Multi-Channel Stochastic Variational Inference for the Joint Analysis of Heterogeneous Biomedical Data in Alzheimer's Disease

International audienceThe joint analysis of biomedical data in Alzheimer's Disease (AD) is important for better clinical diagnosis and to understand the relationship between biomarkers. However, jointly accounting for heterogeneous measures poses important challenges related to the modeling of heterogeneity and to the interpretability of the results. These issues are here addressed by proposing a novel multi-channel stochastic generative model. We assume that a latent variable generates the data observed through different channels (e.g., clinical scores, imaging) and we describe an efficient way to estimate jointly the distribution of the latent variable and the data generative process. Experiments on synthetic data show that the multi-channel formulation allows superior data reconstruction as opposed to the single channel one. Moreover, the derived lower bound of the model evidence represents a promising model selection criterion. Experiments on AD data show that the model parameters can be used for unsupervised patient stratification and for the joint interpretation of the heterogeneous observations. Because of its general and flexible formulation , we believe that the proposed method can find various applications as a general data fusion technique

Sparse Multi-Channel Variational Autoencoder for the Joint Analysis of Heterogeneous Data

International audienceInterpretable modeling of heterogeneous data channels is essential in medical applications, for example when jointly analyzing clinical scores and medical images. Variational Autoencoders (VAE) are powerful generative models that learn representations of complex data. The flexibility of VAE may come at the expense of lack of interpretability in describing the joint relationship between heterogeneous data. To tackle this problem, in this work we extend the variational framework of VAE to bring parsimony and inter-pretability when jointly account for latent relationships across multiple channels. In the latent space, this is achieved by constraining the varia-tional distribution of each channel to a common target prior. Parsimonious latent representations are enforced by variational dropout. Experiments on synthetic data show that our model correctly identifies the prescribed latent dimensions and data relationships across multiple testing scenarios. When applied to imaging and clinical data, our method allows to identify the joint effect of age and pathology in describing clinical condition in a large scale clinical cohort

Sparse Multi-Channel Variational Autoencoder for the Joint Analysis of Heterogeneous Data

International audienceInterpretable modeling of heterogeneous data channels is essential in medical applications, for example when jointly analyzing clinical scores and medical images. Variational Autoencoders (VAE) are powerful generative models that learn representations of complex data. The flexibility of VAE may come at the expense of lack of interpretability in describing the joint relationship between heterogeneous data. To tackle this problem, in this work we extend the variational framework of VAE to bring parsimony and inter-pretability when jointly account for latent relationships across multiple channels. In the latent space, this is achieved by constraining the varia-tional distribution of each channel to a common target prior. Parsimonious latent representations are enforced by variational dropout. Experiments on synthetic data show that our model correctly identifies the prescribed latent dimensions and data relationships across multiple testing scenarios. When applied to imaging and clinical data, our method allows to identify the joint effect of age and pathology in describing clinical condition in a large scale clinical cohort

Supplementary Material of the paper: "Multi-Channel Stochastic Variational Inference for the Joint Analysis of Heterogeneous Biomedical Data in Alzheimer's Disease"

Supplementary Material of the paper: "Multi-Channel Stochastic Variational Inference for the Joint Analysis of Heterogeneous Biomedical Data in Alzheimer's Disease". Paper accepted at the 1st International Workshop on Machine Learning in Clinical Neuroimaging, in conjunction with MICCAI 2018, September 20, Granada (Spain

Deficits in naming pictures of objects are associated with glioma infiltration of the inferior longitudinal fasciculus: A study with diffusion MRI tractography, volumetric MRI, and neuropsychology

It has been suggested that the inferior longitudinal fasciculus (ILF) may play an important role in several aspects of language processing such as visual object recognition, visual memory, lexical retrieval, reading, and specifically, in naming visual stimuli. In particular, the ILF appears to convey visual information from the occipital lobe to the anterior temporal lobe (ATL). However, direct evidence proving the essential role of the ILF in language and semantics remains limited and controversial. The first aim of this study was to prove that patients with a brain glioma damaging the left ILF would be selectively impaired in picture naming of objects; the second aim was to prove that patients with glioma infiltrating the ATL would not be impaired due to functional reorganization of the lexical retrieval network elicited by the tumor. We evaluated 48 right-handed patients with neuropsychological testing and magnetic resonance imaging (MRI) before and after surgery for resection of a glioma infiltrating aspects of the left temporal, occipital, and/or parietal lobes; diffusion tensor imaging (DTI) was acquired preoperatively in all patients. Damage to the ILF, inferior frontal occipital fasciculus (IFOF), uncinate fasciculus (UF), arcuate fasciculus (AF), and associated cortical regions was assessed by means of preoperative tractography and pre-/pos-toperative MRI volumetry. The association of fascicles damage with patients' performance in picture naming and three additional cognitive tasks, namely, verbal fluency (two verbal non-visual tasks) and the Trail Making Test (a visual attentional task), was evaluated. Nine patients were impaired in the naming test before surgery. ILF damage was demonstrated with tractography in six (67%) of these patients. The odds of having an ILF damage was 6.35 (95% CI: 1.27-34.92) times higher among patients with naming deficit than among those without it. The ILF was the only fascicle to be significantly associated with naming deficit when all the fascicles were considered together, achieving an adjusted odds ratio of 15.73 (95% CI: 2.30-178.16, p = .010). Tumor infiltration of temporal and occipital cortices did not contribute to increase the odd of having a naming deficit. ILF damage was found to be selectively associated with picture naming deficit and not with lexical retrieval assessed by means of verbal fluency. Early after surgery, 29 patients were impaired in naming objects. The association of naming deficit with percentage of ILF resection (assessed by 3D-MRI) was confirmed (beta = -56.78 ± 20.34, p = .008) through a robust multiple linear regression model; no significant association was found with damage of IFOF, UF or AF. Crucially, postoperative neuropsychological evaluation showed that naming scores of patients with tumor infiltration of the anterior temporal cortex were not significantly associated with the percentage of ILF damage (rho = .180, p > .999), while such association was significant in patients without ATL infiltration (rho = -.556, p = .004). The ILF is selectively involved in picture naming of objects; however, the naming deficits are less severe in patients with glioma infiltration of the ATL probably due to release of an alternative route that may involve the posterior segment of the AF. The left ILF, connecting the extrastriatal visual cortex to the anterior region of the temporal lobe, is crucial for lexical retrieval on visual stimulus, such as in picture naming. However, when the ATL is also damaged, an alternative route is released and the performance improves

Prevalence of lack of interest and anhedonia in the general population of the UK Biobank

International audienc

Combining Multi-Task Learning and Multi-Channel Variational Auto-Encoders to Exploit Datasets with Missing Observations -Application to Multi-Modal Neuroimaging Studies in Dementia

The joint modeling of neuroimaging data across multiple datasets requires to consistently analyze high-dimensional and heterogeneous information in presence of often non-overlapping sets of views across data samples (e.g. imaging data, clinical scores, biological measurements). This analysis is associated with the problem of missing information across datasets, which can happen in two forms: missing at random (MAR), when the absence of a view is unpredictable and does not depend on the dataset (e.g. due to data corruption); missing not at random (MNAR), when a specific view is absent by design for a specific dataset. In order to take advantage of the increased variability and sample size when pooling together observations from many cohorts and at the same time cope with the ubiquitous problem of missing information, we propose here a multi-task generative latent-variable model where the common variability across datasets stems from the estimation of a shared latent representation across views. Our formulation allows to retrieve a consistent latent representation common to all views and datasets, even in the presence of missing information. Simulations on synthetic data show that our method is able to identify a common latent representation of multi-view datasets, even when the compatibility across datasets is minimal. When jointly analyzing multi-modal neuroimaging and clinical data from real independent dementia studies, our model is able to mitigate the absence of modalities without having to discard any available information. Moreover, the common latent representation inferred with our model can be used to define robust classifiers gathering the combined information across different datasets. To conclude, both on synthetic and real data experiments, our model compared favorably to state of the art benchmark methods, providing a more powerful exploitation of multi-modal observations with missing views

Clinical and dopaminergic imaging characteristics of the FARPRESTO cohort of trial-ready idiopathic rapid eye movement sleep behavior patients

Introduction: Idiopathic/isolated rapid eye movement (REM) sleep behavior disorder (iRBD) is considered the prodromal stage of alpha-synucleinopathies. Thus, iRBD patients are the ideal target for disease-modifying therapy. The risk FActoRs PREdictive of phenoconversion in iRBD Italian STudy (FARPRESTO) is an ongoing Italian database aimed at identifying risk factors of phenoconversion, and eventually to ease clinical trial enrollment of well-characterized subjects.Methods: Polysomnography-confirmed iRBD patients were retrospectively and prospectively enrolled. Baseline harmonized clinical and nigrostriatal functioning data were collected at baseline. Nigrostriatal functioning was evaluated by dopamine transporter-single-photon emission computed tomography (DaT-SPECT) and categorized with visual semi-quantification. Longitudinal data were evaluated to assess phenoconversion. Cox regressions were applied to calculate hazard ratios.Results: 365 patients were enrolled, and 289 patients with follow-up (age 67.7 & PLUSMN; 7.3 years, 237 males, mean follow-up 40 & PLUSMN; 37 months) were included in this study. At follow-up, 97 iRBD patients (33.6%) phenoconverted to an overt synucleinopathy. Older age, motor and cognitive impairment, constipation, urinary and sexual dysfunction, depression, and visual semi-quantification of nigrostriatal functioning predicted phenoconversion. The remaining 268 patients are in follow-up within the FARPRESTO project.Conclusions: Clinical data (older age, motor and cognitive impairment, constipation, urinary and sexual dysfunction, depression) predicted phenoconversion in this multicenter, longitudinal, observational study. A standardized visual approach for semi-quantification of DaT-SPECT is proposed as a practical risk factor for phenoconversion in iRBD patients. Of note, non-converted and newly diagnosed iRBD patients, who represent a trial-ready cohort for upcoming disease-modification trials, are currently being enrolled and followed in the FARPRESTO study. New data are expected to allow better risk characterization

The dementia-associated APOE ε4 allele is not associated with rapid eye movement sleep behavior disorder

The present study aimed to examine whether the APOE ε4 allele, associated with dementia with Lewy bodies (DLB), and possibly with dementia in Parkinson's disease (PD), is also associated with idiopathic rapid eye movement sleep behavior disorder (RBD). Two single nucleotide polymorphisms, rs429358 and rs7412, were genotyped in RBD patients (n = 480) and in controls (n = 823). APOE ε4 allele frequency was 0.14 among RBD patients and 0.13 among controls (OR = 1.11, 95% CI: 0.88-1.40, p = 0.41). APOE ε4 allele frequencies were similar in those who converted to DLB (0.14) and those who converted to Parkinson's disease (0.12) or multiple system atrophy (0.14, p = 1.0). The APOE ε4 allele is neither a risk factor for RBD nor it is associated with conversion from RBD to DLB or other synucleinopathies

GBA variants in REM sleep behavior disorder: a multicenter study

To study the role of GBA variants in the risk for isolated rapid-eye-movement (REM)-sleep behavior disorder (iRBD) and conversion to overt neurodegeneration