Corticosteroids induce an early but limited decrease in IL-6 dependent pro-inflammatory responses in critically ill COVID-19 patients
Tomas URBINA
Paul GABARRE
Vincent BONNY
Jean-Rémi Lavillegrand
Marc GARNIER
Jérémie JOFFRE
Nathalie MARIO
Guillaume Dumas
Geoffroy HARIRI
Matthieu TURPIN
Emmanuel PARDO
Muriel FARTOUKH
Bertrand GUIDET
Eric Maury
Yannick CHANTRAN
Pierre-Yves BOELLE
Guillaume VOIRIOT
Hafid AIT-OUFELLA
2024-01-01
Minerva Anestesiologica (published)
doi.org
Dance of the Neurons: Unraveling Sex from Brain Signals (short paper).
Mohammad-Javad Darvishi Bayazi
Mohammad S. Ghaemi
Jocelyn Faubert
Irina Rish
2024-01-01
ML4CMH@AAAI (published)
dblp.uni-trier.de
Data-access performance anti-patterns in data-intensive systems
Biruk Asmare Muse
Kawser Wazed Nafi
Foutse Khomh
Giuliano Antoniol
Data-intensive systems handle variable, high volume, and high-velocity data generated by human and digital devices. Like traditional softwar… (see more)e, data-intensive systems are prone to technical debts introduced to cope-up with the pressure of time and resource constraints on developers. Data-access is a critical component of data-intensive systems as it determines the overall performance and functionality of such systems. While data access technical debts are getting attention from the research community, technical debts affecting the performance, are not well investigated. Objective: Identify, categorize, and validate data access performance issues in the context of NoSQL-based and polyglot persistence data-intensive systems using qualitative study. Method: We collect issues from NoSQL-based and polyglot persistence open-source data-intensive systems and identify data access performance issues using inductive coding and build a taxonomy of the root causes. Then, we validate the perceived relevance of the newly identified performance issues using a developer survey.
2024-01-01
Empir. Softw. Eng. (published)
doi.org
arxiv.org
Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP.
Chen Su
William A Pastor
Amin Emad
Deciphering the underlying gene regulatory networks (GRNs) that govern early human embryogenesis is critical for understanding developmental… (see more) mechanisms yet remains challenging due to limited sample availability and the inherent complexity of the biological processes involved. To address this, we developed InPheRNo-ChIP, a computational framework that integrates multimodal data, including RNA-seq, transcription factor (TF)-specific ChIP-seq, and phenotypic labels, to reconstruct phenotype-relevant GRNs associated with endoderm development. The core of this method is a probabilistic graphical model that models the simultaneous effect of TFs on their putative target genes to influence a particular phenotypic outcome. Unlike the majority of existing GRN inference methods that are agnostic to the phenotypic outcomes, InPheRNo-ChIP directly incorporates phenotypic information during GRN inference, enabling the distinction between lineage-specific and general regulatory interactions. We integrated data from three experimental studies and applied InPheRNo-ChIP to infer the GRN governing the differentiation of human embryonic stem cells into definitive endoderm. Benchmarking against a scRNA-seq CRISPRi study demonstrated InPheRNo-ChIP's ability to identify regulatory interactions involving endoderm markers FOXA2, SMAD2, and SOX17, outperforming other methods. This highlights the importance of incorporating the phenotypic context during network inference. Furthermore, an ablation study confirms the synergistic contribution of ChIP-seq, RNA-seq, and phenotypic data, highlighting the value of multimodal integration for accurate phenotype-relevant GRN reconstruction.
2024-01-01
Briefings Bioinform. (published)
doi.org
DeCoDEx: Confounder Detector Guidance for Improved Diffusion-based Counterfactual Explanations
Nima Fathi
Amar Kumar
Brennan Nichyporuk
Mohammad Havaei
Tal Arbel
Deep learning classifiers are prone to latching onto dominant confounders present in a dataset rather than on the causal markers associated … (see more)with the target class, leading to poor generalization and biased predictions. Although explainability via counterfactual image generation has been successful at exposing the problem, bias mitigation strategies that permit accurate explainability in the presence of dominant and diverse artifacts remain unsolved. In this work, we propose the DeCoDEx framework and show how an external, pre-trained binary artifact detector can be leveraged during inference to guide a diffusion-based counterfactual image generator towards accurate explainability. Experiments on the CheXpert dataset, using both synthetic artifacts and real visual artifacts (support devices), show that the proposed method successfully synthesizes the counterfactual images that change the causal pathology markers associated with Pleural Effusion while preserving or ignoring the visual artifacts. Augmentation of ERM and Group-DRO classifiers with the DeCoDEx generated images substantially improves the results across underrepresented groups that are out of distribution for each class. The code is made publicly available at https://github.com/NimaFathi/DeCoDEx.
2024-01-01
MIDL (published)
doi.org
openreview.net
Decoding of Polar Codes Using Quadratic Unconstrained Binary Optimization
Huayi Zhou
Ryan Seah
Marwan Jalaleddine
Warren Gross
2024-01-01
IEEE Journal on Selected Areas in Communications (published)
doi.org
Deep Learning Approach for Changepoint Detection: Penalty Parameter Optimization
Tung L. Nguyen
Toby Dylan Hocking
Changepoint detection, a technique for identifying significant shifts within data sequences, is crucial in various fields such as finance, g… (see more)enomics, medicine, etc. Dynamic programming changepoint detection algorithms are employed to identify the locations of changepoints within a sequence, which rely on a penalty parameter to regulate the number of changepoints. To estimate this penalty parameter, previous work uses simple models such as linear models or decision trees. This study introduces a novel deep learning method for predicting penalty parameters, leading to demonstrably improved changepoint detection accuracy on large benchmark supervised labeled datasets compared to previous methods.
2024-01-01
arXiv.org (preprint)
doi.org
Deep reinforcement learning for continuous wood drying production line control
François-Alexandre Tremblay
Audrey Durand
Michael Morin
Philippe Marier
Jonathan Gaudreault
2024-01-01
Computers in industry (Print) (published)
doi.org
Deep reinforcement learning for continuous wood drying production line control
François-Alexandre Tremblay
Audrey Durand
Michael Morin
Philippe Marier
Jonathan Gaudreault
2024-01-01
Computers in Industry (published)
doi.org
In deep reinforcement learning, a pruned network is a good network
Johan Samir Obando Ceron
Aaron Courville
Pablo Samuel Castro
Recent work has shown that deep reinforcement learning agents have difficulty in effectively using their network parameters. We leverage pri… (see more)or insights into the advantages of sparse training techniques and demonstrate that gradual magnitude pruning enables agents to maximize parameter effectiveness. This results in networks that yield dramatic performance improvements over traditional networks and exhibit a type of"scaling law", using only a small fraction of the full network parameters.
2024-01-01
ICML (published)
doi.org
arxiv.org
Designing and Evaluating Dialogue LLMs for Co-Creative Improvised Theatre
Boyd Branch
Piotr Mirowski
Kory Wallace Mathewson
Sophia Ppali
Alexandra Covaci
Social robotics researchers are increasingly interested in multi-party trained conversational agents. With a growing demand for real-world e… (see more)valuations, our study presents Large Language Models (LLMs) deployed in a month-long live show at the Edinburgh Festival Fringe. This case study investigates human improvisers co-creating with conversational agents in a professional theatre setting. We explore the technical capabilities and constraints of on-the-spot multi-party dialogue, providing comprehensive insights from both audience and performer experiences with AI on stage. Our human-in-the-loop methodology underlines the challenges of these LLMs in generating context-relevant responses, stressing the user interface's crucial role. Audience feedback indicates an evolving interest for AI-driven live entertainment, direct human-AI interaction, and a diverse range of expectations about AI's conversational competence and utility as a creativity support tool. Human performers express immense enthusiasm, varied satisfaction, and the evolving public opinion highlights mixed emotions about AI's role in arts.
2024-01-01
ICCC (published)
doi.org
arxiv.org
On diffusion models for amortized inference: Benchmarking and improving stochastic control and sampling
Marcin Sendera
Minsu Kim
Sarthak Mittal
Pablo Lemos
Luca Scimeca
Jarrid Rector-Brooks
Alexandre Adam
Yoshua Bengio
Nikolay Malkin
We study the problem of training diffusion models to sample from a distribution with a given unnormalized density or energy function. We ben… (see more)chmark several diffusion-structured inference methods, including simulation-based variational approaches and off-policy methods (continuous generative flow networks). Our results shed light on the relative advantages of existing algorithms while bringing into question some claims from past work. We also propose a novel exploration strategy for off-policy methods, based on local search in the target space with the use of a replay buffer, and show that it improves the quality of samples on a variety of target distributions. Our code for the sampling methods and benchmarks studied is made public at https://github.com/GFNOrg/gfn-diffusion as a base for future work on diffusion models for amortized inference.
2024-01-01
NeurIPS (published)
doi.org
arxiv.org