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Purpose: In diffusion MRI (dMRI), the volumetric and bundle analyses of whole-brain tissue microstructure and connectivity can be severely impeded by an incomplete field-of-view (FOV). This work aims to develop a method for imputing the missing slices directly from existing dMRI scans with an incomplete FOV. We hypothesize that the imputed image with complete FOV can improve the whole-brain tractography for corrupted data with incomplete FOV. Therefore, our approach provides a desirable alternative to discarding the valuable dMRI data, enabling subsequent tractography analyses that would otherwise be challenging or unattainable with corrupted data. Approach: We propose a framework based on a deep generative model that estimates the absent brain regions in dMRI scans with incomplete FOV. The model is capable of learning both the diffusion characteristics in diffusion-weighted images (DWI) and the anatomical features evident in the corresponding structural images for efficiently imputing missing slices of DWI outside of incomplete FOV. Results: For evaluating the imputed slices, on the WRAP dataset the proposed framework achieved PSNRb0=22.397, SSIMb0=0.905, PSNRb1300=22.479, SSIMb1300=0.893; on the NACC dataset it achieved PSNRb0=21.304, SSIMb0=0.892, PSNRb1300=21.599, SSIMb1300= 0.877. The proposed framework improved the tractography accuracy, as demonstrated by an increased average Dice score for 72 tracts (p < 0.001) on both the WRAP and NACC datasets. Conclusions: Results suggest that the proposed framework achieved sufficient imputation performance in dMRI data with incomplete FOV for improving whole-brain tractography, thereby repairing the corrupted data. Our approach achieved more accurate whole-brain tractography results with extended and complete FOV and reduced the uncertainty when analyzing bundles associated with Alzheimer's Disease., Comment: 20 pages, 11 figures

We introduce an assessment procedure for interactive segmentation models. Based on concepts from Bayesian Experimental Design, the procedure measures a model's understanding of point prompts and their correspondence with the desired segmentation mask. We show that Oracle Dice index measurements are insensitive or even misleading in measuring this property. We demonstrate the use of the proposed procedure on three interactive segmentation models and subsets of two large image segmentation datasets.

Purpose: In order to produce a surgical gesture recognition system that can support a wide variety of procedures, either a very large annotated dataset must be acquired, or fitted models must generalize to new labels (so called "zero-shot" capability). In this paper we investigate the feasibility of latter option. Methods: Leveraging the Bridge-Prompt framework, we prompt-tune a pre-trained vision-text model (CLIP) for gesture recognition in surgical videos. This can utilize extensive outside video data such as text, but also make use of label meta-data and weakly supervised contrastive losses. Results: Our experiments show that prompt-based video encoder outperforms standard encoders in surgical gesture recognition tasks. Notably, it displays strong performance in zero-shot scenarios, where gestures/tasks that were not provided during the encoder training phase are included in the prediction phase. Additionally, we measure the benefit of inclusion text descriptions in the feature extractor training schema. Conclusion Bridge-Prompt and similar pre-trained+prompt-tuned video encoder models present significant visual representation for surgical robotics, especially in gesture recognition tasks. Given the diverse range of surgical tasks (gestures), the ability of these models to zero-shot transfer without the need for any task (gesture) specific retraining makes them invaluable., Comment: 17 pages,4 figures, 7 tables, IPCAI 2024 & IJCARS

Diffusion MRI (dMRI) streamline tractography, the gold standard for in vivo estimation of brain white matter (WM) pathways, has long been considered indicative of macroscopic relationships with WM microstructure. However, recent advances in tractography demonstrated that convolutional recurrent neural networks (CoRNN) trained with a teacher-student framework have the ability to learn and propagate streamlines directly from T1 and anatomical contexts. Training for this network has previously relied on high-resolution dMRI. In this paper, we generalize the training mechanism to traditional clinical resolution data, which allows generalizability across sensitive and susceptible study populations. We train CoRNN on a small subset of the Baltimore Longitudinal Study of Aging (BLSA), which better resembles clinical protocols. Then, we define a metric, termed the epsilon ball seeding method, to compare T1 tractography and traditional diffusion tractography at the streamline level. Under this metric, T1 tractography generated by CoRNN reproduces diffusion tractography with approximately two millimeters of error.

Connectivity matrices derived from diffusion MRI (dMRI) provide an interpretable and generalizable way of understanding the human brain connectome. However, dMRI suffers from inter-site and between-scanner variation, which impedes analysis across datasets to improve robustness and reproducibility of results. To evaluate different harmonization approaches on connectivity matrices, we compared graph measures derived from these matrices before and after applying three harmonization techniques: mean shift, ComBat, and CycleGAN. The sample comprises 168 age-matched, sex-matched normal subjects from two studies: the Vanderbilt Memory and Aging Project (VMAP) and the Biomarkers of Cognitive Decline Among Normal Individuals (BIOCARD). First, we plotted the graph measures and used coefficient of variation (CoV) and the Mann-Whitney U test to evaluate different methods' effectiveness in removing site effects on the matrices and the derived graph measures. ComBat effectively eliminated site effects for global efficiency and modularity and outperformed the other two methods. However, all methods exhibited poor performance when harmonizing average betweenness centrality. Second, we tested whether our harmonization methods preserved correlations between age and graph measures. All methods except for CycleGAN in one direction improved correlations between age and global efficiency and between age and modularity from insignificant to significant with p-values less than 0.05., Comment: 11 pages, 5 figures, to be published in SPIE Medical Imaging 2024: Image Processing

Rigid motion tracking is paramount in many medical imaging applications where movements need to be detected, corrected, or accounted for. Modern strategies rely on convolutional neural networks (CNN) and pose this problem as rigid registration. Yet, CNNs do not exploit natural symmetries in this task, as they are equivariant to translations (their outputs shift with their inputs) but not to rotations. Here we propose EquiTrack, the first method that uses recent steerable SE(3)-equivariant CNNs (E-CNN) for motion tracking. While steerable E-CNNs can extract corresponding features across different poses, testing them on noisy medical images reveals that they do not have enough learning capacity to learn noise invariance. Thus, we introduce a hybrid architecture that pairs a denoiser with an E-CNN to decouple the processing of anatomically irrelevant intensity features from the extraction of equivariant spatial features. Rigid transforms are then estimated in closed-form. EquiTrack outperforms state-of-the-art learning and optimisation methods for motion tracking in adult brain MRI and fetal MRI time series. Our code is available at https://github.com/BBillot/EquiTrack., Comment: Published at IEEE transactions on Medical Imaging

Imaging findings inconsistent with those expected at specific chronological age ranges may serve as early indicators of neurological disorders and increased mortality risk. Estimation of chronological age, and deviations from expected results, from structural MRI data has become an important task for developing biomarkers that are sensitive to such deviations. Complementary to structural analysis, diffusion tensor imaging (DTI) has proven effective in identifying age-related microstructural changes within the brain white matter, thereby presenting itself as a promising additional modality for brain age prediction. Although early studies have sought to harness DTI's advantages for age estimation, there is no evidence that the success of this prediction is owed to the unique microstructural and diffusivity features that DTI provides, rather than the macrostructural features that are also available in DTI data. Therefore, we seek to develop white-matter-specific age estimation to capture deviations from normal white matter aging. Specifically, we deliberately disregard the macrostructural information when predicting age from DTI scalar images, using two distinct methods. The first method relies on extracting only microstructural features from regions of interest. The second applies 3D residual neural networks (ResNets) to learn features directly from the images, which are non-linearly registered and warped to a template to minimize macrostructural variations. When tested on unseen data, the first method yields mean absolute error (MAE) of 6.11 years for cognitively normal participants and MAE of 6.62 years for cognitively impaired participants, while the second method achieves MAE of 4.69 years for cognitively normal participants and MAE of 4.96 years for cognitively impaired participants. We find that the ResNet model captures subtler, non-macrostructural features for brain age prediction., Comment: SPIE Medical Imaging: Image Processing. San Diego, CA. February 2024 (accepted as poster presentation)

Steganography is the art of hiding information in plain sight. This form of covert communication can be used by bad actors to propagate malware, exfiltrate victim data, and communicate with other bad actors. Current image steganography defenses rely upon steganalysis, or the detection of hidden messages. These methods, however, are non-blind as they require information about known steganography techniques and are easily bypassed. Recent work has instead focused on a defense mechanism known as sanitization, which eliminates hidden information from images. In this work, we introduce a novel blind deep learning steganography sanitization method that utilizes a diffusion model framework to sanitize universal and dependent steganography (DM-SUDS), which both sanitizes and preserves image quality. We evaluate this approach against state-of-the-art deep learning sanitization frameworks and provide further detailed analysis through an ablation study. DM-SUDS outperforms previous sanitization methods and improves image preservation MSE by 71.32%, PSNR by 22.43% and SSIM by 17.30%. This is the first blind deep learning image sanitization framework to meet these image quality results.

This work reports the empirical performance of an automated medical landmark detection method for predict clinical markers in hip radiograph images. Notably, the detection method was trained using a label-only augmentation scheme; our results indicate that this form of augmentation outperforms traditional data augmentation and produces highly sample efficient estimators. We train a generic U-Net-based architecture under a curriculum consisting of two phases: initially relaxing the landmarking task by enlarging the label points to regions, then gradually eroding these label regions back to the base task. We measure the benefits of this approach on six datasets of radiographs with gold-standard expert annotations.

Steganography, or hiding messages in plain sight, is a form of information hiding that is most commonly used for covert communication. As modern steganographic mediums include images, text, audio, and video, this communication method is being increasingly used by bad actors to propagate malware, exfiltrate data, and discreetly communicate. Current protection mechanisms rely upon steganalysis, or the detection of steganography, but these approaches are dependent upon prior knowledge, such as steganographic signatures from publicly available tools and statistical knowledge about known hiding methods. These dependencies render steganalysis useless against new or unique hiding methods, which are becoming increasingly common with the application of deep learning models. To mitigate the shortcomings of steganalysis, this work focuses on a deep learning sanitization technique called SUDS that is not reliant upon knowledge of steganographic hiding techniques and is able to sanitize universal and dependent steganography. SUDS is tested using least significant bit method (LSB), dependent deep hiding (DDH), and universal deep hiding (UDH). We demonstrate the capabilities and limitations of SUDS by answering five research questions, including baseline comparisons and an ablation study. Additionally, we apply SUDS to a real-world scenario, where it is able to increase the resistance of a poisoned classifier against attacks by 1375%., Comment: Accepted to European Conference on Artificial Intelligence (ECAI) 2023

Machine learning provides a valuable tool for analyzing high-dimensional functional neuroimaging data, and is proving effective in predicting various neurological conditions, psychiatric disorders, and cognitive patterns. In functional magnetic resonance imaging (MRI) research, interactions between brain regions are commonly modeled using graph-based representations. The potency of graph machine learning methods has been established across myriad domains, marking a transformative step in data interpretation and predictive modeling. Yet, despite their promise, the transposition of these techniques to the neuroimaging domain has been challenging due to the expansive number of potential preprocessing pipelines and the large parameter search space for graph-based dataset construction. In this paper, we introduce NeuroGraph, a collection of graph-based neuroimaging datasets, and demonstrated its utility for predicting multiple categories of behavioral and cognitive traits. We delve deeply into the dataset generation search space by crafting 35 datasets that encompass static and dynamic brain connectivity, running in excess of 15 baseline methods for benchmarking. Additionally, we provide generic frameworks for learning on both static and dynamic graphs. Our extensive experiments lead to several key observations. Notably, using correlation vectors as node features, incorporating larger number of regions of interest, and employing sparser graphs lead to improved performance. To foster further advancements in graph-based data driven neuroimaging analysis, we offer a comprehensive open-source Python package that includes the benchmark datasets, baseline implementations, model training, and standard evaluation., Comment: NeurIPS23

Volumetric reconstruction of fetal brains from multiple stacks of MR slices, acquired in the presence of almost unpredictable and often severe subject motion, is a challenging task that is highly sensitive to the initialization of slice-to-volume transformations. We propose a novel slice-to-volume registration method using Transformers trained on synthetically transformed data, which model multiple stacks of MR slices as a sequence. With the attention mechanism, our model automatically detects the relevance between slices and predicts the transformation of one slice using information from other slices. We also estimate the underlying 3D volume to assist slice-to-volume registration and update the volume and transformations alternately to improve accuracy. Results on synthetic data show that our method achieves lower registration error and better reconstruction quality compared with existing state-of-the-art methods. Experiments with real-world MRI data are also performed to demonstrate the ability of the proposed model to improve the quality of 3D reconstruction under severe fetal motion., Comment: Accepted by MICCAI 2022

Adoption of machine learning models in healthcare requires end users' trust in the system. Models that provide additional supportive evidence for their predictions promise to facilitate adoption. We define consistent evidence to be both compatible and sufficient with respect to model predictions. We propose measures of model inconsistency and regularizers that promote more consistent evidence. We demonstrate our ideas in the context of edema severity grading from chest radiographs. We demonstrate empirically that consistent models provide competitive performance while supporting interpretation., Comment: 13 pages, 6 figures, proceedings of the Machine Learning for Health NeurIPS Workshop, 2021

We demonstrate an object tracking method for 3D images with fixed computational cost and state-of-the-art performance. Previous methods predicted transformation parameters from convolutional layers. We instead propose an architecture that does not include either flattening of convolutional features or fully connected layers, but instead relies on equivariant filters to preserve transformations between inputs and outputs (e.g. rot./trans. of inputs rotate/translate outputs). The transformation is then derived in closed form from the outputs of the filters. This method is useful for applications requiring low latency, such as real-time tracking. We demonstrate our model on synthetically augmented adult brain MRI, as well as fetal brain MRI, which is the intended use-case., Comment: MICCAI 2021 Early Accept

We propose and demonstrate a representation learning approach by maximizing the mutual information between local features of images and text. The goal of this approach is to learn useful image representations by taking advantage of the rich information contained in the free text that describes the findings in the image. Our method trains image and text encoders by encouraging the resulting representations to exhibit high local mutual information. We make use of recent advances in mutual information estimation with neural network discriminators. We argue that the sum of local mutual information is typically a lower bound on the global mutual information. Our experimental results in the downstream image classification tasks demonstrate the advantages of using local features for image-text representation learning., Comment: In Proceedings of International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2021

We show that for a wide class of harmonization/domain-invariance schemes several undesirable properties are unavoidable. If a predictive machine is made invariant to a set of domains, the accuracy of the output predictions (as measured by mutual information) is limited by the domain with the least amount of information to begin with. If a real label value is highly informative about the source domain, it cannot be accurately predicted by an invariant predictor. These results are simple and intuitive, but we believe that it is beneficial to state them for medical imaging harmonization., Comment: Med-NeurIPS 2020 Workshop Paper, updated 4/2021

Machine learning models are commonly trained end-to-end and in a supervised setting, using paired (input, output) data. Examples include recent super-resolution methods that train on pairs of (low-resolution, high-resolution) images. However, these end-to-end approaches require re-training every time there is a distribution shift in the inputs (e.g., night images vs daylight) or relevant latent variables (e.g., camera blur or hand motion). In this work, we leverage state-of-the-art (SOTA) generative models (here StyleGAN2) for building powerful image priors, which enable application of Bayes' theorem for many downstream reconstruction tasks. Our method, Bayesian Reconstruction through Generative Models (BRGM), uses a single pre-trained generator model to solve different image restoration tasks, i.e., super-resolution and in-painting, by combining it with different forward corruption models. We keep the weights of the generator model fixed, and reconstruct the image by estimating the Bayesian maximum a-posteriori (MAP) estimate over the input latent vector that generated the reconstructed image. We further use variational inference to approximate the posterior distribution over the latent vectors, from which we sample multiple solutions. We demonstrate BRGM on three large and diverse datasets: (i) 60,000 images from the Flick Faces High Quality dataset (ii) 240,000 chest X-rays from MIMIC III and (iii) a combined collection of 5 brain MRI datasets with 7,329 scans. Across all three datasets and without any dataset-specific hyperparameter tuning, our simple approach yields performance competitive with current task-specific state-of-the-art methods on super-resolution and in-painting, while being more generalisable and without requiring any training. Our source code and pre-trained models are available online: https://razvanmarinescu.github.io/brgm/., Comment: 27 pages, 17 figures, 5 tables

Estimating mutual information between continuous random variables is often intractable and extremely challenging for high-dimensional data. Recent progress has leveraged neural networks to optimize variational lower bounds on mutual information. Although showing promise for this difficult problem, the variational methods have been theoretically and empirically proven to have serious statistical limitations: 1) many methods struggle to produce accurate estimates when the underlying mutual information is either low or high; 2) the resulting estimators may suffer from high variance. Our approach is based on training a classifier that provides the probability that a data sample pair is drawn from the joint distribution rather than from the product of its marginal distributions. Moreover, we establish a direct connection between mutual information and the average log odds estimate produced by the classifier on a test set, leading to a simple and accurate estimator of mutual information. We show theoretically that our method and other variational approaches are equivalent when they achieve their optimum, while our method sidesteps the variational bound. Empirical results demonstrate high accuracy of our approach and the advantages of our estimator in the context of representation learning. Our demo is available at https://github.com/RayRuizhiLiao/demi_mi_estimator.

Pooled imaging data from multiple sources is subject to bias from each source. Studies that do not correct for these scanner/site biases at best lose statistical power, and at worst leave spurious correlations in their data. Estimation of the bias effects is non-trivial due to the paucity of data with correspondence across sites, so called "traveling phantom" data, which is expensive to collect. Nevertheless, numerous solutions leveraging direct correspondence have been proposed. In contrast to this, Moyer et al. (2019) proposes an unsupervised solution using invariant representations, one which does not require correspondence and thus does not require paired images. By leveraging the data processing inequality, an invariant representation can then be used to create an image reconstruction that is uninformative of its original source, yet still faithful to the underlying structure. In the present abstract we provide an overview of this method., Comment: Accepted as a short paper in MIDL 2020. In accordance with the MIDL 2020 Call for Papers, this short paper is an overview of an already published work arXiv:1904.05375, and was submitted to MIDL in order to allow presentation and discussion at the meeting

Supervised machine learning models often associate irrelevant nuisance factors with the prediction target, which hurts generalization. We propose a framework for training robust neural networks that induces invariance to nuisances through learning to discover and separate predictive and nuisance factors of data. We present an information theoretic formulation of our approach, from which we derive training objectives and its connections with previous methods. Empirical results on a wide array of datasets show that the proposed framework achieves state-of-the-art performance, without requiring nuisance annotations during training., Comment: 10 pages, 3 figures

We propose a novel approach to achieving invariance for deep neural networks in the form of inducing amnesia to unwanted factors of data through a new adversarial forgetting mechanism. We show that the forgetting mechanism serves as an information-bottleneck, which is manipulated by the adversarial training to learn invariance to unwanted factors. Empirical results show that the proposed framework achieves state-of-the-art performance at learning invariance in both nuisance and bias settings on a diverse collection of datasets and tasks., Comment: To appear in Proceedings of the 34th AAAI Conference on Artificial Intelligence (AAAI-20)

Estimating the covariance structure of multivariate time series is a fundamental problem with a wide-range of real-world applications -- from financial modeling to fMRI analysis. Despite significant recent advances, current state-of-the-art methods are still severely limited in terms of scalability, and do not work well in high-dimensional undersampled regimes. In this work we propose a novel method called Temporal Correlation Explanation, or T-CorEx, that (a) has linear time and memory complexity with respect to the number of variables, and can scale to very large temporal datasets that are not tractable with existing methods; (b) gives state-of-the-art results in highly undersampled regimes on both synthetic and real-world datasets; and (c) makes minimal assumptions about the character of the dynamics of the system. T-CorEx optimizes an information-theoretic objective function to learn a latent factor graphical model for each time period and applies two regularization techniques to induce temporal consistency of estimates. We perform extensive evaluation of T-Corex using both synthetic and real-world data and demonstrate that it can be used for detecting sudden changes in the underlying covariance matrix, capturing transient correlations and analyzing extremely high-dimensional complex multivariate time series such as high-resolution fMRI data.

Compression is at the heart of effective representation learning. However, lossy compression is typically achieved through simple parametric models like Gaussian noise to preserve analytic tractability, and the limitations this imposes on learning are largely unexplored. Further, the Gaussian prior assumptions in models such as variational autoencoders (VAEs) provide only an upper bound on the compression rate in general. We introduce a new noise channel, \emph{Echo noise}, that admits a simple, exact expression for mutual information for arbitrary input distributions. The noise is constructed in a data-driven fashion that does not require restrictive distributional assumptions. With its complex encoding mechanism and exact rate regularization, Echo leads to improved bounds on log-likelihood and dominates $\beta$-VAEs across the achievable range of rate-distortion trade-offs. Further, we show that Echo noise can outperform flow-based methods without the need to train additional distributional transformations., Comment: NeurIPS 2019; updated Gaussian baseline results, added disentanglement

Purpose: In the present work we describe the correction of diffusion-weighted MRI for site and scanner biases using a novel method based on invariant representation. Theory and Methods: Pooled imaging data from multiple sources are subject to variation between the sources. Correcting for these biases has become very important as imaging studies increase in size and multi-site cases become more common. We propose learning an intermediate representation invariant to site/protocol variables, a technique adapted from information theory-based algorithmic fairness; by leveraging the data processing inequality, such a representation can then be used to create an image reconstruction that is uninformative of its original source, yet still faithful to underlying structures. To implement this, we use a deep learning method based on variational auto-encoders (VAE) to construct scanner invariant encodings of the imaging data. Results: To evaluate our method, we use training data from the 2018 MICCAI Computational Diffusion MRI (CDMRI) Challenge Harmonization dataset. Our proposed method shows improvements on independent test data relative to a recently published baseline method on each subtask, mapping data from three different scanning contexts to and from one separate target scanning context. Conclusion: As imaging studies continue to grow, the use of pooled multi-site imaging will similarly increase. Invariant representation presents a strong candidate for the harmonization of these data.

We present two related methods for deriving connectivity-based brain atlases from individual connectomes. The proposed methods exploit a previously proposed dense connectivity representation, termed continuous connectivity, by first performing graph-based hierarchical clustering of individual brains, and subsequently aggregating the individual parcellations into a consensus parcellation. The search for consensus minimizes the sum of cluster membership distances, effectively estimating a pseudo-Karcher mean of individual parcellations. We assess the quality of our parcellations using (1) Kullback-Liebler and Jensen-Shannon divergence with respect to the dense connectome representation, (2) inter-hemispheric symmetry, and (3) performance of the simplified connectome in a biological sex classification task. We find that the parcellation based-atlas computed using a greedy search at a hierarchical depth 3 outperforms all other parcellation-based atlases as well as the standard Dessikan-Killiany anatomical atlas in all three assessments.

In the present work, we use information theory to understand the empirical convergence rate of tractography, a widely-used approach to reconstruct anatomical fiber pathways in the living brain. Based on diffusion MRI data, tractography is the starting point for many methods to study brain connectivity. Of the available methods to perform tractography, most reconstruct a finite set of streamlines, or 3D curves, representing probable connections between anatomical regions, yet relatively little is known about how the sampling of this set of streamlines affects downstream results, and how exhaustive the sampling should be. Here we provide a method to measure the information theoretic surprise (self-cross entropy) for tract sampling schema. We then empirically assess four streamline methods. We demonstrate that the relative information gain is very low after a moderate number of streamlines have been generated for each tested method. The results give rise to several guidelines for optimal sampling in brain connectivity analyses., Comment: 11 pages

Representations of data that are invariant to changes in specified factors are useful for a wide range of problems: removing potential biases in prediction problems, controlling the effects of covariates, and disentangling meaningful factors of variation. Unfortunately, learning representations that exhibit invariance to arbitrary nuisance factors yet remain useful for other tasks is challenging. Existing approaches cast the trade-off between task performance and invariance in an adversarial way, using an iterative minimax optimization. We show that adversarial training is unnecessary and sometimes counter-productive; we instead cast invariant representation learning as a single information-theoretic objective that can be directly optimized. We demonstrate that this approach matches or exceeds performance of state-of-the-art adversarial approaches for learning fair representations and for generative modeling with controllable transformations., Comment: NeurIPS 2018, with corrections

There is no consensus on how to construct structural brain networks from diffusion MRI. How variations in pre-processing steps affect network reliability and its ability to distinguish subjects remains opaque. In this work, we address this issue by comparing 35 structural connectome-building pipelines. We vary diffusion reconstruction models, tractography algorithms and parcellations. Next, we classify structural connectome pairs as either belonging to the same individual or not. Connectome weights and eight topological derivative measures form our feature set. For experiments, we use three test-retest datasets from the Consortium for Reliability and Reproducibility (CoRR) comprised of a total of 105 individuals. We also compare pairwise classification results to a commonly used parametric test-retest measure, Intraclass Correlation Coefficient (ICC)., Comment: Accepted for MICCAI 2017, 8 pages, 3 figures

Estimating graphical model structure from high-dimensional and undersampled data is a fundamental problem in many scientific fields. Existing approaches, such as GLASSO, latent variable GLASSO, and latent tree models, suffer from high computational complexity and may impose unrealistic sparsity priors in some cases. We introduce a novel method that leverages a newly discovered connection between information-theoretic measures and structured latent factor models to derive an optimization objective which encourages modular structures where each observed variable has a single latent parent. The proposed method has linear stepwise computational complexity w.r.t. the number of observed variables. Our experiments on synthetic data demonstrate that our approach is the only method that recovers modular structure better as the dimensionality increases. We also use our approach for estimating covariance structure for a number of real-world datasets and show that it consistently outperforms state-of-the-art estimators at a fraction of the computational cost. Finally, we apply the proposed method to high-resolution fMRI data (with more than 10^5 voxels) and show that it is capable of extracting meaningful patterns., Comment: 22 pages, accepted to NeurIPS 2019

We consider the problem of duplicate detection in noisy and incomplete data: given a large data set in which each record has multiple entries (attributes), detect which distinct records refer to the same real world entity. This task is complicated by noise (such as misspellings) and missing data, which can lead to records being different, despite referring to the same entity. Our method consists of three main steps: creating a similarity score between records, grouping records together into "unique entities", and refining the groups. We compare various methods for creating similarity scores between noisy records, considering different combinations of string matching, term frequency-inverse document frequency methods, and n-gram techniques. In particular, we introduce a vectorized soft term frequency-inverse document frequency method, with an optional refinement step. We also discuss two methods to deal with missing data in computing similarity scores. We test our method on the Los Angeles Police Department Field Interview Card data set, the Cora Citation Matching data set, and two sets of restaurant review data. The results show that the methods that use words as the basic units are preferable to those that use 3-grams. Moreover, in some (but certainly not all) parameter ranges soft term frequency-inverse document frequency methods can outperform the standard term frequency-inverse document frequency method. The results also confirm that our method for automatically determining the number of groups typically works well in many cases and allows for accurate results in the absence of a priori knowledge of the number of unique entities in the data set., Comment: 24 pages, 17 figures; this second version has various significant updates compared to version 1 as a result of the peer review process prior to journal publication; we thank the reviewers for their comments

One of the primary objectives of human brain mapping is the division of the cortical surface into functionally distinct regions, i.e. parcellation. While it is generally agreed that at macro-scale different regions of the cortex have different functions, the exact number and configuration of these regions is not known. Methods for the discovery of these regions are thus important, particularly as the volume of available information grows. Towards this end, we present a parcellation method based on a Bayesian non-parametric mixture model of cortical connectivity., Comment: In the Proceedings of Information Processing in Medical Imaging 2017

In the present work we demonstrate the use of a parcellation free connectivity model based on Poisson point processes. This model produces for each subject a continuous bivariate intensity function that represents for every possible pair of points the relative rate at which we observe tracts terminating at those points. We fit this model to explore degree sequence equivalents for spatial continuum graphs, and to investigate the local differences between estimated intensity functions for two different tractography methods. This is a companion paper to Moyer et al. (2016), where the model was originally defined., Comment: Presented at The MICCAI-BACON 16 Workshop (https://arxiv.org/abs/1611.03363)

We present a continuous model for structural brain connectivity based on the Poisson point process. The model treats each streamline curve in a tractography as an observed event in connectome space, here a product space of cortical white matter boundaries. We approximate the model parameter via kernel density estimation. To deal with the heavy computational burden, we develop a fast parameter estimation method by pre-computing associated Legendre products of the data, leveraging properties of the spherical heat kernel. We show how our approach can be used to assess the quality of cortical parcellations with respect to connectivty. We further present empirical results that suggest the discrete connectomes derived from our model have substantially higher test-retest reliability compared to standard methods., Comment: Accepted at MICCAI 2016