Publications

Biomedical image analysis competitions: The state of current participation practice
Matthias Eisenmann
Annika Reinke
Vivienn Weru
Minu Dietlinde Tizabi
Fabian Isensee
T. Adler
PATRICK GODAU
Veronika Cheplygina
Michal Kozubek
Sharib Ali
Anubha Gupta
Jan. Kybic
Alison Professor Noble
Carlos Ortiz de Sol'orzano
Samiksha Pachade
Caroline Petitjean
Daniel Sage
Donglai Wei
Elizabeth Wilden
Deepak Alapatt … (see 334 more)
Vincent Andrearczyk
Ujjwal Baid
Spyridon Bakas
Niranjan Balu
Sophia Bano
Vivek Singh Bawa
Jorge Bernal
Sebastian Bodenstedt
Alessandro Casella
Jinwook Choi
Olivier Commowick
M. Daum
Adrien Depeursinge
Reuben Dorent
J. Egger
H. Eichhorn
Sandy Engelhardt
Melanie Ganz
Gabriel Girard
Lasse Donovan Hansen
Mattias Paul Heinrich
Nicholas Heller
Alessa Hering
Arnaud Huaulm'e
Hyunjeong Kim
Bennett Landman
Hongwei Bran Li
Jianning Li
Junfang Ma
Anne L. Martel
Carlos Mart'in-Isla
Bjoern Menze
Chinedu Innocent Nwoye
Valentin Oreiller
Nicolas Padoy
Sarthak Pati
Kelly Payette
Carole H. Sudre
K. V. Wijnen
Armine Vardazaryan
Tom Kamiel Magda Vercauteren
Martin Wagner
Chuanbo Wang
Moi Hoon Yap
Zeyun Yu
Chuner Yuan
Maximilian Zenk
Aneeq Zia
David Zimmerer
Rina Bao
Chanyeol Choi
Andrew Cohen
Oleh Dzyubachyk
Adrian Galdran
Tianyuan Gan
Tianqi Guo
Pradyumna Gupta
M. Haithami
Edward Ho
Ikbeom Jang
Zhili Li
Zheng Luo
Filip Lux
Sokratis Makrogiannis
Dominikus Muller
Young-Tack Oh
Subeen Pang
Constantin Pape
Gorkem Polat
Charlotte Rosalie Reed
Kanghyun Ryu
Tim Scherr
Vajira L. Thambawita
Haoyu Wang
Xinliang Wang
Kele Xu
H.-I. Yeh
Doyeob Yeo
Yi Yuan
Yan Zeng
Xingwen Zhao
Julian Ronald Abbing
Jannes Adam
Nagesh Adluru
Niklas Agethen
S. Ahmed
Yasmina Al Khalil
Mireia Alenya
Esa J. Alhoniemi
C. An
Talha E Anwar
Tewodros Arega
Netanell Avisdris
D. Aydogan
Yi-Shi Bai
Maria Baldeon Calisto
Berke Doga Basaran
Marcel Beetz
Cheng Bian
Hao-xuan Bian
Kevin Blansit
Louise Bloch
Robert Bohnsack
Sara Bosticardo
J. Breen
Mikael Brudfors
Raphael Brungel
Mariano Cabezas
Alberto Cacciola
Zhiwei Chen
Yucong Chen
Dan Chen
Minjeong Cho
Min-Kook Choi
Chuantao Xie Chuantao Xie
Dana Cobzas
Julien Cohen-Adad
Jorge Corral Acero
Sujit Kumar Das
Marcela de Oliveira
Hanqiu Deng
Guiming Dong
Lars Doorenbos
Cory Efird
Di Fan
Mehdi Fatan Serj
Alexandre Fenneteau
Lucas Fidon
Patryk Filipiak
Ren'e Finzel
Nuno Renato Freitas
C. Friedrich
Mitchell J. Fulton
Finn Gaida
Francesco Galati
Christoforos Galazis
Changna Gan
Zheyao Gao
Sheng Gao
Matej Gazda
Beerend G. A. Gerats
Neil Getty
Adam Gibicar
Ryan J. Gifford
Sajan Gohil
Maria Grammatikopoulou
Daniel Grzech
Orhun Guley
Timo Gunnemann
Chun-Hai Guo
Sylvain Guy
Heonjin Ha
Luyi Han
Ilseok Han
Ali Hatamizadeh
Tianhai He
Ji-Wu Heo
Sebastian Hitziger
SeulGi Hong
Seungbum Hong
Rian Huang
Zi-You Huang
Markus Huellebrand
Stephan Huschauer
M. Hussain
Tomoo Inubushi
Ece Isik Polat
Mojtaba Jafaritadi
Seonghun Jeong
Bailiang Jian
Yu Jiang
Zhifan Jiang
Yu Jin
Smriti Joshi
A. Kadkhodamohammadi
R. A. Kamraoui
Inhak Kang
Jun-Su Kang
Davood Karimi
April Ellahe Khademi
Muhammad Irfan Khan
Suleiman A. Khan
Rishab Khantwal
Kwang-Ju Kim
Timothy Lee Kline
Satoshi Kondo
Elina Kontio
Adrian Krenzer
Artem Kroviakov
Hugo J. Kuijf
Satyadwyoom Kumar
Francesco La Rosa
Abhishek Lad
Doohee Lee
Minho Lee
Chiara Lena
Hao Li
Ling Li
Xingyu Li
F. Liao
Kuan-Ya Liao
Arlindo L. Oliveira
Chaonan Lin
Shanhai Lin
Akis Linardos
M. Linguraru
Han Liu
Tao Liu
Dian Liu
Yanling Liu
Joao Lourencco-Silva
Jing Lu
Jia Lu
Imanol Luengo
Christina Bach Lund
Huan Minh Luu
Yingqi Lv
Uzay Macar
Leon Maechler
L. SinaMansour
Kenji Marshall
Moona Mazher
Richard McKinley
Alfonso Medela
Felix Meissen
Mingyuan Meng
Dylan Bradley Miller
S. Mirjahanmardi
Arnab Kumar Mishra
Samir Mitha
Hassan Mohy-ud-Din
Tony C. W. Mok
Gowtham Krishnan Murugesan
Enamundram Naga Karthik
Sahil Nalawade
Jakub Nalepa
M. Naser
Ramin Nateghi
Hammad Naveed
Quang-Minh Nguyen
Cuong Nguyen Quoc
Brennan Nichyporuk
Bruno Oliveira
David Owen
Jimut Bahan Pal
Junwen Pan
Wei-Dong Pan
Winnie Pang
Bogyu Park
Vivek G. Pawar
Kamlesh Pawar
Michael Peven
Lena Philipp
Tomasz Pieciak
Szymon S Płotka
Marcel Plutat
Fattane Pourakpour
Domen Prelovznik
K. Punithakumar
Abdul Qayyum
Sandro Queir'os
Arman Rahmim
Salar Razavi
Jintao Ren
Mina Rezaei
Jonathan Adam Rico
ZunHyan Rieu
Markus Rink
Johannes Roth
Yusely Ruiz-gonzalez
Numan Saeed
Anindo Saha
Mostafa M. Sami Salem
Ricardo Sanchez-matilla
Kurt G Schilling
Weizhen Shao
Zhiqiang Shen
Ruize Shi
Pengcheng Shi
Daniel Sobotka
Th'eodore Soulier
Bella Specktor Fadida
D. Stoyanov
Timothy Sum Hon Mun
Xiao-Fu Sun
Rong Tao
Franz Thaler
Antoine Th'eberge
Felix Thielke
Helena R. Torres
K. Wahid
Jiacheng Wang
Yifei Wang
Wei David Wang
Xiong Jun Wang
Jianhui Wen
Ning Wen
Marek Wodziński
Yehong Wu
Fangfang Xia
Tianqi Xiang
Cheng Xiaofei
Lizhang Xu
Tingting Xue
Yu‐Xia Yang
Lingxian Yang
Kai Yao
Huifeng Yao
Amirsaeed Yazdani
Michael Yip
Hwa-Seong Yoo
Fereshteh Yousefirizi
Shu-Fen Yu
Lei Yu
Jonathan Zamora
Ramy A. Zeineldin
Dewen Zeng
Jianpeng Zhang
Bokai Zhang
Jiapeng Zhang
Fangxi Zhang
Huahong Zhang
Zhongchen Zhao
Zixuan Zhao
Jia Zhao
Can Zhao
Qiuyue Zheng
Yuheng Zhi
Ziqi Zhou
Baosheng Zou
Klaus Maier-Hein
PAUL F. JÄGER
Annette Kopp-Schneider
Lena Maier-Hein
2022-12-15
ArXiv (preprint)
doi.org
arxiv.org
Rethinking Generalization: The Impact of Annotation Style on Medical Image Segmentation
Brennan Nichyporuk
Jillian Cardinell
Justin Szeto
Raghav Mehta
Jean-Pierre R. Falet
Douglas L. Arnold
Sotirios A. Tsaftaris
Tal Arbel
Generalization is an important attribute of machine learning models, particularly for those that are to be deployed in a medical context, wh… (see more)ere unreliable predictions can have real world consequences. While the failure of models to generalize across datasets is typically attributed to a mismatch in the data distributions, performance gaps are often a consequence of biases in the "ground-truth" label annotations. This is particularly important in the context of medical image segmentation of pathological structures (e.g. lesions), where the annotation process is much more subjective, and affected by a number underlying factors, including the annotation protocol, rater education/experience, and clinical aims, among others. In this paper, we show that modeling annotation biases, rather than ignoring them, poses a promising way of accounting for differences in annotation style across datasets. To this end, we propose a generalized conditioning framework to (1) learn and account for different annotation styles across multiple datasets using a single model, (2) identify similar annotation styles across different datasets in order to permit their effective aggregation, and (3) fine-tune a fully trained model to a new annotation style with just a few samples. Next, we present an image-conditioning approach to model annotation styles that correlate with specific image features, potentially enabling detection biases to be more easily identified.
2022-12-14
Journal of Machine Learning for Biomedical Imaging (published)
doi.org
arxiv.org
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
2022-12-13
Nature Machine Intelligence (published)
doi.org
Redefining Relationships in Music
Christian Detweiler
Beth Coleman
Fernando Diaz
Lieke Dom
Chris Donahue
Jesse Engel
Cheng-Zhi Anna Huang
Larry James
Ethan Manilow
Amanda McCroskery
Kyle Pedersen
Pamela Peter-Agbia
Negar Rostamzadeh
Thomas Robert
Marco Zamarato
Ben Zevenbergen
AI tools increasingly shape how we discover, make and experience music. While these tools can have the potential to empower creativity, they… (see more) may fundamentally redefine relationships between stakeholders, to the benefit of some and the detriment of others. In this position paper, we argue that these tools will fundamentally reshape our music culture, with profound effects (for better and for worse) on creators, consumers and the commercial enterprises that often connect them. By paying careful attention to emerging Music AI technologies and developments in other creative domains and understanding the implications, people working in this space could decrease the possible negative impacts on the practice, consumption and meaning of music. Given that many of these technologies are already available, there is some urgency in conducting analyses of these technologies now. It is important that people developing and working with these tools address these issues now to help guide their evolution to be equitable and empower creativity. We identify some potential risks and opportunities associated with existing and forthcoming AI tools for music, though more work is needed to identify concrete actions which leverage the opportunities while mitigating risks.
2022-12-12
arXiv (Cornell University) (preprint)
doi.org
arxiv.org
Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data
Melissa Zwaig
Audrey Baguette
Bo Hu
Michael Johnston
Hussein Lakkis
Emily M. Nakada
Damien Faury
Nikoleta Juretic
Benjamin Ellezam
Alexandre G. Weil
Jason Karamchandani
Jacek Majewski
Mathieu Blanchette
Michael D. Taylor
Marco Gallo
Claudia L. Kleinman
Nada Jabado
Jiannis Ragoussis
Juvenile Pilocytic Astrocytomas (JPAs) are one of the most common pediatric brain tumors, and they are driven by aberrant activation of the … (see more)mitogen-activated protein kinase (MAPK) signaling pathway. RAF-fusions are the most common genetic alterations identified in JPAs, with the prototypical KIAA1549-BRAF fusion leading to loss of BRAF’s auto-inhibitory domain and subsequent constitutive kinase activation. JPAs are highly vascular and show pervasive immune infiltration, which can lead to low tumor cell purity in clinical samples. This can result in gene fusions that are difficult to detect with conventional omics approaches including RNA-Seq. To this effect, we applied RNA-Seq as well as linked-read whole-genome sequencing and in situ Hi-C as new approaches to detect and characterize low-frequency gene fusions at the genomic, transcriptomic and spatial level. Integration of these datasets allowed the identification and detailed characterization of two novel BRAF fusion partners, PTPRZ1 and TOP2B, in addition to the canonical fusion with partner KIAA1549. Additionally, our Hi-C datasets enabled investigations of 3D genome architecture in JPAs which showed a high level of correlation in 3D compartment annotations between JPAs compared to other pediatric tumors, and high similarity to normal adult astrocytes. We detected interactions between BRAF and its fusion partners exclusively in tumor samples containing BRAF fusions. We demonstrate the power of integrating multi-omic datasets to identify low frequency fusions and characterize the JPA genome at high resolution. We suggest that linked-reads and Hi-C could be used in clinic for the detection and characterization of JPAs.
2022-12-11
BMC Cancer (published)
doi.org
VDGraph2Vec: Vulnerability Detection in Assembly Code using Message Passing Neural Networks
Ashita Diwan
Miles Q. Li
Benjamin C. M. Fung
Software vulnerability detection is one of the most challenging tasks faced by reverse engineers. Recently, vulnerability detection has rece… (see more)ived a lot of attention due to a drastic increase in the volume and complexity of software. Reverse engineering is a time-consuming and labor-intensive process for detecting malware and software vulnerabilities. However, with the advent of deep learning and machine learning, it has become possible for researchers to automate the process of identifying potential security breaches in software by developing more intelligent technologies. In this research, we propose VDGraph2Vec, an automated deep learning method to generate representations of assembly code for the task of vulnerability detection. Previous approaches failed to attend to topological characteristics of assembly code while discovering the weakness in the software. VDGraph2Vec embeds the control flow and semantic information of assembly code effectively using the expressive capabilities of message passing neural networks and the RoBERTa model. Our model is able to learn the important features that help distinguish between vulnerable and non-vulnerable software. We carry out our experimental analysis for performance benchmark on three of the most common weaknesses and demonstrate that our model can identify vulnerabilities with high accuracy and outperforms the current state-of-the-art binary vulnerability detection models.
2022-12-11
2022 21st IEEE International Conference on Machine Learning and Applications (ICMLA) (published)
doi.org
Galaxies on graph neural networks: towards robust synthetic galaxy catalogs with deep generative models
Yesukhei Jagvaral
François Lanusse
Sukhdeep Singh
Rachel Mandelbaum
Siamak Ravanbakhsh
Duncan Campbell
The future astronomical imaging surveys are set to provide precise constraints on cosmological parameters, such as dark energy. However, pro… (see more)-duction of synthetic data for these surveys, to test and validate analysis methods, suffers from a very high computational cost. In particular, generating mock galaxy catalogs at sufficiently large volume and high resolution will soon become computa-tionally unreachable. In this paper, we address this problem with a Deep Generative Model to create robust mock galaxy catalogs that may be used to test and develop the analysis pipelines of future weak lensing surveys. We build our model on a custom built Graph Convolutional Networks, by placing each galaxy on a graph node and then connecting the graphs within each gravitationally bound system. We train our model on a cosmological simulation with realistic galaxy populations to capture the 2D and 3D orientations of galaxies. The samples from the model exhibit comparable statistical properties to those in the simulations. To the best of our knowledge, this is the first instance of a generative model on graphs in an astrophysical/cosmological context.
2022-12-10
ArXiv (preprint)
arxiv.org
arxiv.org
Neural Bandits for Data Mining: Searching for Dangerous Polypharmacy
Alexandre Larouche
Audrey Durand
Richard Khoury
Caroline Sirois
2022-12-09
ArXiv (preprint)
doi.org
arxiv.org
Bayesian Q-learning With Imperfect Expert Demonstrations
Fengdi Che
Xiru Zhu
Doina Precup
David Meger
Gregory Dudek
Guided exploration with expert demonstrations improves data efficiency for reinforcement learning, but current algorithms often overuse expe… (see more)rt information. We propose a novel algorithm to speed up Q-learning with the help of a limited amount of imperfect expert demonstrations. The algorithm avoids excessive reliance on expert data by relaxing the optimal expert assumption and gradually reducing the usage of uninformative expert data. Experimentally, we evaluate our approach on a sparse-reward chain environment and six more complicated Atari games with delayed rewards. With the proposed methods, we can achieve better results than Deep Q-learning from Demonstrations (Hester et al., 2017) in most environments.
2022-12-08
NeurIPS.cc/2022/Workshop/DeepRL (accepted)
doi.org
openreview.net
Energy efficiency as a normative account for predictive coding
Shahab Bakhtiari
2022-12-08
Patterns (published)
doi.org
Imitation from Observation With Bootstrapped Contrastive Learning
Medric Sonwa
Johanna Hansen
Eugene Belilovsky
2022-12-08
NeurIPS.cc/2022/Workshop/DeepRL (accepted)
doi.org
openreview.net
Implicit Offline Reinforcement Learning via Supervised Learning
Alexandre Piché
Rafael Pardinas
David Vázquez
Igor Mordatch
Christopher Pal
Offline Reinforcement Learning (RL) via Supervised Learning is a simple and effective way to learn robotic skills from a dataset of varied b… (see more)ehaviors. It is as simple as supervised learning and Behavior Cloning (BC) but takes advantage of the return information. On BC tasks, implicit models have been shown to match or outperform explicit ones. Despite the benefits of using implicit models to learn robotic skills via BC, Offline RL via Supervised Learning algorithms have been limited to explicit models. We show how implicit models leverage return information and match or outperform explicit algorithms to acquire robotic skills from fixed datasets. Furthermore, we show how closely related our implicit methods are to other popular RL via Supervised Learning algorithms.
2022-12-08
NeurIPS.cc/2022/Workshop/DeepRL (accepted)
doi.org
openreview.net