Publications

Video Game Bad Smells: What They Are and How Developers Perceive Them
Vittoria Nardone
Biruk Asmare Muse
Mouna Abidi
Foutse Khomh
Massimiliano Di Penta
Video games represent a substantial and increasing share of the software market. However, their development is particularly challenging as i… (see more)t requires multi-faceted knowledge, which is not consolidated in computer science education yet. This article aims at defining a catalog of bad smells related to video game development. To achieve this goal, we mined discussions on general-purpose and video game-specific forums. After querying such a forum, we adopted an open coding strategy on a statistically significant sample of 572 discussions, stratified over different forums. As a result, we obtained a catalog of 28 bad smells, organized into five categories, covering problems related to game design and logic, physics, animation, rendering, or multiplayer. Then, we assessed the perceived relevance of such bad smells by surveying 76 game development professionals. The survey respondents agreed with the identified bad smells but also provided us with further insights about the discussed smells. Upon reporting results, we discuss bad smell examples, their consequences, as well as possible mitigation/fixing strategies and trade-offs to be pursued by developers. The catalog can be used not only as a guideline for developers and educators but also can pave the way toward better automated tool support for video game developers.
2022-09-14
ACM Transactions on Software Engineering and Methodology (published)
doi.org
Accurate machine learning prediction of sexual orientation based on brain morphology and intrinsic functional connectivity
Benjamin Clemens
Jeremy Lefort-Besnard
Christoph Ritter
Elke Smith
Mikhail Votinov
Birgit Derntl
Ute Habel
Danilo Bzdok
Sexual orientation in humans represents a multilevel construct that is grounded in both neurobiological and environmental factors. Here, we… (see more) bring to bear a machine learning approach to predict sexual orientation from gray matter volumes (GMVs) or resting-state functional connectivity (RSFC) in a cohort of 45 heterosexual and 41 homosexual participants.  In both brain assessments, we used penalized logistic regression models and nonparametric permutation.  We found an average accuracy of 62% (±6.72) for predicting sexual orientation based on GMV and an average predictive accuracy of 92% (±9.89) using RSFC. Regions in the precentral gyrus, precuneus and the prefrontal cortex were significantly informative for distinguishing heterosexual from homosexual participants in both the GMV and RSFC settings.  These results indicate that, aside from self-reports, RSFC offers neurobiological information valuable for highly accurate prediction of sexual orientation. We demonstrate for the first time that sexual orientation is reflected in specific patterns of RSFC, which enable personalized, brain-based predictions of this highly complex human trait. While these results are preliminary, our neurobiologically based prediction framework illustrates the great value and potential of RSFC for revealing biologically meaningful and generalizable predictive patterns in the human brain.
2022-09-13
Cerebral Cortex (unknown)
doi.org
Designing Biological Sequences via Meta-Reinforcement Learning and Bayesian Optimization
Leo Feng
Padideh Nouri
Aneri Muni
Yoshua Bengio
Pierre-Luc Bacon
The ability to accelerate the design of biological sequences can have a substantial impact on the progress of the medical field. The problem… (see more) can be framed as a global optimization problem where the objective is an expensive black-box function such that we can query large batches restricted with a limitation of a low number of rounds. Bayesian Optimization is a principled method for tackling this problem. However, the astronomically large state space of biological sequences renders brute-force iterating over all possible sequences infeasible. In this paper, we propose MetaRLBO where we train an autoregressive generative model via Meta-Reinforcement Learning to propose promising sequences for selection via Bayesian Optimization. We pose this problem as that of finding an optimal policy over a distribution of MDPs induced by sampling subsets of the data acquired in the previous rounds. Our in-silico experiments show that meta-learning over such ensembles provides robustness against reward misspecification and achieves competitive results compared to existing strong baselines.
2022-09-12
ArXiv (preprint)
doi.org
arxiv.org
Measuring Commonality in Recommendation of Cultural Content: Recommender Systems to Enhance Cultural Citizenship
Andres Ferraro
Gustavo Ferreira
Fernando Diaz
Georgina Born
2022-09-12
Proceedings of the 16th ACM Conference on Recommender Systems (published)
doi.org
arxiv.org
Towards Fair Federated Recommendation Learning: Characterizing the Inter-Dependence of System and Data Heterogeneity
Kiwan Maeng
Haiyu Lu
Luca Melis
John Nguyen
Michael G. Rabbat
Carole-Jean Wu
2022-09-12
Proceedings of the 16th ACM Conference on Recommender Systems (published)
doi.org
arxiv.org
Rapidly Inferring Personalized Neurostimulation Parameters with Meta-Learning: A Case Study of Individualized Fiber Recruitment in Vagus Nerve Stimulation
Ximeng Mao
Yao-Chuan Chang
Stavros Zanos
Guillaume Lajoie
Our meta-learning framework is general and can be adapted to many input-response neurostimulation mapping problems. Moreover, this method le… (see more)verages information from growing data sets of past patients, as a treatment is deployed. It can also be combined with several model types, including regression, Gaussian processes with Bayesian optimization, and beyond.
2022-09-07
bioRxiv (preprint)
doi.org
Unifying Generative Models with GFlowNets
Dinghuai Zhang
Ricky T. Q. Chen
Nikolay Malkin
Yoshua Bengio
There are many frameworks for deep generative modeling, each often presented with their own specific training algorithms and inference metho… (see more)ds. Here, we demonstrate the connections between existing deep generative models and the recently introduced GFlowNet framework, a probabilistic inference machine which treats sampling as a decision-making process. This analysis sheds light on their overlapping traits and provides a unifying viewpoint through the lens of learning with Markovian trajectories. Our framework provides a means for unifying training and inference algorithms, and provides a route to shine a unifying light over many generative models. Beyond this, we provide a practical and experimentally verified recipe for improving generative modeling with insights from the GFlowNet perspective.
2022-09-05
ArXiv (preprint)
doi.org
arxiv.org
Assessing Intrapartum Risk of Hypoxic-Ischemic Encephalopathy using Fetal Heart Rate with Long Short-term Memory Networks
"Derek Kweku DEGBEDZUI
Michael Kuzniewicz
Cornet Marie-Coralie
Yvonne Wu
Heather Forquer
Lawrence Gerstley
Emily Hamilton
Doina Precup
Philip Warrick
Robert Kearney"
This study investigated the prediction of the risk of hypoxic ischemic encephalopathy using intrapartum cardiotocography records with a long… (see more) short-term memory re-current neural network. Across the 12 hours of labour, HIE sensitivity rose from 0.25 to 0.56 as delivery approached while specificity remained approximately constant with a mean of 0.71 and standard deviation of 0.04. The results show that classification improves as delivery approaches but that performance needs improvement. Future work will address the limitations of this preliminary study by investigating input signal transformations and the use of other network architectures to improve the model performance.
2022-09-03
2022 Computing in Cardiology (CinC) (published)
doi.org
Re-expression of CA1 and entorhinal activity patterns preserves temporal context memory at long timescales
Futing Zou
Wanjia Guo
Emily J. Allen
Yihan Wu
Ian Charest
Thomas Naselaris
Kendrick Kay
Brice A. Kuhl
J. Benjamin Hutchinson
Sarah DuBrow
Converging, cross-species evidence indicates that memory for time is supported by hippocampal area CA1 and entorhinal cortex. However, limit… (see more)ed evidence characterizes how these regions preserve temporal memories over long timescales (e.g., months). At long timescales, memoranda may be encountered in multiple temporal contexts, potentially creating interference. Here, using 7T fMRI, we measured CA1 and entorhinal activity patterns as human participants viewed thousands of natural scene images distributed, and repeated, across many months. We show that memory for an image’s original temporal context was predicted by the degree to which CA1/entorhinal activity patterns from the first encounter with an image were re-expressed during re-encounters occurring minutes to months later. Critically, temporal memory signals were dissociable from predictors of recognition confidence, which were carried by distinct medial temporal lobe expressions. These findings suggest that CA1 and entorhinal cortex preserve temporal memories across long timescales by coding for and reinstating temporal context information.
2022-09-02
bioRxiv (preprint)
doi.org
Digitalization and the Anthropocene
Felix Creutzig
Daron Acemoglu
Xuemei Bai
Paul N. Edwards
Marie Josefine Hintz
Lynn H. Kaack
Siir Kilkis
Stefanie Kunkel
Amy Luers
Nikola Milojevic-Dupont
Dave Rejeski
Jürgen Renn
David Rolnick
Christoph Rosol
Daniela Russ
Thomas Turnbull
Elena Verdolini
Felix Wagner
Charlie Wilson
Aicha Zekar … (see 1 more)
Marius Zumwald
Great claims have been made about the benefits of dematerialization in a digital service economy. However, digitalization has historically i… (see more)ncreased environmental impacts at local and planetary scales, affecting labor markets, resource use, governance, and power relationships. Here we study the past, present, and future of digitalization through the lens of three interdependent elements of the Anthropocene: ( a) planetary boundaries and stability, ( b) equity within and between countries, and ( c) human agency and governance, mediated via ( i) increasing resource efficiency, ( ii) accelerating consumption and scale effects, ( iii) expanding political and economic control, and ( iv) deteriorating social cohesion. While direct environmental impacts matter, the indirect and systemic effects of digitalization are more profoundly reshaping the relationship between humans, technosphere and planet. We develop three scenarios: planetary instability, green but inhumane, and deliberate for the good. We conclude with identifying leverage points that shift human–digital–Earth interactions toward sustainability.
2022-09-01
Annual Review Environment and Resources (published)
doi.org
Researcher perspectives on ethics considerations in epigenetics: an international survey
Charles Dupras
Terese Knoppers
Nicole Palmour
Elisabeth Beauchamp
Stamatina Liosi
Reiner Siebert
Alison May Berner
Stephan Beck
Ian Charest
Yann Joly
Over the past decade, bioethicists, legal scholars and social scientists have started to investigate the potential implications of epigeneti… (see more)c research and technologies on medicine and society. There is growing literature discussing the most promising opportunities, as well as arising ethical, legal and social issues (ELSI). This paper explores the views of epigenetic researchers about some of these discussions. From January to March 2020, we conducted an online survey of 189 epigenetic researchers working in 31 countries. We questioned them about the scope of their field, opportunities in different areas of specialization, and ELSI in the conduct of research and knowledge translation. We also assessed their level of concern regarding four emerging non-medical applications of epigenetic testing—i.e., in life insurance, forensics, immigration and direct-to-consumer testing. Although there was strong agreement on DNA methylation, histone modifications, 3D structure of chromatin and nucleosomes being integral elements of the field, there was considerable disagreement on transcription factors, RNA interference, RNA splicing and prions. The most prevalent ELSI experienced or witnessed by respondents were in obtaining timely access to epigenetic data in existing databases, and in the communication of epigenetic findings by the media. They expressed high levels of concern regarding non-medical applications of epigenetics, echoing cautionary appraisals in the social sciences and humanities literature.
2022-09-01
Clinical Epigenetics (published)
doi.org
Small, correlated changes in synaptic connectivity may facilitate rapid motor learning
Barbara Feulner
Matthew G Perich
Raeed H. Chowdhury
Lee Miller
Juan A. Gallego
Claudia Clopath
2022-09-01
Nature Communications (published)
doi.org