700 research outputs found
Tensor Analysis and Fusion of Multimodal Brain Images
Current high-throughput data acquisition technologies probe dynamical systems
with different imaging modalities, generating massive data sets at different
spatial and temporal resolutions posing challenging problems in multimodal data
fusion. A case in point is the attempt to parse out the brain structures and
networks that underpin human cognitive processes by analysis of different
neuroimaging modalities (functional MRI, EEG, NIRS etc.). We emphasize that the
multimodal, multi-scale nature of neuroimaging data is well reflected by a
multi-way (tensor) structure where the underlying processes can be summarized
by a relatively small number of components or "atoms". We introduce
Markov-Penrose diagrams - an integration of Bayesian DAG and tensor network
notation in order to analyze these models. These diagrams not only clarify
matrix and tensor EEG and fMRI time/frequency analysis and inverse problems,
but also help understand multimodal fusion via Multiway Partial Least Squares
and Coupled Matrix-Tensor Factorization. We show here, for the first time, that
Granger causal analysis of brain networks is a tensor regression problem, thus
allowing the atomic decomposition of brain networks. Analysis of EEG and fMRI
recordings shows the potential of the methods and suggests their use in other
scientific domains.Comment: 23 pages, 15 figures, submitted to Proceedings of the IEE
3d Face Reconstruction And Emotion Analytics With Part-Based Morphable Models
3D face reconstruction and facial expression analytics using 3D facial data are new
and hot research topics in computer graphics and computer vision. In this proposal, we first
review the background knowledge for emotion analytics using 3D morphable face model, including
geometry feature-based methods, statistic model-based methods and more advanced
deep learning-bade methods. Then, we introduce a novel 3D face modeling and reconstruction
solution that robustly and accurately acquires 3D face models from a couple of images
captured by a single smartphone camera. Two selfie photos of a subject taken from the
front and side are used to guide our Non-Negative Matrix Factorization (NMF) induced
part-based face model to iteratively reconstruct an initial 3D face of the subject. Then, an
iterative detail updating method is applied to the initial generated 3D face to reconstruct
facial details through optimizing lighting parameters and local depths. Our iterative 3D
face reconstruction method permits fully automatic registration of a part-based face representation
to the acquired face data and the detailed 2D/3D features to build a high-quality
3D face model. The NMF part-based face representation learned from a 3D face database
facilitates effective global and adaptive local detail data fitting alternatively. Our system
is flexible and it allows users to conduct the capture in any uncontrolled environment. We
demonstrate the capability of our method by allowing users to capture and reconstruct their
3D faces by themselves.
Based on the 3D face model reconstruction, we can analyze the facial expression and
the related emotion in 3D space. We present a novel approach to analyze the facial expressions
from images and a quantitative information visualization scheme for exploring this
type of visual data. From the reconstructed result using NMF part-based morphable 3D face
model, basis parameters and a displacement map are extracted as features for facial emotion
analysis and visualization. Based upon the features, two Support Vector Regressions (SVRs)
are trained to determine the fuzzy Valence-Arousal (VA) values to quantify the emotions.
The continuously changing emotion status can be intuitively analyzed by visualizing the
VA values in VA-space. Our emotion analysis and visualization system, based on 3D NMF
morphable face model, detects expressions robustly from various head poses, face sizes and
lighting conditions, and is fully automatic to compute the VA values from images or a sequence
of video with various facial expressions. To evaluate our novel method, we test our
system on publicly available databases and evaluate the emotion analysis and visualization
results. We also apply our method to quantifying emotion changes during motivational interviews.
These experiments and applications demonstrate effectiveness and accuracy of
our method.
In order to improve the expression recognition accuracy, we present a facial expression
recognition approach with 3D Mesh Convolutional Neural Network (3DMCNN) and a visual
analytics guided 3DMCNN design and optimization scheme. The geometric properties of the
surface is computed using the 3D face model of a subject with facial expressions. Instead of
using regular Convolutional Neural Network (CNN) to learn intensities of the facial images,
we convolve the geometric properties on the surface of the 3D model using 3DMCNN. We
design a geodesic distance-based convolution method to overcome the difficulties raised from
the irregular sampling of the face surface mesh. We further present an interactive visual
analytics for the purpose of designing and modifying the networks to analyze the learned
features and cluster similar nodes in 3DMCNN. By removing low activity nodes in the network,
the performance of the network is greatly improved. We compare our method with the regular CNN-based method by interactively visualizing each layer of the networks and
analyze the effectiveness of our method by studying representative cases. Testing on public
datasets, our method achieves a higher recognition accuracy than traditional image-based
CNN and other 3D CNNs. The presented framework, including 3DMCNN and interactive
visual analytics of the CNN, can be extended to other applications
Matrix and tensor comparisons of genomic profiles to predict cancer survival and drug targets
disseratationDespite recent large-scale profiling efforts, the best predictor of a glioblastoma (GBM) brain cancer patient's survival remains the patient's age at diagnosis. The best predictor of an ovarian serous cystadenocarcinoma (OV) patient's survival remains the tumor's stage, an assessment - numbering I to IV - of the spread of the cancer. To identify DNA copy-number alterations (CNAs) that might predict GBM or OV patients' survival, we comparatively modeled matched genomic profiles from The Cancer Genome Atlas (TCGA). Generalized singular value decomposition (GSVD) of patient-matched but probe- independent GBM and normal profiles uncovered a previously unknown global pattern of tumor-exclusive co-occurring CNAs that is correlated, and possibly causally related to, GBM patients' survival and response to chemotherapy. This suggests that the GBM survival phenotype is an outcome of its global genotype. The GSVD, formulated as a framework for comparatively modeling two composite datasets, removes from the pattern variations that occur in the normal human genome (e.g., female-specific X chromosome amplification) and experimental variations, without a-priori knowledge of these variations. The pattern is independent of age, and combined with age, makes a better predictor than age alone. The pattern suggests previously unrecognized targets for personalized GBM drug therapy, the kinase TLK2 and the methyltransferase METTL2A. A novel tensor GSVD of patient- and platform-matched OV and normal genomic profiles revealed multiple chromosome arm-wide patterns of CNAs that are correlated with OV patients' survival. These indicate several, previously unrecognized, subtypes of OV. The tensor GSVD is an exact simultaneous decomposition of two high-dimensional datasets arranged in higher-order tensors. The tensor GSVD generalizes the GSVD, which is limited to two second-order tensors, i.e., matrices. The chromosome arm-wide patterns of CNAs are independent of the OV tumor stage. Combined with stage, each of the patterns makes a better predictor than stage alone. We conclude that the GSVD and the novel tensor GSVD can uncover the relations, and possibly causal coordinations, between different recorded aspects of the same medical phenomenon. GSVD and tensor GSVD comparisons can be used to determine one patient's medical status in relation to other patients in a set, and inform the patient's prognosis, and possibly also treatment
Statistical Techniques for Exploratory Analysis of Structured Three-Way and Dynamic Network Data.
In this thesis, I develop different techniques for the pattern
extraction and visual exploration of a collection of data matrices.
Specifically, I present methods to help home in on and visualize an
underlying structure and its evolution over ordered (e.g., time) or
unordered (e.g., experimental conditions) index sets. The first part
of the thesis introduces a biclustering technique for such three
dimensional data arrays. This technique is capable of discovering
potentially overlapping groups of samples and variables that evolve
similarly with respect to a subset of conditions. To facilitate and
enhance visual exploration, I introduce a framework that utilizes
kernel smoothing to guide the estimation of bicluster responses over
the array. In the second part of the thesis, I introduce two matrix
factorization models. The first is a data integration model that
decomposes the data into two factors: a basis common to all data
matrices, and a coefficient matrix that varies for each data matrix.
The second model is meant for visual clustering of nodes in dynamic
network data, which often contains complex evolving structure. Hence,
this approach is more flexible and additionally lets the basis evolve
for each matrix in the array. Both models utilize a regularization
within the framework of non-negative matrix factorization to encourage
local smoothness of the basis and coefficient matrices, which improves
interpretability and highlights the structural patterns underlying the
data, while mitigating noise effects. I also address computational
aspects of applying regularized non-negative matrix factorization
models to large data arrays by presenting multiple algorithms,
including an approximation algorithm based on alternating least
squares.PhDStatisticsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/99838/1/smankad_1.pd
Modern Views of Machine Learning for Precision Psychiatry
In light of the NIMH's Research Domain Criteria (RDoC), the advent of
functional neuroimaging, novel technologies and methods provide new
opportunities to develop precise and personalized prognosis and diagnosis of
mental disorders. Machine learning (ML) and artificial intelligence (AI)
technologies are playing an increasingly critical role in the new era of
precision psychiatry. Combining ML/AI with neuromodulation technologies can
potentially provide explainable solutions in clinical practice and effective
therapeutic treatment. Advanced wearable and mobile technologies also call for
the new role of ML/AI for digital phenotyping in mobile mental health. In this
review, we provide a comprehensive review of the ML methodologies and
applications by combining neuroimaging, neuromodulation, and advanced mobile
technologies in psychiatry practice. Additionally, we review the role of ML in
molecular phenotyping and cross-species biomarker identification in precision
psychiatry. We further discuss explainable AI (XAI) and causality testing in a
closed-human-in-the-loop manner, and highlight the ML potential in multimedia
information extraction and multimodal data fusion. Finally, we discuss
conceptual and practical challenges in precision psychiatry and highlight ML
opportunities in future research
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