Bertrand Thirion

Bio: Bertrand Thirion is an academic researcher from Université Paris-Saclay. The author has contributed to research in topics: Cluster analysis & Cognition. The author has an hindex of 51, co-authored 311 publications receiving 73839 citations. Previous affiliations of Bertrand Thirion include French Institute for Research in Computer Science and Automation & French Institute of Health and Medical Research.

Compressed Online Dictionary Learning for Fast fMRI Decomposition

Abstract: We present a method for fast resting-state fMRI spatial decomposi-tions of very large datasets, based on the reduction of the temporal dimension before applying dictionary learning on concatenated individual records from groups of subjects. Introducing a measure of correspondence between spatial decompositions of rest fMRI, we demonstrates that time-reduced dictionary learning produces result as reliable as non-reduced decompositions. We also show that this reduction significantly improves computational scalability.

Extracting representations of cognition across neuroimaging studies improves brain decoding

Abstract: Cognitive brain imaging is accumulating datasets about the neural substrate of many different mental processes. Yet, most studies are based on few subjects and have low statistical power. Analyzing data across studies could bring more statistical power; yet the current brain-imaging analytic framework cannot be used at scale as it requires casting all cognitive tasks in a unified theoretical framework. We introduce a new methodology to analyze brain responses across tasks without a joint model of the psychological processes. The method boosts statistical power in small studies with specific cognitive focus by analyzing them jointly with large studies that probe less focal mental processes. Our approach improves decoding performance for 80% of 35 widely-different functional-imaging studies. It finds commonalities across tasks in a data-driven way, via common brain representations that predict mental processes. These are brain networks tuned to psychological manipulations. They outline interpretable and plausible brain structures. The extracted networks have been made available; they can be readily reused in new neuro-imaging studies. We provide a multi-study decoding tool to adapt to new data.

Neural Language Models are not Born Equal to Fit Brain Data, but Training Helps

Abstract: Neural Language Models (NLMs) have made tremendous advances during the last years, achieving impressive performance on various linguistic tasks. Capitalizing on this, studies in neuroscience have started to use NLMs to study neural activity in the human brain during language processing. However, many questions remain unan-swered regarding which factors determine the ability of a neural language model to capture brain activity (aka its ’brain score’). Here, we make first steps in this direction and examine the impact of test loss, training corpus and model architecture (comparing GloVe, LSTM, GPT-2 and BERT), on the prediction of functional Magnetic Resonance Imaging timecourses of participants listening to an audiobook. We find that (1) untrained versions of each model already explain significant amount of signal in the brain by capturing similarity in brain responses across identical words, with the untrained LSTM outperforming the transformer-based models, being less impacted by the effect of context; (2) that training NLP models improves brain scores in the same brain regions irrespective of the model’s architecture; (3) that Perplexity (test loss) is not a good predictor of brain score; (4) that training data have a strong influence on the outcome and, notably, that off-the-shelf models may lack statistical power to detect brain activations. Overall, we outline the impact of model-training choices, and suggest good practices for future studies aiming at explaining the human language system using neural language models.

Inference of a HARDI fiber bundle atlas using a two-level clustering strategy

Abstract: This paper presents a method inferring a model of the brain white matter organisation from HARDI tractography results computed for a group of subjects. This model is made up of a set of generic fiber bundles that can be detected in most of the population. Our approach is based on a two-level clustering strategy. The first level is a multiresolution intra-subject clustering of the million tracts that are computed for each brain. This analysis reduces the complexity of the data to a few thousands fiber bundles for each subject. The second level is an intersubject clustering over fiber bundle centroids from all the subjects using a pairwise distance computed after spatial normalization. The resulting model includes the large bundles of anatomical literature and about 20 U-fiber bundles in each hemisphere.

Speeding-Up Model-Selection in Graphnet via Early-Stopping and Univariate Feature-Screening

Abstract: The Graph Net (aka S-Lasso), as well as other "spar-sity + structure" priors like TV-L1, are not easily applicable to brain data because of technical problems concerning the selection of the regularization parameters. Also, in their own right, such models lead to challenging high-dimensional optimization problems. In this manuscript, we present some heuristics for speeding up the overall optimization process: (a) Early-stopping, whereby one halts the optimization process when the test score(performance on left out data) for the internal cross validation for model-selection stops improving, and (b) univariate feature-screening, whereby irrelevant (non-predictive) voxels are detected and eliminated before the optimization problem is entered, thus reducing the size of the problem. Empirical results with Graph Net on real MRI (Magnetic Resonance Imaging) datasets indicate that these heuristics are a win-win strategy, as they add speed without sacrificing the quality of the predictions. We expect the proposed heuristics to work on other models like TV-L1, etc.

Scikit-learn: Machine Learning in Python

Abstract: Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from http://scikit-learn.sourceforge.net.

Scikit-learn: Machine Learning in Python

Abstract: Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems. This package focuses on bringing machine learning to non-specialists using a general-purpose high-level language. Emphasis is put on ease of use, performance, documentation, and API consistency. It has minimal dependencies and is distributed under the simplified BSD license, encouraging its use in both academic and commercial settings. Source code, binaries, and documentation can be downloaded from this http URL.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

XGBoost: A Scalable Tree Boosting System

Abstract: Tree boosting is a highly effective and widely used machine learning method. In this paper, we describe a scalable end-to-end tree boosting system called XGBoost, which is used widely by data scientists to achieve state-of-the-art results on many machine learning challenges. We propose a novel sparsity-aware algorithm for sparse data and weighted quantile sketch for approximate tree learning. More importantly, we provide insights on cache access patterns, data compression and sharding to build a scalable tree boosting system. By combining these insights, XGBoost scales beyond billions of examples using far fewer resources than existing systems.

XGBoost: A Scalable Tree Boosting System

Abstract: Tree boosting is a highly effective and widely used machine learning method. In this paper, we describe a scalable end-to-end tree boosting system called XGBoost, which is used widely by data scientists to achieve state-of-the-art results on many machine learning challenges. We propose a novel sparsity-aware algorithm for sparse data and weighted quantile sketch for approximate tree learning. More importantly, we provide insights on cache access patterns, data compression and sharding to build a scalable tree boosting system. By combining these insights, XGBoost scales beyond billions of examples using far fewer resources than existing systems.