Elvis Dohmatob, Michael Eickenberg, B. Thirion, G. Varoquaux
{"title":"Speeding-Up Model-Selection in Graphnet via Early-Stopping and Univariate Feature-Screening","authors":"Elvis Dohmatob, Michael Eickenberg, B. Thirion, G. Varoquaux","doi":"10.1109/PRNI.2015.19","DOIUrl":"https://doi.org/10.1109/PRNI.2015.19","url":null,"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.","PeriodicalId":380902,"journal":{"name":"2015 International Workshop on Pattern Recognition in NeuroImaging","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129108977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Nikolaidis, Drew Goatz, P. Smaragdis, A. Kramer
{"title":"Predicting Skill-Based Task Performance and Learning with fMRI Motor and Subcortical Network Connectivity","authors":"A. Nikolaidis, Drew Goatz, P. Smaragdis, A. Kramer","doi":"10.1109/PRNI.2015.35","DOIUrl":"https://doi.org/10.1109/PRNI.2015.35","url":null,"abstract":"Procedural learning is the process of skill acquisition that is regulated by the basal ganglia, and this learning becomes automated over time through cortico-striatal and cortico-cortical connectivity. In the current study, we use a common machine learning regression technique to investigate how fMRI network connectivity in the subcortical and motor networks are able to predict initial performance and traininginduced improvement in a skill-based cognitive training game, Space Fortress, and how these predictions interact with the strategy the trainees were given during training. To explore the reliability and validity of our findings, we use a range of regression lambda values, sizes of model complexity, and connectivity measurements.","PeriodicalId":380902,"journal":{"name":"2015 International Workshop on Pattern Recognition in NeuroImaging","volume":"61 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117330029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Predicting Numerical Processing in Naturalistic Settings from Controlled Experimental Conditions","authors":"J. Schrouff, C. Phillips, J. Parvizi, J. Miranda","doi":"10.1109/PRNI.2015.13","DOIUrl":"https://doi.org/10.1109/PRNI.2015.13","url":null,"abstract":"Machine learning research is interested in building models based on a training set that can then be applied to new data, whether this unseen data comes from new examples (e.g. New subjects, other tasks) or new features (e.g. Different modalities). In this work, we present a simple approach to transfer learning using intracranial EEG (also known as electrocorticographic, ECoG) data from three patients. More specifically, we aimed at detecting numerical processing during naturalistic settings based on a model trained with controlled experimental conditions. Our results showed significant prediction accuracy of numerical events in naturalistic settings when considering a priori knowledge of the target task.","PeriodicalId":380902,"journal":{"name":"2015 International Workshop on Pattern Recognition in NeuroImaging","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129520795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. Monteiro, A. Rao, J. Ashburner, J. Shawe-Taylor, J. Miranda
{"title":"Multivariate Effect Ranking via Adaptive Sparse PLS","authors":"J. Monteiro, A. Rao, J. Ashburner, J. Shawe-Taylor, J. Miranda","doi":"10.1109/PRNI.2015.27","DOIUrl":"https://doi.org/10.1109/PRNI.2015.27","url":null,"abstract":"Unsupervised learning approaches, such as Sparse Partial Least Squares (SPLS), may provide useful insights into the brain mechanisms by finding relationships between two sets of variables (i.e. Views) from the same subjects. The algorithm outputs two sets of paired weight vectors, where each pair expresses an \"effect\" between both views. However, each effect can be described by a different number of variables. In this paper, we propose a novel approach to find multivariate associations between combinations of clinical/behavioural variables and brain voxels/regions which provides an unique solution with different levels of sparsity per weight vector pair. The effects described by the weight vector pairs are ranked by how much data covariance they explain. The proposed method was able to find statistically significant effects or relationships in a dementia dataset between clinical/demographic information and brain scans. Its adaptive nature allowed not only to determine an optimal sparse solution, but also provided the flexibility to select the adequate number of clinical/demographic variables and voxels to describe each effect, which enabled it to distinguish the effects associated with age from the ones associated with dementia.","PeriodicalId":380902,"journal":{"name":"2015 International Workshop on Pattern Recognition in NeuroImaging","volume":"47 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122686819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andrés Hoyos Idrobo, Y. Schwartz, G. Varoquaux, B. Thirion
{"title":"Improving Sparse Recovery on Structured Images with Bagged Clustering","authors":"Andrés Hoyos Idrobo, Y. Schwartz, G. Varoquaux, B. Thirion","doi":"10.1109/PRNI.2015.30","DOIUrl":"https://doi.org/10.1109/PRNI.2015.30","url":null,"abstract":"The identification of image regions associated with external variables through discriminative approaches yields ill-posed estimation problems. This estimation challenge can be tackled by imposing sparse solutions. However, the sensitivity of sparse estimators to correlated variables leads to non-reproducible results, and only a subset of the important variables are selected. In this paper, we explore an approach based on bagging clustering-based data compression in order to alleviate the instability of sparse models. Specifically, we design a new framework in which the estimator is built by averaging multiple models estimated after feature clustering, to improve the conditioning of the model. We show that this combination of model averaging with spatially consistent compression can have the virtuous effect of increasing the stability of the weight maps, allowing a better interpretation of the results. Finally, we demonstrate the benefit of our approach on several predictive modeling problems.","PeriodicalId":380902,"journal":{"name":"2015 International Workshop on Pattern Recognition in NeuroImaging","volume":"54 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123113195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Variational Physiologically Informed Solution to Hemodynamic and Perfusion Response Estimation from ASL fMRI Data","authors":"Aina Frau-Pascual, F. Forbes, P. Ciuciu","doi":"10.1109/PRNI.2015.12","DOIUrl":"https://doi.org/10.1109/PRNI.2015.12","url":null,"abstract":"Functional Arterial Spin Labeling (fASL) MRI can provide a quantitative measurement of cerebral blood flow. A joint detection-estimation (JDE) framework has been considered to extract task-related perfusion and hemodynamic responses not restricted to canonical response function shapes. In this work, we provide a variational expectation-maximization (VEM) algorithm for hemodynamic and perfusion responses estimation. This approach provides a lower computational load compared to previous attempts, and facilitates the incorporation of prior knowledge and constraints in the estimation. Validation on simulated and real data sets has been performed.","PeriodicalId":380902,"journal":{"name":"2015 International Workshop on Pattern Recognition in NeuroImaging","volume":"369 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122834969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yuhong Li, Q. Dou, Jinze Yu, F. Jia, Jing Qin, P. Heng
{"title":"Automatic Brain Tumor Segmentation from MR Images via a Multimodal Sparse Coding Based Probabilistic Model","authors":"Yuhong Li, Q. Dou, Jinze Yu, F. Jia, Jing Qin, P. Heng","doi":"10.1109/PRNI.2015.18","DOIUrl":"https://doi.org/10.1109/PRNI.2015.18","url":null,"abstract":"Accurate segmentation of brain tumor from MR image is crucial for the diagnosis and treatment of brain cancer. We propose a novel automated brain tumor segmentation method based on a probabilistic model combining sparse coding and Markov random field (MRF). We formulate the brain tumor segmentation task as a pixel-wise labeling problem with regard to three classes: tumor, edema and healthy issue. For each class, dictionary learning is performed independently on multi-modality gray scale patches. Sparse representation is then extracted based on a joint dictionary which is constructed by combing the three independent dictionaries. Finally, we build the probabilistic model aiming to estimate maximum a posterior (MAP) probability by introducing the sparse representation into likelihood probability and prior probability using the Markov random field (MRF) assumption. Compared with traditional methods, which employed hand-crafted low level features to construct the probabilistic model, our model can better represent the characteristics of a pixel and its relation with neighbors based on the sparse coefficients obtained from the learned dictionary. We validated our method on the MICAAI 2012 BRATS challenge brain MRI dataset and achieved comparable or better results compared with state-of the-art methods.","PeriodicalId":380902,"journal":{"name":"2015 International Workshop on Pattern Recognition in NeuroImaging","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132612358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Modeling Voxel Connectivity for Brain Decoding","authors":"Itir Önal, M. Ozay, F. Yarman-Vural","doi":"10.1109/PRNI.2015.26","DOIUrl":"https://doi.org/10.1109/PRNI.2015.26","url":null,"abstract":"The massively dynamic nature of human brain cannot be represented by considering only a collection of voxel intensity values obtained from fMRI measurements. It has been observed that the degree of connectivity among voxels provide important information for modeling cognitive activities. Moreover, spatially close voxels act together to generate similar BOLD responses to the same stimuli. In this study, we propose a local mesh model, called Local Mesh Model with Temporal Measurements (LMM-TM), to first estimate spatial relationship among a set of voxels using spatial and temporal data measured at each voxel, and then employ the relationship for the construction of a connectivity model for brain decoding. For this purpose, we first construct a local mesh around each voxel (called seed voxel) by connecting it to its spatially nearest neighbors. Then, we represent the BOLD response of each seed voxel in terms of linear combination of the BOLD responses of its p-nearest neighbors. The relationship between a seed voxel and its neighbors is estimated by solving a linear regression problem. The estimated mesh arc weights are used to model local connectivity among the voxels that reside in a spatial neighborhood. Using these weights as features, we train Support Vector Machines and k-Nearest Neighbor classifiers. We test our model on a visual object recognition experiment. In the experimental analysis, we observe that classifiers that employ our features perform better than classifiers that employ raw voxel intensity values, local mesh model weights and features extracted using distance metrics such as Euclidean distance, cosine similarity and Pearson correlation.","PeriodicalId":380902,"journal":{"name":"2015 International Workshop on Pattern Recognition in NeuroImaging","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131141967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Bayesian Test for Comparing Classifier Errors","authors":"E. Olivetti, Dirk Bernhardt-Walther","doi":"10.1109/PRNI.2015.11","DOIUrl":"https://doi.org/10.1109/PRNI.2015.11","url":null,"abstract":"Multi-class classification algorithms have become an important tool for the analysis of neuroimaging data. Classification errors contain potentially important information that often goes unreported. It is therefore desirable to quantitatively compare patterns of errors between different experimental conditions. Here we present a Bayesian test that is based on comparing evidence in favor of two competing hypotheses, one stating dependence and one stating independence of two given error patterns. We derive analytical solutions for the likelihoods of both hypotheses. We compare the results from our new test with two other methods of comparing error patterns using data from an fMRI experiment and we substantiate reasons for adopting our proposal and for future work.","PeriodicalId":380902,"journal":{"name":"2015 International Workshop on Pattern Recognition in NeuroImaging","volume":"88 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133909456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alex F. Mendelson, Maria A. Zuluaga, B. Hutton, S. Ourselin
{"title":"Bolstering Heuristics for Statistical Validation of Prediction Algorithms","authors":"Alex F. Mendelson, Maria A. Zuluaga, B. Hutton, S. Ourselin","doi":"10.1109/PRNI.2015.16","DOIUrl":"https://doi.org/10.1109/PRNI.2015.16","url":null,"abstract":"Machine learning research in image-based computer aided diagnosis is a field characterised by rich models and relatively small datasets. In this regime, conventional statistical tests for cross validation results may no longer be optimal due to variability in training set quality. We present a principle by which existing statistical tests can be conservatively extended to make use of arbitrary numbers of repeated experiments. We apply this to the problems of interval estimation and pair wise comparison for the accuracy of classification algorithms, and test the resulting procedures on real and synthetic classification tasks. The interval coverages in the synthetic task are notably improved, and the comparison has both increased power and reduced type I error. Experiments in the ADNI dataset show that the low replicability of split-half based tests can be dramatically improved.","PeriodicalId":380902,"journal":{"name":"2015 International Workshop on Pattern Recognition in NeuroImaging","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130753197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}