kevin R. Moon

A fundamental task in data exploration is to extract simplified low dimensional representations that capture intrinsic geometry in data, esp… (voir plus)ecially for faithfully visualizing data in two or three dimensions. Common approaches to this task use kernel methods for manifold learning. However, these methods typically only provide an embedding of fixed input data and cannot extend to new data points. Autoencoders have also recently become popular for representation learning. But while they naturally compute feature extractors that are both extendable to new data and invertible (i.e., reconstructing original features from latent representation), they have limited capabilities to follow global intrinsic geometry compared to kernel-based manifold learning. We present a new method for integrating both approaches by incorporating a geometric regularization term in the bottleneck of the autoencoder. Our regularization, based on the diffusion potential distances from the recently-proposed PHATE visualization method, encourages the learned latent representation to follow intrinsic data geometry, similar to manifold learning algorithms, while still enabling faithful extension to new data and reconstruction of data in the original feature space from latent coordinates. We compare our approach with leading kernel methods and autoencoder models for manifold learning to provide qualitative and quantitative evidence of our advantages in preserving intrinsic structure, out of sample extension, and reconstruction. Our method is easily implemented for big-data applications, whereas other methods are limited in this regard.

2020-12-10

2020 IEEE International Conference on Big Data (Big Data) (publié)

Extendable and invertible manifold learning with geometry regularized autoencoders

Andres F. Duque Correa

Sacha Morin

Kevin R. Moon

A fundamental task in data exploration is to extract simplified low dimensional representations that capture intrinsic geometry in data, esp… (voir plus)ecially for faithfully visualizing data in two or three dimensions. Common approaches to this task use kernel methods for manifold learning. However, these methods typically only provide an embedding of fixed input data and cannot extend to new data points. Autoencoders have also recently become popular for representation learning. But while they naturally compute feature extractors that are both extendable to new data and invertible (i.e., reconstructing original features from latent representation), they have limited capabilities to follow global intrinsic geometry compared to kernel-based manifold learning. We present a new method for integrating both approaches by incorporating a geometric regularization term in the bottleneck of the autoencoder. Our regularization, based on the diffusion potential distances from the recently-proposed PHATE visualization method, encourages the learned latent representation to follow intrinsic data geometry, similar to manifold learning algorithms, while still enabling faithful extension to new data and reconstruction of data in the original feature space from latent coordinates. We compare our approach with leading kernel methods and autoencoder models for manifold learning to provide qualitative and quantitative evidence of our advantages in preserving intrinsic structure, out of sample extension, and reconstruction. Our method is easily implemented for big-data applications, whereas other methods are limited in this regard.

2020-07-14

ArXiv (preprint)