Publications

Physics-Guided Adversarial Machine Learning for Aircraft Systems Simulation

Thomas Reid

In the context of aircraft system performance assessment, deep learning technologies allow us to quickly infer models from experimental meas… (see more)urements, with less detailed system knowledge than usually required by physics-based modeling. However, this inexpensive model development also comes with new challenges regarding model trustworthiness. This article presents a novel approach, physics-guided adversarial machine learning (ML), which improves the confidence over the physics consistency of the model. The approach performs, first, a physics-guided adversarial testing phase to search for test inputs revealing behavioral system inconsistencies, while still falling within the range of foreseeable operational conditions. Then, it proceeds with a physics-informed adversarial training to teach the model the system-related physics domain foreknowledge through iteratively reducing the unwanted output deviations on the previously uncovered counterexamples. Empirical evaluation on two aircraft system performance models shows the effectiveness of our adversarial ML approach in exposing physical inconsistencies of both the models and in improving their propensity to be consistent with physics domain knowledge.

2022-12-31

IEEE Transactions on Reliability (published)

doi.org

arxiv.org

Preclinical-to-clinical Anti-cancer Drug Response Prediction and Biomarker Identification Using TINDL

David Earl Hostallero

Lixuan Wei

Liewei Wang

Junmei Cairns

Amin Emad

Prediction of the response of cancer patients to different treatments and identification of biomarkers of drug response are two major goals … (see more)of individualized medicine. Here, we developed a deep learning framework called TINDL, completely trained on preclinical cancer cell lines (CCLs), to predict the response of cancer patients to different treatments. TINDL utilizes a tissue-informed normalization to account for the tissue type and cancer type of the tumors and to reduce the statistical discrepancies between CCLs and patient tumors. Moreover, by making the deep learning black box interpretable, this model identifies a small set of genes whose expression levels are predictive of drug response in the trained model, enabling identification of biomarkers of drug response. Using data from two large databases of CCLs and cancer tumors, we showed that this model can distinguish between sensitive and resistant tumors for 10 (out of 14) drugs, outperforming various other machine learning models. In addition, our small interfering RNA (siRNA) knockdown experiments on 10 genes identified by this model for one of the drugs (tamoxifen) confirmed that tamoxifen sensitivity is substantially influenced by all of these genes in MCF7 cells, and seven of these genes in T47D cells. Furthermore, genes implicated for multiple drugs pointed to shared mechanism of action among drugs and suggested several important signaling pathways. In summary, this study provides a powerful deep learning framework for prediction of drug response and identification of biomarkers of drug response in cancer. The code can be accessed at https://github.com/ddhostallero/tindl.

2022-12-31

Genomics, Proteomics & Bioinformatics (published)

doi.org

Predicting Time to and Average Quality of Future Offers for Kidney Transplant Candidates Declining a Current Deceased Donor Kidney Offer: A Retrospective Cohort Study

Jonathan Jalbert

Jean-Noel Weller

Pierre-Luc Boivin

Sylvain Lavigne

Mehdi Taobane

Mike Pieper

Andrea Lodi

Heloise Cardinal

By providing personalized quantitative estimates of time to and quality of future offers, our new approach can inform the shared decision-ma… (see more)king process between transplant candidates and physicians when a kidney offer from a deceased donor is made by an ODO.

2022-12-31

Canadian Journal of Kidney Health and Disease (published)

doi.org

Preference-Based Offline Evaluation

C. Clarke

Fernando Diaz

Negar Arabzadeh

A core step in production model research and development involves the offline evaluation of a system before production deployment. Tradition… (see more)al offline evaluation of search, recommender, and other systems involves gathering item relevance labels from human editors. These labels can then be used to assess system performance using offline evaluation metrics. Unfortunately, this approach does not work when evaluating highly effective ranking systems, such as those emerging from the advances in machine learning. Recent work demonstrates that moving away from pointwise item and metric evaluation can be a more effective approach to the offline evaluation of systems. This tutorial, intended for both researchers and practitioners, reviews early work in preference-based evaluation and covers recent developments in detail.

2022-12-31

WSDM (published)

doi.org

Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction

Zuobai Zhang

Minghao Xu

Aurelie Lozano

Vijil Chenthamarakshan

Payel Das

Jian Tang

Self-supervised pre-training methods on proteins have recently gained attention, with most approaches focusing on either protein sequences o… (see more)r structures, neglecting the exploration of their joint distribution, which is crucial for a comprehensive understanding of protein functions by integrating co-evolutionary information and structural characteristics. In this work, inspired by the success of denoising diffusion models in generative tasks, we propose the DiffPreT approach to pre-train a protein encoder by sequence-structure joint diffusion modeling. DiffPreT guides the encoder to recover the native protein sequences and structures from the perturbed ones along the joint diffusion trajectory, which acquires the joint distribution of sequences and structures. Considering the essential protein conformational variations, we enhance DiffPreT by a method called Siamese Diffusion Trajectory Prediction (SiamDiff) to capture the correlation between different conformers of a protein. SiamDiff attains this goal by maximizing the mutual information between representations of diffusion trajectories of structurally-correlated conformers. We study the effectiveness of DiffPreT and SiamDiff on both atom- and residue-level structure-based protein understanding tasks. Experimental results show that the performance of DiffPreT is consistently competitive on all tasks, and SiamDiff achieves new state-of-the-art performance, considering the mean ranks on all tasks. Our implementation is available at https://github.com/DeepGraphLearning/SiamDiff.

2022-12-31

arXiv.org (preprint)

doi.org

openreview.net

Price forecasting in the Ontario electricity market via TriConvGRU hybrid model: Univariate vs. multivariate frameworks

Behdad Ehsani

Pierre-Olivier Pineau

Laurent Charlin

Electricity price forecasting is a challenging task for decision-makers in deregulated power markets due to the inherent characteristics of … (see more)electricity prices, e.g., high frequency and volatility. Therefore, accurate forecasting of electricity prices can assist market participants in maximizing their profit. Accordingly, we proposed a novel hybrid Deep Learning model to forecast one-step, two-step, and three-step ahead Ontario electricity prices based on a Convolutional Neural Network (CNN) and Gated Recurrent Unit (GRU). Our model consists of three consecutive CNN-GRU models combined in parallel with different input data. We downsampled input data via pooling layers at the beginning of two streams of the model to capture different frequencies of price patterns concurrently. Also, a set of external variables, including previous prices, electricity load, generation, import and export, and weather data, were considered in our forecasting models to test whether these features improve the efficiency of the models. Finally, three experiments in various weeks of 2022 were carried out in the Ontario electricity market to assess the model. The results indicate that the proposed model reduced the forecasting error significantly by 63.3% in the first experiment, 41.8% in the second, and 28.2% in the third, on average, with respect to a Root Mean Square Error (RMSE). Also, the proposed model was compared with outperformed several baseline models, including statistical time-series, Machine Learning, and Deep Learning models. Furthermore, the comparison of results in univariate and multivariate settings indicated that adding variables to forecasting models did not help reduce forecasting errors.

2022-12-31

SSRN Electronic Journal (unknown)

doi.org

PromptMix: A Class Boundary Augmentation Method for Large Language Model Distillation

Gaurav Sahu

Olga Vechtomova

Dzmitry Bahdanau

Issam Laradji

Data augmentation is a widely used technique to address the problem of text classification when there is a limited amount of training data. … (see more)Recent work often tackles this problem using large language models (LLMs) like GPT3 that can generate new examples given already available ones. In this work, we propose a method to generate more helpful augmented data by utilizing the LLM's abilities to follow instructions and perform few-shot classifications. Our specific PromptMix method consists of two steps: 1) generate challenging text augmentations near class boundaries; however, generating borderline examples increases the risk of false positives in the dataset, so we 2) relabel the text augmentations using a prompting-based LLM classifier to enhance the correctness of labels in the generated data. We evaluate the proposed method in challenging 2-shot and zero-shot settings on four text classification datasets: Banking77, TREC6, Subjectivity (SUBJ), and Twitter Complaints. Our experiments show that generating and, crucially, relabeling borderline examples facilitates the transfer of knowledge of a massive LLM like GPT3.5-turbo into smaller and cheaper classifiers like DistilBERT

2022-12-31

EMNLP (published)

doi.org

openreview.net

Prototype-Sample Relation Distillation: Towards Replay-Free Continual Learning

Nader Asadi

MohammadReza Davari

Sudhir Mudur

Rahaf Aljundi

Eugene Belilovsky

In Continual learning (CL) balancing effective adaptation while combating catastrophic forgetting is a central challenge. Many of the recent… (see more) best-performing methods utilize various forms of prior task data, e.g. a replay buffer, to tackle the catastrophic forgetting problem. Having access to previous task data can be restrictive in many real-world scenarios, for example when task data is sensitive or proprietary. To overcome the necessity of using previous tasks' data, in this work, we start with strong representation learning methods that have been shown to be less prone to forgetting. We propose a holistic approach to jointly learn the representation and class prototypes while maintaining the relevance of old class prototypes and their embedded similarities. Specifically, samples are mapped to an embedding space where the representations are learned using a supervised contrastive loss. Class prototypes are evolved continually in the same latent space, enabling learning and prediction at any point. To continually adapt the prototypes without keeping any prior task data, we propose a novel distillation loss that constrains class prototypes to maintain relative similarities as compared to new task data. This method yields state-of-the-art performance in the task-incremental setting, outperforming methods relying on large amounts of data, and provides strong performance in the class-incremental setting without using any stored data points.

2022-12-31

ICML (published)

doi.org

proceedings.mlr.press

Publisher Correction: Advancing ethics review practices in AI research

Madhulika Srikumar

Rebecca Finlay

Grace M. Abuhamad

Carolyn Ashurst

Rosie Campbell

Emily Campbell-Ratcliffe

Hudson Hongo

Sara Rene Jordan

Joseph Lindley

Aviv Ovadya

Joelle Pineau

2022-12-31

Nature Machine Intelligence (published)

doi.org

Questions Are All You Need to Train a Dense Passage Retriever

Devendra Singh Sachan

Mike Lewis

Dani Yogatama

Luke Zettlemoyer

Joelle Pineau

Manzil Zaheer

We introduce ART, a new corpus-level autoencoding approach for training dense retrieval models that does not require any labeled training da… (see more)ta. Dense retrieval is a central challenge for open-domain tasks, such as Open QA, where state-of-the-art methods typically require large supervised datasets with custom hard-negative mining and denoising of positive examples. ART, in contrast, only requires access to unpaired inputs and outputs (e.g. questions and potential answer documents). It uses a new document-retrieval autoencoding scheme, where (1) an input question is used to retrieve a set of evidence documents, and (2) the documents are then used to compute the probability of reconstructing the original question. Training for retrieval based on question reconstruction enables effective unsupervised learning of both document and question encoders, which can be later incorporated into complete Open QA systems without any further finetuning. Extensive experiments demonstrate that ART obtains state-of-the-art results on multiple QA retrieval benchmarks with only generic initialization from a pre-trained language model, removing the need for labeled data and task-specific losses.

2022-12-31

Transactions of the Association for Computational Linguistics (published)

doi.org

arxiv.org

A rapid review for developing a co-design framework for a pediatric surgical communication application

Michelle Cwintal

Hamed Ranjbar

Parsa Bandamiri

Elena Guadagno

Esli Osmanlliu

Dan Poenaru

2022-12-31