Publications

Spinal cord perfusion impairments in the M83 mouse model of Parkinson’s disease

Benjamin F. Combes

Sandeep Kumar Kalva

Pierre-Louis Benveniste

Agathe Tournant

Man Hoi Law

Joshua Newton

Maik Krüger

Rebecca Z. Weber

Inês Dias

Daniela Noain

Xose Luis Dean-Ben

Uwe Konietzko

Christian R. Baumann

Per-Göran Gillberg

Christoph Hock

Roger M. Nitsch

Julien Cohen-Adad

Daniel Razansky

Ruiqing Ni

Metabolism and bioenergetics in the central nervous system play important roles in the pathophysiology of Parkinson’s disease (PD). Here, … (voir plus)we employed a multimodal imaging approach to assess oxygenation changes in the spinal cord of a transgenic M83 murine model of PD in comparison to non-transgenic littermates at 9-12 months-of-age. A lower oxygen saturation (SO 2 ) SVOT was detected in vivo with spiral volumetric optoacoustic tomography (SVOT) in the spinal cord of M83 mice compared to non-transgenic littermate mice. Ex-vivo high-field T1-weighted magnetic resonance imaging (MRI) and immunostaining for alpha-synuclein (phospho-S129) and vascular organisation (CD31 and GLUT1) were used to investigate the nature of the abnormalities detected via in vivo imaging. Ex-vivo analysis showed that the vascular network in the spinal cord was not impaired in the spinal cord of M83 mice. Ex-vivo MRI assisted with deep learning-based automatic segmentation showed no volumetric atrophy in the spinal cord of M83 mice compared to non-transgenic littermates, whereas nuclear alpha-synuclein phosphorylated at Ser129 site could be linked to early pathology and metabolic dysfunction. The proposed and validated non-invasive high-resolution imaging tool to study oxygen saturation in the spinal cord of PD mice holds promise for assessing early changes preceding motor deficits in PD mice.

2024-04-28

bioRxiv (prépublication)

doi.org

Comparing LLM prompting with Cross-lingual transfer performance on Indigenous and Low-resource Brazilian Languages

David Ifeoluwa Adelani

A. Seza Doğruöz

Andr'e Coneglian

Atul Kr. Ojha

Large Language Models are transforming NLP for a variety of tasks. However, how LLMs perform NLP tasks for low-resource languages (LRLs) is … (voir plus)less explored. In line with the goals of the AmericasNLP workshop, we focus on 12 LRLs from Brazil, 2 LRLs from Africa and 2 high-resource languages (HRLs) (e.g., English and Brazilian Portuguese). Our results indicate that the LLMs perform worse for the part of speech (POS) labeling of LRLs in comparison to HRLs. We explain the reasons behind this failure and provide an error analysis through examples observed in our data set.

2024-04-27

ArXiv (prépublication)

doi.org

arxiv.org

EkoHate: Abusive Language and Hate Speech Detection for Code-switched Political Discussions on Nigerian Twitter

Comfort Eseohen Ilevbare

Jesujoba Oluwadara Alabi

David Ifeoluwa Adelani

Firdous Damilola Bakare

Oluwatoyin Bunmi Abiola

Oluwaseyi A. Adeyemo

Nigerians have a notable online presence and actively discuss political and topical matters. This was particularly evident throughout the 20… (voir plus)23 general election, where Twitter was used for campaigning, fact-checking and verification, and even positive and negative discourse. However, little or none has been done in the detection of abusive language and hate speech in Nigeria. In this paper, we curated code-switched Twitter data directed at three musketeers of the governorship election on the most populous and economically vibrant state in Nigeria; Lagos state, with the view to detect offensive speech in political discussions. We developed EkoHate -- an abusive language and hate speech dataset for political discussions between the three candidates and their followers using a binary (normal vs offensive) and fine-grained four-label annotation scheme. We analysed our dataset and provided an empirical evaluation of state-of-the-art methods across both supervised and cross-lingual transfer learning settings. In the supervised setting, our evaluation results in both binary and four-label annotation schemes show that we can achieve 95.1 and 70.3 F1 points respectively. Furthermore, we show that our dataset adequately transfers very well to three publicly available offensive datasets (OLID, HateUS2020, and FountaHate), generalizing to political discussions in other regions like the US.

2024-04-27

ArXiv (prépublication)

doi.org

arxiv.org

Contrast-agnostic Spinal Cord Segmentation: A Comparative Study of ConvNets and Vision Transformers

Enamundram Naga Karthik

Sandrine Bédard

Jan Valosek

A. Chandar

Julien Cohen-Adad

The cross-sectional area (CSA) of the spinal cord (SC) computed from its segmentation is a relevant clinical biomarker for the diagnosis and… (voir plus) monitoring of cord compression and atrophy. One key limitation of existing automatic methods is that their SC segmentations depend on the MRI contrast, resulting in different CSA across contrasts. Furthermore, these methods rely on CNNs, leaving a gap in the literature for exploring the performance of modern deep learning (DL) architectures. In this study, we extend our recent work \cite{Bdard2023TowardsCS} by evaluating the contrast-agnostic SC segmentation capabilities of different classes of DL architectures, namely, ConvNeXt, vision transformers (ViTs), and hierarchical ViTs. We compared 7 different DL models using the open-source \textit{Spine Generic} Database of healthy participants

2024-04-26

MIDL.io/2024/Short_Papers (accepté)

openreview.net

Human local field potentials in motor and non-motor brain areas encode upcoming movement direction.

Etienne Combrisson

Franck Di Rienzo

Anne-Lise Saive

Marcela Perrone-Bertolotti

Juan LP Soto

Philippe Kahane

Jean-Philippe Lachaux

Aymeric Guillot

Karim Jerbi CoCo Lab

2024-04-26

Communications Biology (publié)

doi.org

Discrete Probabilistic Inference as Control in Multi-path Environments

Nikolay Malkin

We consider the problem of sampling from a discrete and structured distribution as a sequential decision problem, where the objective is to … (voir plus)find a stochastic policy such that objects are sampled at the end of this sequential process proportionally to some predefined reward. While we could use maximum entropy Reinforcement Learning (MaxEnt RL) to solve this problem for some distributions, it has been shown that in general, the distribution over states induced by the optimal policy may be biased in cases where there are multiple ways to generate the same object. To address this issue, Generative Flow Networks (GFlowNets) learn a stochastic policy that samples objects proportionally to their reward by approximately enforcing a conservation of flows across the whole Markov Decision Process (MDP). In this paper, we extend recent methods correcting the reward in order to guarantee that the marginal distribution induced by the optimal MaxEnt RL policy is proportional to the original reward, regardless of the structure of the underlying MDP. We also prove that some flow-matching objectives found in the GFlowNet literature are in fact equivalent to well-established MaxEnt RL algorithms with a corrected reward. Finally, we study empirically the performance of multiple MaxEnt RL and GFlowNet algorithms on multiple problems involving sampling from discrete distributions.

2024-04-25

Conference on Uncertainty in Artificial Intelligence (poster)

doi.org

proceedings.mlr.press

Neural Active Learning Meets the Partial Monitoring Framework

Maxime Heuillet

Ola Ahmad

Audrey Durand

2024-04-25

auai.org/UAI/2024/Conference (poster)

doi.org

proceedings.mlr.press

Penalty weight tuning in high dose rate brachytherapy using multi-objective Bayesian optimization

Hossein Jafarzadeh

Majd Antaki

Ximeng Mao

Marie Duclos

Farhard Maleki

Shirin A Enger

Objective. Treatment plan optimization in high dose rate brachytherapy often requires manual fine-tuning of penalty weights for each objecti… (voir plus)ve, which can be time-consuming and dependent on the planner's experience. To automate this process, this study used a multi-criteria approach called multi-objective Bayesian optimization with q-noisy expected hypervolume improvement as its acquisition function (MOBO-qNEHVI). Approach. The treatment plans of 13 prostate cancer patients were retrospectively imported to a research treatment planning system, RapidBrachyMTPS, where fast mixed integer optimization (FMIO) performs dwell time optimization given a set of penalty weights to deliver 15 Gy to the target volume. MOBO-qNEHVI was used to find patient-specific Pareto optimal penalty weight vectors that yield clinically acceptable dose volume histogram metrics. The relationship between the number of MOBO-qNEHVI iterations and the number of clinically acceptable plans per patient (acceptance rate) was investigated. The performance time was obtained for various parameter configurations. Main results. MOBO-qNEHVI found clinically acceptable treatment plans for all patients. With increasing the number of MOBO-qNEHVI iterations, the acceptance rate grew logarithmically while the performance time grew exponentially. Fixing the penalty weight of the tumour volume to maximum value, adding the target dose as a parameter, initiating MOBO-qNEHVI with 25 parallel sampling of FMIO, and running 6 MOBO-qNEHVI iterations found solutions that delivered 15 Gy to the hottest 95% of the clinical target volume while respecting the dose constraints to the organs at risk. The average acceptance rate for each patient was 89.74% ± 8.11%, and performance time was 66.6 ± 12.6 s. The initiation took 22.47 ± 7.57 s, and each iteration took 7.35 ± 2.45 s to find one Pareto solution.Significance. MOBO-qNEHVI combined with FMIO can automatically explore the trade-offs between treatment plan objectives in a patient specific manner within a minute. This approach can reduce the dependency of plan quality on planner’s experience and reduce dose to the organs at risk.

2024-04-25

Physics in Medicine and Biology (publié)

doi.org

Autoregressive Networks with Dependent Edges

Jinyuan Chang

Qin Fang

Eric D. Kolaczyk

Peter W. MacDonald

Qiwei Yao

2024-04-23

ArXiv (prépublication)

arxiv.org