Publications

Data Cleaning and Machine Learning: A Systematic Literature Review
Pierre-Olivier Cot'e
Amin Nikanjam
Nafisa Ahmed
Dmytro Humeniuk
Foutse Khomh
Context: Machine Learning (ML) is integrated into a growing number of systems for various applications. Because the performance of an ML mod… (see more)el is highly dependent on the quality of the data it has been trained on, there is a growing interest in approaches to detect and repair data errors (i.e., data cleaning). Researchers are also exploring how ML can be used for data cleaning; hence creating a dual relationship between ML and data cleaning. To the best of our knowledge, there is no study that comprehensively reviews this relationship. Objective: This paper's objectives are twofold. First, it aims to summarize the latest approaches for data cleaning for ML and ML for data cleaning. Second, it provides future work recommendations. Method: We conduct a systematic literature review of the papers published between 2016 and 2022 inclusively. We identify different types of data cleaning activities with and for ML: feature cleaning, label cleaning, entity matching, outlier detection, imputation, and holistic data cleaning. Results: We summarize the content of 101 papers covering various data cleaning activities and provide 24 future work recommendations. Our review highlights many promising data cleaning techniques that can be further extended. Conclusion: We believe that our review of the literature will help the community develop better approaches to clean data.
2023-10-03
ArXiv (preprint)
doi.org
arxiv.org
Differential Chromatin Architecture and Risk Variants in Deep Layer Excitatory Neurons and Grey Matter Microglia Contribute to Major Depressive Disorder
Anjali Chawla
Doruk Cakmakci
Wenmin Zhang
Malosree Maitra
Reza Rahimian
Haruka Mitsuhashi
MA Davoli
Jenny Yang
Gary Gang Chen
Ryan Denniston
Deborah Mash
Naguib Mechawar
Matthew Suderman
Yue Li
Corina Nagy
Gustavo Turecki
2023-10-03
bioRxiv (preprint)
doi.org
Learning Reliable Logical Rules with SATNet
Zhaoyu Li
Jinpei Guo
Yuhe Jiang
Xujie Si
2023-10-03
ArXiv (preprint)
doi.org
arxiv.org
Leveraging Diffusion Disentangled Representations to Mitigate Shortcuts in Underspecified Visual Tasks
Luca Scimeca
Alexander Rubinstein
Armand Nicolicioiu
Damien Teney
Yoshua Bengio
Spurious correlations in the data, where multiple cues are predictive of the target labels, often lead to shortcut learning phenomena, where… (see more) a model may rely on erroneous, easy-to-learn, cues while ignoring reliable ones. In this work, we propose an ensemble diversification framework exploiting the generation of synthetic counterfactuals using Diffusion Probabilistic Models (DPMs). We discover that DPMs have the inherent capability to represent multiple visual cues independently, even when they are largely correlated in the training data. We leverage this characteristic to encourage model diversity and empirically show the efficacy of the approach with respect to several diversification objectives. We show that diffusion-guided diversification can lead models to avert attention from shortcut cues, achieving ensemble diversity performance comparable to previous methods requiring additional data collection.
2023-10-03
ArXiv (preprint)
doi.org
arxiv.org
Aberrant functional brain network organization is associated with relapse during 1‐year follow‐up in alcohol‐dependent patients
Justin Böhmer
Pablo Reinhardt
Maria Garbusow
Michael Marxen
Michael N. Smolka
Ulrich S. Zimmermann
Andreas Heinz
Danilo Bzdok
Eva Friedel
Johann D. Kruschwitz
Henrik Walter
2023-10-02
Addiction Biology (published)
doi.org
GraphText: Graph Reasoning in Text Space
Jianan Zhao
Le Zhuo
Yikang Shen
Meng Qu
Kai Liu
Michael Bronstein
Zhaocheng Zhu
Jian Tang
Large Language Models (LLMs) have gained the ability to assimilate human knowledge and facilitate natural language interactions with both hu… (see more)mans and other LLMs. However, despite their impressive achievements, LLMs have not made significant advancements in the realm of graph machine learning. This limitation arises because graphs encapsulate distinct relational data, making it challenging to transform them into natural language that LLMs understand. In this paper, we bridge this gap with a novel framework, GraphText, that translates graphs into natural language. GraphText derives a graph-syntax tree for each graph that encapsulates both the node attributes and inter-node relationships. Traversal of the tree yields a graph text sequence, which is then processed by an LLM to treat graph tasks as text generation tasks. Notably, GraphText offers multiple advantages. It introduces training-free graph reasoning: even without training on graph data, GraphText with ChatGPT can achieve on par with, or even surpassing, the performance of supervised-trained graph neural networks through in-context learning (ICL). Furthermore, GraphText paves the way for interactive graph reasoning, allowing both humans and LLMs to communicate with the model seamlessly using natural language. These capabilities underscore the vast, yet-to-be-explored potential of LLMs in the domain of graph machine learning.
2023-10-02
ArXiv (preprint)
doi.org
arxiv.org
Imitation Learning from Observation through Optimal Transport
Wei-Di Chang
Scott Fujimoto
David Meger
Gregory Dudek
2023-10-02
ArXiv (preprint)
doi.org
arxiv.org
TACTiS-2: Better, Faster, Simpler Attentional Copulas for Multivariate Time Series
Arjun Ashok
Étienne Marcotte
Valentina Zantedeschi
Nicolas Chapados
Alexandre Drouin
We introduce a new model for multivariate probabilistic time series prediction, designed to flexibly address a range of tasks including fore… (see more)casting, interpolation, and their combinations. Building on copula theory, we propose a simplified objective for the recently-introduced transformer-based attentional copulas (TACTiS), wherein the number of distributional parameters now scales linearly with the number of variables instead of factorially. The new objective requires the introduction of a training curriculum, which goes hand-in-hand with necessary changes to the original architecture. We show that the resulting model has significantly better training dynamics and achieves state-of-the-art performance across diverse real-world forecasting tasks, while maintaining the flexibility of prior work, such as seamless handling of unaligned and unevenly-sampled time series. Code is made available at https://github.com/ServiceNow/TACTiS.
2023-10-02
ArXiv (preprint)
doi.org
arxiv.org
AI and Catastrophic Risk
Yoshua Bengio
2023-10-01
Journal of Democracy (published)
doi.org
Bootstrapping Adaptive Human-Machine Interfaces with Offline Reinforcement Learning
Jensen Gao
Siddharth Reddy
Glen Berseth
Anca Dragan
Sergey Levine
Adaptive interfaces can help users perform sequential decision-making tasks like robotic teleoperation given noisy, high-dimensional command… (see more) signals (e.g., from a brain-computer interface). Recent advances in human-in-the-loop machine learning enable such systems to improve by interacting with users, but tend to be limited by the amount of data that they can collect from individual users in practice. In this paper, we propose a reinforcement learning algorithm to address this by training an interface to map raw command signals to actions using a combination of offline pre-training and online fine-tuning. To address the challenges posed by noisy command signals and sparse rewards, we develop a novel method for representing and inferring the user's long-term intent for a given trajectory. We primarily evaluate our method's ability to assist users who can only communicate through noisy, high-dimensional input channels through a user study in which 12 participants performed a simulated navigation task by using their eye gaze to modulate a 128-dimensional command signal from their webcam. The results show that our method enables successful goal navigation more often than a baseline directional interface, by learning to denoise user commands signals and provide shared autonomy assistance. We further evaluate on a simulated Sawyer pushing task with eye gaze control, and the Lunar Lander game with simulated user commands, and find that our method improves over baseline interfaces in these domains as well. Extensive ablation experiments with simulated user commands empirically motivate each component of our method.
2023-10-01
2023 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS) (published)
doi.org
arxiv.org
Comparison of Radiologists and Deep Learning for US Grading of Hepatic Steatosis.
Pedro Vianna
Sara-Ivana Calce
Pamela Boustros
Cassandra Larocque-Rigney
Laurent Patry-Beaudoin
Yi Hui Luo
Emre Aslan
John Marinos
Talal M. Alamri
Kim-Nhien Vu
Jessica Murphy-Lavallée
Jean-Sébastien Billiard
Emmanuel Montagnon
Hongliang Li
Samuel Kadoury
Bich Nguyen
Shanel Gauthier
Benjamin Thérien
Irina Rish
Eugene Belilovsky … (see 4 more)
Guy Wolf
Michael Chassé
Guy Cloutier
An Tang
Background Screening for nonalcoholic fatty liver disease (NAFLD) is suboptimal due to the subjective interpretation of US images. Purpose T… (see more)o evaluate the agreement and diagnostic performance of radiologists and a deep learning model in grading hepatic steatosis in NAFLD at US, with biopsy as the reference standard. Materials and Methods This retrospective study included patients with NAFLD and control patients without hepatic steatosis who underwent abdominal US and contemporaneous liver biopsy from September 2010 to October 2019. Six readers visually graded steatosis on US images twice, 2 weeks apart. Reader agreement was assessed with use of κ statistics. Three deep learning techniques applied to B-mode US images were used to classify dichotomized steatosis grades. Classification performance of human radiologists and the deep learning model for dichotomized steatosis grades (S0, S1, S2, and S3) was assessed with area under the receiver operating characteristic curve (AUC) on a separate test set. Results The study included 199 patients (mean age, 53 years ± 13 [SD]; 101 men). On the test set (n = 52), radiologists had fair interreader agreement (0.34 [95% CI: 0.31, 0.37]) for classifying steatosis grades S0 versus S1 or higher, while AUCs were between 0.49 and 0.84 for radiologists and 0.85 (95% CI: 0.83, 0.87) for the deep learning model. For S0 or S1 versus S2 or S3, radiologists had fair interreader agreement (0.30 [95% CI: 0.27, 0.33]), while AUCs were between 0.57 and 0.76 for radiologists and 0.73 (95% CI: 0.71, 0.75) for the deep learning model. For S2 or lower versus S3, radiologists had fair interreader agreement (0.37 [95% CI: 0.33, 0.40]), while AUCs were between 0.52 and 0.81 for radiologists and 0.67 (95% CI: 0.64, 0.69) for the deep learning model. Conclusion Deep learning approaches applied to B-mode US images provided comparable performance with human readers for detection and grading of hepatic steatosis. Published under a CC BY 4.0 license. Supplemental material is available for this article. See also the editorial by Tuthill in this issue.
2023-10-01
Radiology (published)
doi.org
Deploying Deep Reinforcement Learning Systems: A Taxonomy of Challenges
Ahmed Haj Yahmed
Altaf Allah Abbassi
Amin Nikanjam
Heng Li
Foutse Khomh
Deep reinforcement learning (DRL), leveraging Deep Learning (DL) in reinforcement learning, has shown significant potential in achieving hum… (see more)an-level autonomy in a wide range of domains, including robotics, computer vision, and computer games. This potential justifies the enthusiasm and growing interest in DRL in both academia and industry. However, the community currently focuses mostly on the development phase of DRL systems, with little attention devoted to DRL deployment. In this paper, we propose an empirical study on Stack Overflow (SO), the most popular Q&A forum for developers, to uncover and understand the challenges practitioners faced when deploying DRL systems. Specifically, we categorized relevant SO posts by deployment platforms: server/cloud, mobile/embedded system, browser, and game engine. After filtering and manual analysis, we examined 357 SO posts about DRL deployment, investigated the current state, and identified the challenges related to deploying DRL systems. Then, we investigate the prevalence and difficulty of these challenges. Results show that the general interest in DRL deployment is growing, confirming the study’s relevance and importance. Results also show that DRL deployment is more difficult than other DRL issues. Additionally, we built a taxonomy of 31 unique challenges in deploying DRL to different platforms. On all platforms, RL environment-related challenges are the most popular, and communication-related challenges are the most difficult among practitioners. We hope our study inspires future research and helps the community overcome the most common and difficult challenges practitioners face when deploying DRL systems.
2023-10-01
2023 IEEE International Conference on Software Maintenance and Evolution (ICSME) (published)
doi.org
arxiv.org