Publications

Bugs in machine learning-based systems: a faultload benchmark

Mohammad Mehdi Morovati

Amin Nikanjam

Foutse Khomh

Z. Jiang

2023-04-05

Empirical Software Engineering (published)

doi.org

arxiv.org

Abstract 2987: BamQuery: a new proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens

Maria-Virginia Ruiz Cuevas

Marie-Pierre Hardy

Jean-David Larouche

Anca Apavaloaei

Eralda Kina

Krystel Vincent

Patrick Gendron

Jean-Philippe Laverdure

Chantal Durette

Pierre Thibault

Sébastien Lemieux

Claude Perreault

Grégory Ehx

MHC class I-associated peptides (MAPs), collectively referred to as the immunopeptidome, have a pivotal role in cancer immunosurveillance. W… (see more)hile MAPs were long thought to be solely generated by the degradation of canonical proteins, recent advances in the field of proteogenomics (genomically-informed proteomics) evidenced that ∼10% of them originate from allegedly noncoding genomic sequences. Among these sequences, endogenous retroelements (EREs) are under intense scrutiny as a possible source of actionable tumor antigens (TAs). With the increasing number of cancer-oriented immunopeptidomic and proteogenomic studies comes the need to accurately attribute an RNA expression level to each MAP identified by mass-spectrometry. Here, we introduce BamQuery (BQ), a computational tool to attribute an exhaustive RNA expression to MAPs of any genomic origin (exon, intron, UTR, intergenic) from bulk and single-cell RNA-sequencing data. By using BQ on large datasets of published MAPs identified by mass spectrometry, we show that many of them can arise from more than one genomic region. Indeed, 27% of MAPs reported as deriving from protein-coding exons (canonical MAPs) could also arise from non-canonical genomic regions, sometimes with greater probability, and 61% of non-canonical MAPs could arise from more than a single genomic origin (334 possible regions on average per non-canonical MAP; up to 35,343 for EREs). The consideration of all these origins evidenced an unsuspected high RNA expression in normal human tissues of (i) published neoantigens/TAs (mutated or not); (ii) MAPs derived from proteasomal splicing, supposedly not genomically templated, and (iii) MAPs derived from viruses. In particular, the high expression of candidate immunotherapeutic targets such as TAs highlights the relevance of BamQuery and the necessity of using it to validate such antigens before translating their usage in clinical trials. We also demonstrate that BamQuery can be used to directly identify safe and actionable TAs as well as to predict their immunogenicity through our freely accessible web portal (https://bamquery.iric.ca/search). Therefore, BQ could become an essential tool in any TA prioritization pipeline in the near future. Citation Format: Maria-Virginia Ruiz Cuevas, Marie-Pierre Hardy, Jean-David Larouche, Anca Apavaloaei, Eralda Kina, Krystel Vincent, Patrick Gendron, Jean-Philippe Laverdure, Chantal Durette, Pierre Thibault, Sebastien Lemieux, Claude Perreault, Gregory Ehx. BamQuery: a new proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2987.

2023-04-04

Cancer Research (published)

doi.org

Abstract 2993: Unmutated tumor antigens are abundant and contribute to tumor control in melanoma

Anca Apavaloaei

Qingchuan Zhao

Leslie Hesnard

Krystel Vincent

Marie-Pierre Hardy

Chantal Durette

Joël Lanoix

Jean-Philippe Laverdure

Jean-David Larouche

Maria-Virginia Ruiz Cuevas

Grégory Ehx

Sébastien Lemieux

Pierre Thibault

Claude Perreault

Recognition of MHC-I-associated tumor antigens (TAs) by CD8+ T cells is central to antitumor immunity. Owing to the elevated tumor mutationa… (see more)l burden (TMB) in melanoma, the marked efficacy of immune checkpoint blockade (ICB) has been attributed to the recognition of mutated TAs. However, recent reports showed that response to ICB in melanomas with low TMB is associated with CD8+ T-cell reactivity against melanocyte lineage-associated antigens (LSAs). Here, we systematically evaluated the contribution of all TA classes, i.e., mutated and unmutated, canonical and non-canonical, to the antigenic landscape of melanoma. We characterized the TAs from melanoma biopsies and patient-derived cell lines using proteogenomics. Out of 79450 MHC-I-associated peptides (MAPs) identified from 19 samples, we found 557 unmutated TAs classified as tumor-specific (TSA), tumor-associated (TAA), or LSAs. These TAs most often derived from annotated open-reading frames, followed by ncRNAs and intergenic regions. By contrast, only 6 MAPs were mutated and tumor-specific, which could be partially explained by a decreased expression of mutations within MAP-generating genomic regions. While the number of unmutated TAs with predicted presentation (TApres) in melanoma patients was similar between responders and non-responders pre-ICB, non-responders showed marks of inefficient antigen presentation. In consequence, only responders lost TApres upon treatment, in tandem with an expansion in tumor-infiltrating lymphocytes. These results reveal a previously underappreciated contribution of unmutated TAs to tumor control in melanoma and suggest that enhancing their recognition could improve the ICB efficacy in non-responders. Citation Format: Anca Apavaloaei, Qingchuan Zhao, Leslie Hesnard, Krystel Vincent, Marie-Pierre Hardy, Chantal Durette, Joël Lanoix, Jean-Philippe Laverdure, Jean-David Larouche, Maria Virginia Ruiz Cuevas, Grégory Ehx, Sébastien Lemieux, Pierre Thibault, Claude Perreault. Unmutated tumor antigens are abundant and contribute to tumor control in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2993.

2023-04-04

Cancer Research (published)

doi.org

Evaluating the Fairness of Deep Learning Uncertainty Estimates in Medical Image Analysis

Raghav Mehta

Changjian Shui

Tal Arbel

2023-04-04

MIDL.io/2023/Conference (poster)

doi.org

openreview.net

Evaluating the Fairness of Deep Learning Uncertainty Estimates in Medical Image Analysis

Raghav Mehta

Changjian Shui

Tal Arbel

Although deep learning (DL) models have shown great success in many medical image analysis tasks, deployment of the resulting models into r… (see more)eal clinical contexts requires: (1) that they exhibit robustness and fairness across different sub-populations, and (2) that the confidence in DL model predictions be accurately expressed in the form of uncertainties. Unfortunately, recent studies have indeed shown significant biases in DL models across demographic subgroups (e.g., race, sex, age) in the context of medical image analysis, indicating a lack of fairness in the models. Although several methods have been proposed in the ML literature to mitigate a lack of fairness in DL models, they focus entirely on the absolute performance between groups without considering their effect on uncertainty estimation. In this work, we present the first exploration of the effect of popular fairness models on overcoming biases across subgroups in medical image analysis in terms of bottom-line performance, and their effects on uncertainty quantification. We perform extensive experiments on three different clinically relevant tasks: (i) skin lesion classification, (ii) brain tumour segmentation, and (iii) Alzheimer's disease clinical score regression. Our results indicate that popular ML methods, such as data-balancing and distributionally robust optimization, succeed in mitigating fairness issues in terms of the model performances for some of the tasks. However, this can come at the cost of poor uncertainty estimates associated with the model predictions. This tradeoff must be mitigated if fairness models are to be adopted in medical image analysis.

2023-04-04

MIDL.io/2023/Conference (poster)

doi.org

openreview.net

Intent-aware Multi-source Contrastive Alignment for Tag-enhanced Recommendation

Haolun Wu

Yingxue Zhang

Chen Ma

Wei Guo

Ruiming Tang

Xue (Steve) Liu

Mark Coates

To offer accurate and diverse recommendation services, recent methods use auxiliary information to foster the learning process of user and i… (see more)tem representations. Many state-of-the-art (SOTA) methods fuse different sources of information (user, item, knowledge graph, tags, etc.) into a graph and use Graph Neural Networks (GNNs) to introduce the auxiliary information through the message passing paradigm. In this work, we seek an alternative framework that is light and effective through self-supervised learning across different sources of information, particularly for the commonly accessible item tag information. We use a self-supervision signal to pair users with the auxiliary information (tags) associated with the items they have interacted with before. To achieve the pairing, we create a proxy training task. For a given item, the model predicts which is the correct pairing between the representations obtained from the users that have interacted with this item and the tags assigned to it. This design provides an efficient solution, using the auxiliary information directly to enhance the quality of user and item embeddings. User behavior in recommendation systems is driven by the complex interactions of many factors behind the users’ decision-making processes. To make the pairing process more fine-grained and avoid embedding collapse, we propose a user intent-aware self-supervised pairing process where we split the user embeddings into multiple sub-embedding vectors. Each sub-embedding vector captures a specific user intent via self-supervised alignment with a particular cluster of tags. We integrate our designed framework with various recommendation models, demonstrating its flexibility and compatibility. Through comparison with numerous SOTA methods on seven real-world datasets, we show that our method can achieve better performance while requiring less training time. This indicates the potential of applying our approach on web-scale datasets.

2023-04-03

2023 IEEE 39th International Conference on Data Engineering (ICDE) (published)

doi.org

arxiv.org

Assessing the inclusion of children’s surgical care in National Surgical, Obstetric and Anaesthesia Plans: a policy content analysis

Sabrina Wimmer

Paul Truche

Elena Guadagno

Emmanuel Ameh

Lubna Samad

Emmanuel Mwenda Malabo Makasa

Sarah Greenberg

John G Meara

Tonnis H van Dijk

Dan Poenaru

Objective While National Surgical, Obstetric and Anaesthesia Plans (NSOAPs) have emerged as a strategy to strengthen and scale up surgical h… (see more)ealthcare systems in low/middle-income countries (LMICs), the degree to which children’s surgery is addressed is not well-known. This study aims to assess the inclusion of children’s surgical care among existing NSOAPs, identify practice examples and provide recommendations to guide inclusion of children’s surgical care in future policies. Design We performed two qualitative content analyses to assess the inclusion of children’s surgical care among NSOAPs. We applied a conventional (inductive) content analysis approach to identify themes and patterns, and developed a framework based on the Global Initiative for Children’s Surgery’s Optimal Resources for Children’s Surgery document. We then used this framework to conduct a directed (deductive) content analysis of the NSOAPs of Ethiopia, Nigeria, Rwanda, Senegal, Tanzania and Zambia. Results Our framework for the inclusion of children’s surgical care in NSOAPs included seven domains. We evaluated six NSOAPs with all addressing at least two of the domains. All six NSOAPs addressed ‘human resources and training’ and ‘infrastructure’, four addressed ‘service delivery’, three addressed ‘governance and financing’, two included ‘research, evaluation and quality improvement’, and one NSOAP addressed ‘equipment and supplies’ and ‘advocacy and awareness’. Conclusions Additional focus must be placed on the development of surgical healthcare systems for children in LMICs. This requires a focus on children’s surgical care separate from adult surgical care in the scaling up of surgical healthcare systems, including children-focused needs assessments and the inclusion of children’s surgery providers in the process. This study proposes a framework for evaluating NSOAPs, highlights practice examples and suggests recommendations for the development of future policies.

2023-04-01

BMJ Open (published)

doi.org

Biomedical discovery through the integrative biomedical knowledge hub (iBKH).

Chang Su

Yu Hou

Manqi Zhou

Suraj Rajendran

Jacqueline R.M. A. Maasch

Zehra Abedi

Haotan Zhang

Zilong Bai

Anthony Cuturrufo

Winston Guo

Fayzan F. Chaudhry

Gregory Ghahramani

Jian Tang

Feixiong Cheng

Yue Li

Rui Zhang

Steven T. DeKosky

Jiang Bian

Fei Wang

2023-04-01

iScience (published)

doi.org

Can Ensembling Preprocessing Algorithms Lead to Better Machine Learning Fairness?

Khaled Badran

Pierre-Olivier Côté

Amanda Kolopanis

Rached Bouchoucha

Antonio Collante

Diego Elias Costa

Emad Shihab

Foutse Khomh

In this work, we evaluate three popular fairness preprocessing algorithms and investigate the potential for combining all algorithms into a … (see more)more robust preprocessing ensemble. We report on lessons learned that can help practitioners better select fairness algorithms for their models.

2023-04-01

Computer (published)

doi.org

arxiv.org

Deep learning-enabled anomaly detection for IoT systems

Adel Abusitta 0001

Adel Abusitta

Glaucio H.S. Carvalho

Omar Abdel Wahab

Talal Halabi

Benjamin Fung

Saja Al-Mamoori