Publications

Problèmes associés au déploiement des modèles fondés sur l’apprentissage machine en santé
Joseph Paul Cohen
Tianshi Cao
Joseph D Viviano
Chin-wei Huang
Michael Fralick
Marzyeh Ghassemi
Muhammad Mamdani
Russell Greiner
Yoshua Bengio
2021-11-06
Canadian Medical Association Journal (published)
doi.org
Learned Image Compression for Machine Perception
Felipe Codevilla
Jean Gabriel Simard
Ross Goroshin
Chris Pal
Recent work has shown that learned image compression strategies can outperform standard hand-crafted compression algorithms that have been d… (see more)eveloped over decades of intensive research on the rate-distortion trade-off. With growing applications of computer vision, high quality image reconstruction from a compressible representation is often a secondary objective. Compression that ensures high accuracy on computer vision tasks such as image segmentation, classification, and detection therefore has the potential for significant impact across a wide variety of settings. In this work, we develop a framework that produces a compression format suitable for both human perception and machine perception. We show that representations can be learned that simultaneously optimize for compression and performance on core vision tasks. Our approach allows models to be trained directly from compressed representations, and this approach yields increased performance on new tasks and in low-shot learning settings. We present results that improve upon segmentation and detection performance compared to standard high quality JPGs, but with representations that are four to ten times smaller in terms of bits per pixel. Further, unlike naive compression methods, at a level ten times smaller than standard JEPGs, segmentation and detection models trained from our format suffer only minor degradation in performance.
2021-11-02
ArXiv (preprint)
doi.org
arxiv.org
Vesicular trafficking is a key determinant of the statin response in acute myeloid leukemia
Jana Krosl
Marie-Eve Bordeleau
Céline Moison
Tara MacRae
Isabel Boivin
Nadine Mayotte
Deanne Gracias
Irène Baccelli
Vincent-Philippe Lavallee
Richard Bisaillon
Bernhard Lehnertz
Rodrigo Mendoza-Sanchez
Réjean Ruel
Thierry Bertomeu
Jasmin Coulombe-Huntington
Geneviève Boucher
Nandita Noronha
Caroline Pabst
Mike Tyers
Patrick Gendron … (see 5 more)
S. Lemieux
Frederic Barabe
Anne Marinier
Josée Hébert
Guy Sauvageau
Key Points Inhibition of RAB protein function mediates the anti–acute myeloid leukemia activity of statins. Statin sensitivity is associat… (see more)ed with enhanced vesicle-mediated traffic.
2021-11-02
Blood Advances (published)
doi.org
Back-Training excels Self-Training at Unsupervised Domain Adaptation of Question Generation and Passage Retrieval
Devang Kulshreshtha
Robert Belfer
Iulian V. Serban
Siva Reddy
In this work, we introduce back-training, an alternative to self-training for unsupervised domain adaptation (UDA). While self-training gene… (see more)rates synthetic training data where natural inputs are aligned with noisy outputs, back-training results in natural outputs aligned with noisy inputs. This significantly reduces the gap between target domain and synthetic data distribution, and reduces model overfitting to source domain. We run UDA experiments on question generation and passage retrieval from the Natural Questions domain to machine learning and biomedical domains. We find that back-training vastly outperforms self-training by a mean improvement of 7.8 BLEU-4 points on generation, and 17.6% top-20 retrieval accuracy across both domains. We further propose consistency filters to remove low-quality synthetic data before training. We also release a new domain-adaptation dataset - MLQuestions containing 35K unaligned questions, 50K unaligned passages, and 3K aligned question-passage pairs.
2021-10-31
Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing (published)
doi.org
arxiv.org
Estimating individual treatment effect on disability progression in multiple sclerosis using deep learning
Jean-Pierre R. Falet
Joshua Durso-finley
Brennan Nichyporuk
Julien Schroeter
Francesca Bovis
Maria-Pia Sormani
Doina Precup
Tal Arbel
Douglas Lorne Arnold
Disability progression in multiple sclerosis remains resistant to treatment. The absence of a suitable biomarker to allow for phase 2 clinic… (see more)al trials presents a high barrier for drug development. We propose to enable short proof-of-concept trials by increasing statistical power using a deep-learning predictive enrichment strategy. Specifically, a multi-headed multilayer perceptron is used to estimate the conditional average treatment effect (CATE) using baseline clinical and imaging features, and patients predicted to be most responsive are preferentially randomized into a trial. Leveraging data from six randomized clinical trials ( n  = 3,830), we first pre-trained the model on the subset of relapsing-remitting MS patients ( n  = 2,520), then fine-tuned it on a subset of primary progressive MS (PPMS) patients ( n  = 695). In a separate held-out test set of PPMS patients randomized to anti-CD20 antibodies or placebo ( n  = 297), the average treatment effect was larger for the 50% (HR, 0.492; 95% CI, 0.266-0.912; p  = 0.0218) and 30% (HR, 0.361; 95% CI, 0.165-0.79; p  = 0.008) predicted to be most responsive, compared to 0.743 (95% CI, 0.482-1.15; p  = 0.179) for the entire group. The same model could also identify responders to laquinimod in another held-out test set of PPMS patients ( n  = 318). Finally, we show that using this model for predictive enrichment results in important increases in power.
2021-10-31
medRxiv (preprint)
doi.org
Masked Language Modeling and the Distributional Hypothesis: Order Word Matters Pre-training for Little
Koustuv Sinha
Robin Jia
Dieuwke Hupkes
Joelle Pineau
Adina Williams
Douwe Kiela
A possible explanation for the impressive performance of masked language model (MLM) pre-training is that such models have learned to repres… (see more)ent the syntactic structures prevalent in classical NLP pipelines. In this paper, we propose a different explanation: MLMs succeed on downstream tasks almost entirely due to their ability to model higher-order word co-occurrence statistics. To demonstrate this, we pre-train MLMs on sentences with randomly shuffled word order, and show that these models still achieve high accuracy after fine-tuning on many downstream tasks—including tasks specifically designed to be challenging for models that ignore word order. Our models perform surprisingly well according to some parametric syntactic probes, indicating possible deficiencies in how we test representations for syntactic information. Overall, our results show that purely distributional information largely explains the success of pre-training, and underscore the importance of curating challenging evaluation datasets that require deeper linguistic knowledge.
2021-10-31
Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing (published)
doi.org
arxiv.org
Opioid prescribing among new users for non-cancer pain in the USA, Canada, UK, and Taiwan: A population-based cohort study
Meghna Jani
Nadyne Girard
David W. Bates
David L Buckeridge
Therese Sheppard
Jack Li
Usman Iqbal
Shelly Vik
Colin Weaver
Judy Seidel
William G. Dixon
Robyn Tamblyn
Background The opioid epidemic in North America has been driven by an increase in the use and potency of prescription opioids, with ensuing … (see more)excessive opioid-related deaths. Internationally, there are lower rates of opioid-related mortality, possibly because of differences in prescribing and health system policies. Our aim was to compare opioid prescribing rates in patients without cancer, across 5 centers in 4 countries. In addition, we evaluated differences in the type, strength, and starting dose of medication and whether these characteristics changed over time. Methods and findings We conducted a retrospective multicenter cohort study of adults who are new users of opioids without prior cancer. Electronic health records and administrative health records from Boston (United States), Quebec and Alberta (Canada), United Kingdom, and Taiwan were used to identify patients between 2006 and 2015. Standard dosages in morphine milligram equivalents (MMEs) were calculated according to The Centers for Disease Control and Prevention. Age- and sex-standardized opioid prescribing rates were calculated for each jurisdiction. Of the 2,542,890 patients included, 44,690 were from Boston (US), 1,420,136 Alberta, 26,871 Quebec (Canada), 1,012,939 UK, and 38,254 Taiwan. The highest standardized opioid prescribing rates in 2014 were observed in Alberta at 66/1,000 persons compared to 52, 51, and 18/1,000 in the UK, US, and Quebec, respectively. The median MME/day (IQR) at initiation was highest in Boston at 38 (20 to 45); followed by Quebec, 27 (18 to 43); Alberta, 23 (9 to 38); UK, 12 (7 to 20); and Taiwan, 8 (4 to 11). Oxycodone was the first prescribed opioid in 65% of patients in the US cohort compared to 14% in Quebec, 4% in Alberta, 0.1% in the UK, and none in Taiwan. One of the limitations was that data were not available from all centers for the entirety of the 10-year period. Conclusions In this study, we observed substantial differences in opioid prescribing practices for non-cancer pain between jurisdictions. The preference to start patients on higher MME/day and more potent opioids in North America may be a contributing cause to the opioid epidemic.
2021-10-31
PLoS Medicine (published)
doi.org
Refining BERT Embeddings for Document Hashing via Mutual Information Maximization
Zijing Ou
Qinliang Su
Jianxing Yu
Ruihui Zhao
Yefeng Zheng
Bang Liu
Existing unsupervised document hashing methods are mostly established on generative models. Due to the difficulties of capturing long depend… (see more)ency structures, these methods rarely model the raw documents directly, but instead to model the features extracted from them (e.g. bag-of-words (BOW), TFIDF). In this paper, we propose to learn hash codes from BERT embeddings after observing their tremendous successes on downstream tasks. As a first try, we modify existing generative hashing models to accommodate the BERT embeddings. However, little improvement is observed over the codes learned from the old BOW or TFIDF features. We attribute this to the reconstruction requirement in the generative hashing, which will enforce irrelevant information that is abundant in the BERT embeddings also compressed into the codes. To remedy this issue, a new unsupervised hashing paradigm is further proposed based on the mutual information (MI) maximization principle. Specifically, the method first constructs appropriate global and local codes from the documents and then seeks to maximize their mutual information. Experimental results on three benchmark datasets demonstrate that the proposed method is able to generate hash codes that outperform existing ones learned from BOW features by a substantial margin.
2021-10-31
Findings of the Association for Computational Linguistics: EMNLP 2021 (published)
doi.org
arxiv.org
The meaning of significant mean group differences for biomarker discovery
Eva Loth
Jumana Ahmad
Chris Chatham
Beatriz López
Ben Carter
Daisy Crawley
Bethany Oakley
Hannah Hayward
Jennifer Cooke
Antonia San José Cáceres
Danilo Bzdok
Emily Jones
Tony Charman
Christian Beckmann
Thomas Bourgeron
Roberto Toro
Jan Buitelaar
Declan Murphy
Guillaume Dumas
Over the past decade, biomarker discovery has become a key goal in psychiatry to aid in the more reliable diagnosis and prognosis of heterog… (see more)eneous psychiatric conditions and the development of tailored therapies. Nevertheless, the prevailing statistical approach is still the mean group comparison between “cases” and “controls,” which tends to ignore within-group variability. In this educational article, we used empirical data simulations to investigate how effect size, sample size, and the shape of distributions impact the interpretation of mean group differences for biomarker discovery. We then applied these statistical criteria to evaluate biomarker discovery in one area of psychiatric research—autism research. Across the most influential areas of autism research, effect size estimates ranged from small (d = 0.21, anatomical structure) to medium (d = 0.36 electrophysiology, d = 0.5, eye-tracking) to large (d = 1.1 theory of mind). We show that in normal distributions, this translates to approximately 45% to 63% of cases performing within 1 standard deviation (SD) of the typical range, i.e., they do not have a deficit/atypicality in a statistical sense. For a measure to have diagnostic utility as defined by 80% sensitivity and 80% specificity, Cohen’s d of 1.66 is required, with still 40% of cases falling within 1 SD. However, in both normal and nonnormal distributions, 1 (skewness) or 2 (platykurtic, bimodal) biologically plausible subgroups may exist despite small or even nonsignificant mean group differences. This conclusion drastically contrasts the way mean group differences are frequently reported. Over 95% of studies omitted the “on average” when summarising their findings in their abstracts (“autistic people have deficits in X”), which can be misleading as it implies that the group-level difference applies to all individuals in that group. We outline practical approaches and steps for researchers to explore mean group comparisons for the discovery of stratification biomarkers.
2021-10-31
PLoS Computational Biology (published)
doi.org
The Topic Confusion Task: A Novel Evaluation Scenario for Authorship Attribution
Malik H. Altakrori
Jackie CK Cheung
Benjamin C. M. Fung
2021-10-31
Findings of the Association for Computational Linguistics: EMNLP 2021 (published)
doi.org
arxiv.org
Visually Grounded Reasoning across Languages and Cultures
Fangyu Liu
Emanuele Bugliarello
Edoardo Ponti
Siva Reddy
Nigel Collier
Desmond Elliott
The design of widespread vision-and-language datasets and pre-trained encoders directly adopts, or draws inspiration from, the concepts and … (see more)images of ImageNet. While one can hardly overestimate how much this benchmark contributed to progress in computer vision, it is mostly derived from lexical databases and image queries in English, resulting in source material with a North American or Western European bias. Therefore, we devise a new protocol to construct an ImageNet-style hierarchy representative of more languages and cultures. In particular, we let the selection of both concepts and images be entirely driven by native speakers, rather than scraping them automatically. Specifically, we focus on a typologically diverse set of languages, namely, Indonesian, Mandarin Chinese, Swahili, Tamil, and Turkish. On top of the concepts and images obtained through this new protocol, we create a multilingual dataset for Multicultural Reasoning over Vision and Language (MaRVL) by eliciting statements from native speaker annotators about pairs of images. The task consists of discriminating whether each grounded statement is true or false. We establish a series of baselines using state-of-the-art models and find that their cross-lingual transfer performance lags dramatically behind supervised performance in English. These results invite us to reassess the robustness and accuracy of current state-of-the-art models beyond a narrow domain, but also open up new exciting challenges for the development of truly multilingual and multicultural systems.
2021-10-31
Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing (published)
doi.org
openreview.net
From Machine Learning to Robotics: Challenges and Opportunities for Embodied Intelligence
Nicholas Roy
Ingmar Posner
T. Barfoot
Philippe Beaudoin
Yoshua Bengio
Jeannette Bohg
Oliver Brock
Isabelle Depatie
Dieter Fox
D. Koditschek
Tom'as Lozano-p'erez
Vikash K. Mansinghka
Christopher Pal
Blake Aaron Richards
Dorsa Sadigh
Stefan Schaal
G. Sukhatme
Denis Therien
Marc Emile Toussaint
Michiel van de Panne
2021-10-27
ArXiv (preprint)
arxiv.org
arxiv.org