Publications

Science-Software Linkage: The Challenges of Traceability between Scientific Knowledge and Software Artifacts
Hideaki Hata
Jin L.C. Guo
Raula Gaikovina Kula
Christoph Treude
Although computer science papers are often accompanied by software artifacts, connecting research papers to their software artifacts and vic… (see more)e versa is not always trivial. First of all, there is a lack of well-accepted standards for how such links should be provided. Furthermore, the provided links, if any, often become outdated: they are affected by link rot when pre-prints are removed, when repositories are migrated, or when papers and repositories evolve independently. In this paper, we summarize the state of the practice of linking research papers and associated source code, highlighting the recent efforts towards creating and maintaining such links. We also report on the results of several empirical studies focusing on the relationship between scientific papers and associated software artifacts, and we outline challenges related to traceability and opportunities for overcoming these challenges.
2021-04-12
ArXiv (preprint)
arxiv.org
arxiv.org
Common Limitations of Image Processing Metrics: A Picture Story
Annika Reinke
Matthias Eisenmann
Minu Dietlinde Tizabi
Carole H. Sudre
TIM RÄDSCH
Michela Antonelli
Tal Arbel
Spyridon Bakas
M. Jorge Cardoso
Veronika Cheplygina
Keyvan Farahani
B. Glocker
DOREEN HECKMANN-NÖTZEL
Fabian Isensee
Pierre Jannin
Charles E. Jr. Kahn
Jens Kleesiek
Tahsin Kurc
Michal Kozubek
Bennett Landman … (see 14 more)
GEERT LITJENS
Klaus Maier-Hein
Bjoern Menze
Henning Müller
Jens Petersen
Mauricio Reyes
Nicola Rieke
Bram Stieltjes
R. Summers
Sotirios A. Tsaftaris
Bram van Ginneken
Annette Kopp-Schneider
PAUL F. JÄGER
Lena Maier-Hein
2021-04-11
ArXiv (preprint)
arxiv.org
arxiv.org
Maintenance of a collection of machines under partial observability: Indexability and computation of Whittle index
Nima Akbarzadeh
Aditya Mahajan
We consider the problem of scheduling maintenance for a collection of machines under partial observations when the state of each machine det… (see more)eriorates stochastically in a Markovian manner. We consider two observational models: first, the state of each machine is not observable at all, and second, the state of each machine is observable only if a service-person visits them. The agent takes a maintenance action, e.g., machine replacement, if he is chosen for the task. We model both problems as restless multi-armed bandit problem and propose the Whittle index policy for scheduling the visits. We show that both models are indexable. For the first model, we derive a closed-form expression for the Whittle index. For the second model, we propose an efficient algorithm to compute the Whittle index by exploiting the qualitative properties of the optimal policy. We present detailed numerical experiments which show that for multiple instances of the model, the Whittle index policy outperforms myopic policy and can be close-to-optimal in different setups.
2021-04-11
arXiv.org (preprint)
dblp.uni-trier.de
Safe Option-Critic: Learning Safety in the Option-Critic Architecture
Arushi Jain
Khimya Khetarpal
Doina Precup
Designing hierarchical reinforcement learning algorithms that exhibit safe behaviour is not only vital for practical applications but also, … (see more)facilitates a better understanding of an agent's decisions. We tackle this problem in the options framework, a particular way to specify temporally abstract actions which allow an agent to use sub-policies with start and end conditions. We consider a behaviour as safe that avoids regions of state-space with high uncertainty in the outcomes of actions. We propose an optimization objective that learns safe options by encouraging the agent to visit states with higher behavioural consistency. The proposed objective results in a trade-off between maximizing the standard expected return and minimizing the effect of model uncertainty in the return. We propose a policy gradient algorithm to optimize the constrained objective function. We examine the quantitative and qualitative behaviour of the proposed approach in a tabular grid-world, continuous-state puddle-world, and three games from the Arcade Learning Environment: Ms.Pacman, Amidar, and Q*Bert. Our approach achieves a reduction in the variance of return, boosts performance in environments with intrinsic variability in the reward structure, and compares favorably both with primitive actions as well as with risk-neutral options.
2021-04-06
The Knowledge Engineering Review (published)
doi.org
arxiv.org
Comparing Transfer and Meta Learning Approaches on a Unified Few-Shot Classification Benchmark
Vincent Dumoulin
Neil Houlsby
Utku Evci
Xiaohua Zhai
Ross Goroshin
Sylvain Gelly
Hugo Larochelle
Meta and transfer learning are two successful families of approaches to few-shot learning. Despite highly related goals, state-of-the-art ad… (see more)vances in each family are measured largely in isolation of each other. As a result of diverging evaluation norms, a direct or thorough comparison of different approaches is challenging. To bridge this gap, we perform a cross-family study of the best transfer and meta learners on both a large-scale meta-learning benchmark (Meta-Dataset, MD), and a transfer learning benchmark (Visual Task Adaptation Benchmark, VTAB). We find that, on average, large-scale transfer methods (Big Transfer, BiT) outperform competing approaches on MD, even when trained only on ImageNet. In contrast, meta-learning approaches struggle to compete on VTAB when trained and validated on MD. However, BiT is not without limitations, and pushing for scale does not improve performance on highly out-of-distribution MD tasks. In performing this study, we reveal a number of discrepancies in evaluation norms and study some of these in light of the performance gap. We hope that this work facilitates sharing of insights from each community, and accelerates progress on few-shot learning.
2021-04-05
ArXiv (preprint)
arxiv.org
arxiv.org
Understanding Continual Learning Settings with Data Distribution Drift Analysis
Timothee LESORT
Massimo Caccia
Irina Rish
Classical machine learning algorithms often assume that the data are drawn i.i.d. from a stationary probability distribution. Recently, cont… (see more)inual learning emerged as a rapidly growing area of machine learning where this assumption is relaxed, i.e. where the data distribution is non-stationary and changes over time. This paper represents the state of data distribution by a context variable
2021-04-03
ArXiv (preprint)
arxiv.org
arxiv.org
Differentially private data publishing for arbitrarily partitioned data
Rongli Wang
Benjamin C. M. Fung
Yan Zhu
Qiang Peng
2021-03-31
Information Sciences (published)
doi.org
Discourse-Aware Unsupervised Summarization for Long Scientific Documents
Yue Dong
Andrei Mircea
Jackie CK Cheung
2021-03-31
Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: Main Volume (published)
doi.org
Generative lesion pattern decomposition of cognitive impairment after stroke
Anna K. Bonkhoff
Jae-Sung Lim
Hee-Joon Bae
Nick A. Weaver
Hugo J. Kuijf
J. Matthijs Biesbroek
Natalia S. Rost
Danilo Bzdok
Cognitive impairment is a frequent and disabling sequela of stroke. There is however incomplete understanding of how lesion topographies in … (see more)the left and right cerebral hemisphere brain interact to cause distinct cognitive deficits. We integrated machine learning and Bayesian hierarchical modelling to enable a hemisphere-aware analysis of 1080 acute ischaemic stroke patients with deep profiling ∼3 months after stroke. We show the relevance of the left hemisphere in the prediction of language and memory assessments and relevance of the right hemisphere in the prediction of visuospatial functioning. Global cognitive impairments were equally well predicted by lesion topographies from both sides. Damage to the hippocampal and occipital regions on the left was particularly informative about lost naming and memory functions, while damage to these regions on the right was linked to lost visuospatial functioning. Global cognitive impairment was predominantly linked to lesioned tissue in the supramarginal and angular gyrus, the post-central gyrus as well as the lateral occipital and opercular cortices of the left hemisphere. Hence, our analysis strategy uncovered that lesion patterns with unique hemispheric distributions are characteristic of how cognitive capacity is lost due to ischaemic brain tissue damage.
2021-03-31
Brain Communications (published)
doi.org
Smart about medications (SAM): a digital solution to enhance medication management following hospital discharge
Santiago Márquez Fosser
Nadar Mahmoud
Bettina Habib
Daniala L. Weir
Fiona Chan
Rola El Halabieh
Jeanne Vachon
Manish Thakur
Thai Tran
Melissa Bustillo
Caroline Beauchamp
André Bonnici
David L. Buckeridge
Robyn Tamblyn
To outline the development of a software solution to improve medication management after hospital discharge, including its design, data sour… (see more)ces, intrinsic features, and to evaluate the usability and the perception of use by end-users. Patients were directly involved in the development using a User Center Design (UCD) approach. We conducted usability interviews prior to hospital discharge, before a user started using the application. A technology acceptance questionnaire was administered to evaluate user self-perception after 2 weeks of use. The following features were developed; pill identification, patient-friendly drug information leaflet, side effect checker, and interaction checker, adherence monitoring and alerts, weekly medication schedule, daily pill reminders, messaging service, and patient medication reviews. The usability interviews show a 98.3% total success rate for all features, severity (on a scale of 1–4) 1.4 (SD 0.79). Regarding the self-perception of use (1–7 agreement scale) the 3 highest-rated domains were: (1) perceived ease of use 5.65 (SD 2.02), (2) output quality 5.44 (SD 1.65), and (3) perceived usefulness 5.29 (SD 2.11). Many medication management apps solutions have been created and most of them have not been properly evaluated. SAM (Smart About Medications) includes the user perspective, integration between a province drug database and the pharmacist workflow in real time. Its features are not limited to maintaining a medication list through manual entry. We can conclude after evaluation that the application is usable and has been self-perceived as easy to use by end-users. Future studies are required to assess the health benefits associated with its use.
2021-03-31
JAMIA Open (published)
doi.org
Touch-based Curiosity for Sparse-Reward Tasks
Sai Rajeswar
Cyril Ibrahim
Nitin Surya
Florian Golemo
David Vázquez
Aaron Courville
Pedro O. Pinheiro
2021-03-31
ArXiv (preprint)
arxiv.org
arxiv.org
Age differences in the functional architecture of the human brain
Roni Setton
Laetitia Mwilambwe-Tshilobo
Manesh Girn
Amber W. Lockrow
Giulia Baracchini
Colleen Hughes
Alexander J. Lowe
Benjamin N. Cassidy
Jian Li
Wen-Ming Luh
Danilo Bzdok
Richard M. Leahy
Tian Ge
Daniel S. Margulies
Bratislav Misic
Boris C. Bernhardt
W. Dale Stevens
Felipe De Brigard
Prantik Kundu
Gary R. Turner … (see 2 more)
R. Nathan Spreng
Montreal Neurological
The intrinsic functional organization of the brain changes into older adulthood. Age differences are observed at multiple spatial scales, fr… (see more)om global reductions in modularity and segregation of distributed brain systems, to network-specific patterns of dedifferentiation. Whether dedifferentiation reflects an inevitable, global shift in brain function with age, circumscribed, experience dependent changes, or both, is uncertain. We employed a multi-method strategy to interrogate dedifferentiation at multiple spatial scales. Multi-echo (ME) resting-state fMRI was collected in younger (n=181) and older (n=120) healthy adults. Cortical parcellation sensitive to individual variation was implemented for precision functional mapping of each participant, while preserving group-level parcel and network labels. ME-fMRI processing and gradient mapping identified global and macroscale network differences. Multivariate functional connectivity methods tested for microscale, edge-level differences. Older adults had lower BOLD signal dimensionality, consistent with global network dedifferentiation. Gradients were largely age-invariant. Edge-level analyses revealed discrete, network-specific dedifferentiation patterns in older adults. Visual and somatosensory regions were more integrated within the functional connectome; default and frontoparietal control network regions showed greater connectivity; and the dorsal attention network was more integrated with heteromodal regions. These findings highlight the importance of multi-scale, multi-method approaches to characterize the architecture of functional brain aging.
2021-03-30
bioRxiv (preprint)
doi.org