Publications

GRouNdGAN: GRN-guided simulation of single-cell RNA-seq data using causal generative adversarial networks
Yazdan Zinati
Abdulrahman Takiddeen
We introduce GRouNdGAN, a gene regulatory network (GRN)-guided causal implicit generative model for simulating single-cell RNA-seq data, in-… (see more)silico perturbation experiments, and benchmarking GRN inference methods. Through the imposition of a user-defined GRN in its architecture, GRouNdGAN simulates steady-state and transient-state single-cell datasets where genes are causally expressed under the control of their regulating transcription factors (TFs). Training on three experimental datasets, we show that our model captures non-linear TF-gene dependences and preserves gene identities, cell trajectories, pseudo-time ordering, and technical and biological noise, with no user manipulation and only implicit parameterization. Despite imposing rigid causality constraints, it outperforms state-of-the-art simulators in generating realistic cells. GRouNdGAN learns meaningful causal regulatory dynamics, allowing sampling from both observational and interventional distributions. This enables it to synthesize cells under conditions that do not occur in the dataset at inference time, allowing to perform in-silico TF knockout experiments. Our results show that in-silico knockout of cell type-specific TFs significantly reduces cells of that type being generated. Interactions imposed through the GRN are emphasized in the simulated datasets, resulting in GRN inference algorithms assigning them much higher scores than interactions not imposed but of equal importance in the experimental training dataset. Benchmarking various GRN inference algorithms reveals that GRouNdGAN effectively bridges the existing gap between simulated and biological data benchmarks of GRN inference algorithms, providing gold standard ground truth GRNs and realistic cells corresponding to the biological system of interest. Our results show that GRouNdGAN is a stable, realistic, and effective simulator with various applications in single-cell RNA-seq analysis.
Imitation Learning from Observation through Optimal Transport
Wei-Di Chang
Scott Fujimoto
More Efficient Randomized Exploration for Reinforcement Learning via Approximate Sampling
Haque Ishfaq
Yixin Tan
Yu Yang
Qingfeng Lan
Jianfeng Lu
A. Rupam Mahmood
Pan Xu
Preface of UniReps: the First Workshop on Unifying Representations in Neural Models
Marco Fumero
Emanuele Rodolá
Clementine Domine
Francesco Locatello
Karolina Dziugaite
Caron Mathilde
Discover why, when and how distinct learning processes yield similar representations, and the degree to which these can be unified.
Protocol to perform integrative analysis of high-dimensional single-cell multimodal data using an interpretable deep learning technique
Manqi Zhou
Hao Zhang
Zilong Bai
Dylan Mann-Krzisnik
Fei Wang
Surprise-Adaptive Intrinsic Motivation for Unsupervised Reinforcement Learning
Adriana Hugessen
Roger Creus Castanyer
Faisal Mohamed
Both entropy-minimizing and entropy-maximizing (curiosity) objectives for unsupervised reinforcement learning (RL) have been shown to be eff… (see more)ective in different environments, depending on the environment's level of natural entropy. However, neither method alone results in an agent that will consistently learn intelligent behavior across environments. In an effort to find a single entropy-based method that will encourage emergent behaviors in any environment, we propose an agent that can adapt its objective online, depending on the entropy conditions by framing the choice as a multi-armed bandit problem. We devise a novel intrinsic feedback signal for the bandit, which captures the agent's ability to control the entropy in its environment. We demonstrate that such agents can learn to control entropy and exhibit emergent behaviors in both high- and low-entropy regimes and can learn skillful behaviors in benchmark tasks. Videos of the trained agents and summarized findings can be found on our project page https://sites.google.com/view/surprise-adaptive-agents
On the consistency of hyper-parameter selection in value-based deep reinforcement learning
Johan Samir Obando Ceron
João Guilherme Madeira Araújo
Deep reinforcement learning (deep RL) has achieved tremendous success on various domains through a combination of algorithmic design and car… (see more)eful selection of hyper-parameters. Algorithmic improvements are often the result of iterative enhancements built upon prior approaches, while hyper-parameter choices are typically inherited from previous methods or fine-tuned specifically for the proposed technique. Despite their crucial impact on performance, hyper-parameter choices are frequently overshadowed by algorithmic advancements. This paper conducts an extensive empirical study focusing on the reliability of hyper-parameter selection for value-based deep reinforcement learning agents, including the introduction of a new score to quantify the consistency and reliability of various hyper-parameters. Our findings not only help establish which hyper-parameters are most critical to tune, but also help clarify which tunings remain consistent across different training regimes.
What Mechanisms Does Knowledge Distillation Distill?
Cindy Wu
Ekdeep Singh Lubana
Bruno Mlodozeniec
Robert Kirk
Knowledge distillation is a commonly-used compression method in ML due to the popularity of increasingly large-scale models, but it is uncle… (see more)ar if all the information a teacher model contains is distilled into the smaller student model. We aim to formalize the concept of ‘knowledge’ to investigate how knowledge is transferred during distillation, focusing on shared invariant outputs to counterfactual changes of dataset latent variables (we call these latents mechanisms). We define a student model to be a good stand-in model for a teacher if it shares the teacher’s learned mechanisms, and find that Jacobian matching and contrastive representation learning are viable methods by which to train such models. While these methods do not result in perfect transfer of mechanisms, we show they often improve student fidelity or mitigate simplicity bias (as measured by the teacher-to-student KL divergence and accuracy on various out-of-distribution test datasets), especially on datasets with spurious statistical correlations.
CARTIER: Cartographic lAnguage Reasoning Targeted at Instruction Execution for Robots
Nikhil Kakodkar
Dmitriy Rivkin
Bobak H. Baghi
Francois Hogan
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… (see more)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 )
Divergent Creativity in Humans and Large Language Models
Antoine Bellemare-Pepin
Franccois Lespinasse
Philipp Thölke
Yann Harel
Jay A. Olson
Karim Jerbi CoCo Lab
Psychology Department
U. Montr'eal
Montreal
Qc
Canada
Music department
C. University
Sociology
Anthropology department
Mila
Departmentof Psychology
University of Toronto Mississauga … (see 5 more)
Mississauga
On
Department of Computer Science
Operations Research
Unique Center
The recent surge in the capabilities of Large Language Models (LLMs) has led to claims that they are approaching a level of creativity akin … (see more)to human capabilities. This idea has sparked a blend of excitement and apprehension. However, a critical piece that has been missing in this discourse is a systematic evaluation of LLM creativity, particularly in comparison to human divergent thinking. To bridge this gap, we leverage recent advances in creativity science to build a framework for in-depth analysis of divergent creativity in both state-of-the-art LLMs and a substantial dataset of 100,000 humans. We found evidence suggesting that LLMs can indeed surpass human capabilities in specific creative tasks such as divergent association and creative writing. Our quantitative benchmarking framework opens up new paths for the development of more creative LLMs, but it also encourages more granular inquiries into the distinctive elements that constitute human inventive thought processes, compared to those that can be artificially generated.
GAGE: Genetic Algorithm-Based Graph Explainer for Malware Analysis
Mohd Saqib
Philippe Charland
Andrew Walenstein
Malware analysts often prefer reverse engineering using Call Graphs, Control Flow Graphs (CFGs), and Data Flow Graphs (DFGs), which involves… (see more) the utilization of black-box Deep Learning (DL) models. The proposed research introduces a structured pipeline for reverse engineering-based analysis, offering promising results compared to state-of-the-art methods and providing high-level interpretability for malicious code blocks in subgraphs. We propose the Canonical Executable Graph (CEG) as a new representation of Portable Executable (PE) files, uniquely incorporating syntactical and semantic information into its node embeddings. At the same time, edge features capture structural aspects of PE files. This is the first work to present a PE file representation encompassing syntactical, semantic, and structural characteristics, whereas previous efforts typically focused solely on syntactic or structural properties. Furthermore, recognizing the limitations of existing graph explanation methods within Explainable Artificial Intelligence (XAI) for malware analysis, primarily due to the specificity of malicious files, we introduce Genetic Algorithm-based Graph Explainer (GAGE). GAGE operates on the CEG, striving to identify a precise subgraph relevant to predicted malware families. Through experiments and comparisons, our proposed pipeline exhibits substantial improvements in model robustness scores and discriminative power compared to the previous benchmarks. Furthermore, we have successfully used GAGE in practical applications on real-world data, producing meaningful insights and interpretability. This research offers a robust solution to enhance cybersecurity by delivering a transparent and accurate understanding of malware behaviour. Moreover, the proposed algorithm is specialized in handling graph-based data, effectively dissecting complex content and isolating influential nodes.