Models, code, and papers for "Mohammad Javad Shafiee":

Discovery Radiomics via Deep Multi-Column Radiomic Sequencers for Skin Cancer Detection

Sep 24, 2017
Mohammad Javad Shafiee, Alexander Wong

While skin cancer is the most diagnosed form of cancer in men and women, with more cases diagnosed each year than all other cancers combined, sufficiently early diagnosis results in very good prognosis and as such makes early detection crucial. While radiomics have shown considerable promise as a powerful diagnostic tool for significantly improving oncological diagnostic accuracy and efficiency, current radiomics-driven methods have largely rely on pre-defined, hand-crafted quantitative features, which can greatly limit the ability to fully characterize unique cancer phenotype that distinguish it from healthy tissue. Recently, the notion of discovery radiomics was introduced, where a large amount of custom, quantitative radiomic features are directly discovered from the wealth of readily available medical imaging data. In this study, we present a novel discovery radiomics framework for skin cancer detection, where we leverage novel deep multi-column radiomic sequencers for high-throughput discovery and extraction of a large amount of custom radiomic features tailored for characterizing unique skin cancer tissue phenotype. The discovered radiomic sequencer was tested against 9,152 biopsy-proven clinical images comprising of different skin cancers such as melanoma and basal cell carcinoma, and demonstrated sensitivity and specificity of 91% and 75%, respectively, thus achieving dermatologist-level performance and \break hence can be a powerful tool for assisting general practitioners and dermatologists alike in improving the efficiency, consistency, and accuracy of skin cancer diagnosis.


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Evolutionary Synthesis of Deep Neural Networks via Synaptic Cluster-driven Genetic Encoding

Nov 22, 2016
Mohammad Javad Shafiee, Alexander Wong

There has been significant recent interest towards achieving highly efficient deep neural network architectures. A promising paradigm for achieving this is the concept of evolutionary deep intelligence, which attempts to mimic biological evolution processes to synthesize highly-efficient deep neural networks over successive generations. An important aspect of evolutionary deep intelligence is the genetic encoding scheme used to mimic heredity, which can have a significant impact on the quality of offspring deep neural networks. Motivated by the neurobiological phenomenon of synaptic clustering, we introduce a new genetic encoding scheme where synaptic probability is driven towards the formation of a highly sparse set of synaptic clusters. Experimental results for the task of image classification demonstrated that the synthesized offspring networks using this synaptic cluster-driven genetic encoding scheme can achieve state-of-the-art performance while having network architectures that are not only significantly more efficient (with a ~125-fold decrease in synapses for MNIST) compared to the original ancestor network, but also tailored for GPU-accelerated machine learning applications.

* 5 pages 

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Efficient Inference on Deep Neural Networks by Dynamic Representations and Decision Gates

Nov 06, 2018
Mohammad Saeed Shafiee, Mohammad Javad Shafiee, Alexander Wong

The current trade-off between depth and computational cost makes it difficult to adopt deep neural networks for many industrial applications, especially when computing power is limited. Here, we are inspired by the idea that, while deeper embeddings are needed to discriminate difficult samples, a large number of samples can be well discriminated via much shallower embeddings. In this study, we introduce the concept of decision gates (d-gate), modules trained to decide whether a sample needs to be projected into a deeper embedding or if an early prediction can be made at the d-gate, thus enabling the computation of dynamic representations at different depths. The proposed d-gate modules can be integrated with any deep neural network and reduces the average computational cost of the deep neural networks while maintaining modeling accuracy. Experimental results show that leveraging the proposed d-gate modules led to a ~38% speed-up and ~39% FLOPS reduction on ResNet-101 and ~46% speed-up and ~36% FLOPS reduction on DenseNet-201 trained on the CIFAR10 dataset with only ~2\% drop in accuracy.

* 4 pages 

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Exploring the Imposition of Synaptic Precision Restrictions For Evolutionary Synthesis of Deep Neural Networks

Jul 01, 2017
Mohammad Javad Shafiee, Francis Li, Alexander Wong

A key contributing factor to incredible success of deep neural networks has been the significant rise on massively parallel computing devices allowing researchers to greatly increase the size and depth of deep neural networks, leading to significant improvements in modeling accuracy. Although deeper, larger, or complex deep neural networks have shown considerable promise, the computational complexity of such networks is a major barrier to utilization in resource-starved scenarios. We explore the synaptogenesis of deep neural networks in the formation of efficient deep neural network architectures within an evolutionary deep intelligence framework, where a probabilistic generative modeling strategy is introduced to stochastically synthesize increasingly efficient yet effective offspring deep neural networks over generations, mimicking evolutionary processes such as heredity, random mutation, and natural selection in a probabilistic manner. In this study, we primarily explore the imposition of synaptic precision restrictions and its impact on the evolutionary synthesis of deep neural networks to synthesize more efficient network architectures tailored for resource-starved scenarios. Experimental results show significant improvements in synaptic efficiency (~10X decrease for GoogLeNet-based DetectNet) and inference speed (>5X increase for GoogLeNet-based DetectNet) while preserving modeling accuracy.


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Evolution in Groups: A deeper look at synaptic cluster driven evolution of deep neural networks

Apr 07, 2017
Mohammad Javad Shafiee, Elnaz Barshan, Alexander Wong

A promising paradigm for achieving highly efficient deep neural networks is the idea of evolutionary deep intelligence, which mimics biological evolution processes to progressively synthesize more efficient networks. A crucial design factor in evolutionary deep intelligence is the genetic encoding scheme used to simulate heredity and determine the architectures of offspring networks. In this study, we take a deeper look at the notion of synaptic cluster-driven evolution of deep neural networks which guides the evolution process towards the formation of a highly sparse set of synaptic clusters in offspring networks. Utilizing a synaptic cluster-driven genetic encoding, the probabilistic encoding of synaptic traits considers not only individual synaptic properties but also inter-synaptic relationships within a deep neural network. This process results in highly sparse offspring networks which are particularly tailored for parallel computational devices such as GPUs and deep neural network accelerator chips. Comprehensive experimental results using four well-known deep neural network architectures (LeNet-5, AlexNet, ResNet-56, and DetectNet) on two different tasks (object categorization and object detection) demonstrate the efficiency of the proposed method. Cluster-driven genetic encoding scheme synthesizes networks that can achieve state-of-the-art performance with significantly smaller number of synapses than that of the original ancestor network. ($\sim$125-fold decrease in synapses for MNIST). Furthermore, the improved cluster efficiency in the generated offspring networks ($\sim$9.71-fold decrease in clusters for MNIST and a $\sim$8.16-fold decrease in clusters for KITTI) is particularly useful for accelerated performance on parallel computing hardware architectures such as those in GPUs and deep neural network accelerator chips.

* 8 pages. arXiv admin note: substantial text overlap with arXiv:1609.01360 

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Deep Learning with Darwin: Evolutionary Synthesis of Deep Neural Networks

Feb 06, 2017
Mohammad Javad Shafiee, Akshaya Mishra, Alexander Wong

Taking inspiration from biological evolution, we explore the idea of "Can deep neural networks evolve naturally over successive generations into highly efficient deep neural networks?" by introducing the notion of synthesizing new highly efficient, yet powerful deep neural networks over successive generations via an evolutionary process from ancestor deep neural networks. The architectural traits of ancestor deep neural networks are encoded using synaptic probability models, which can be viewed as the `DNA' of these networks. New descendant networks with differing network architectures are synthesized based on these synaptic probability models from the ancestor networks and computational environmental factor models, in a random manner to mimic heredity, natural selection, and random mutation. These offspring networks are then trained into fully functional networks, like one would train a newborn, and have more efficient, more diverse network architectures than their ancestor networks, while achieving powerful modeling capabilities. Experimental results for the task of visual saliency demonstrated that the synthesized `evolved' offspring networks can achieve state-of-the-art performance while having network architectures that are significantly more efficient (with a staggering $\sim$48-fold decrease in synapses by the fourth generation) compared to the original ancestor network.

* 5 pages 

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StochasticNet: Forming Deep Neural Networks via Stochastic Connectivity

Nov 10, 2015
Mohammad Javad Shafiee, Parthipan Siva, Alexander Wong

Deep neural networks is a branch in machine learning that has seen a meteoric rise in popularity due to its powerful abilities to represent and model high-level abstractions in highly complex data. One area in deep neural networks that is ripe for exploration is neural connectivity formation. A pivotal study on the brain tissue of rats found that synaptic formation for specific functional connectivity in neocortical neural microcircuits can be surprisingly well modeled and predicted as a random formation. Motivated by this intriguing finding, we introduce the concept of StochasticNet, where deep neural networks are formed via stochastic connectivity between neurons. As a result, any type of deep neural networks can be formed as a StochasticNet by allowing the neuron connectivity to be stochastic. Stochastic synaptic formations, in a deep neural network architecture, can allow for efficient utilization of neurons for performing specific tasks. To evaluate the feasibility of such a deep neural network architecture, we train a StochasticNet using four different image datasets (CIFAR-10, MNIST, SVHN, and STL-10). Experimental results show that a StochasticNet, using less than half the number of neural connections as a conventional deep neural network, achieves comparable accuracy and reduces overfitting on the CIFAR-10, MNIST and SVHN dataset. Interestingly, StochasticNet with less than half the number of neural connections, achieved a higher accuracy (relative improvement in test error rate of ~6% compared to ConvNet) on the STL-10 dataset than a conventional deep neural network. Finally, StochasticNets have faster operational speeds while achieving better or similar accuracy performances.

* 8 pages 

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Forming A Random Field via Stochastic Cliques: From Random Graphs to Fully Connected Random Fields

Jun 30, 2015
Mohammad Javad Shafiee, Alexander Wong, Paul Fieguth

Random fields have remained a topic of great interest over past decades for the purpose of structured inference, especially for problems such as image segmentation. The local nodal interactions commonly used in such models often suffer the short-boundary bias problem, which are tackled primarily through the incorporation of long-range nodal interactions. However, the issue of computational tractability becomes a significant issue when incorporating such long-range nodal interactions, particularly when a large number of long-range nodal interactions (e.g., fully-connected random fields) are modeled. In this work, we introduce a generalized random field framework based around the concept of stochastic cliques, which addresses the issue of computational tractability when using fully-connected random fields by stochastically forming a sparse representation of the random field. The proposed framework allows for efficient structured inference using fully-connected random fields without any restrictions on the potential functions that can be utilized. Several realizations of the proposed framework using graph cuts are presented and evaluated, and experimental results demonstrate that the proposed framework can provide competitive performance for the purpose of image segmentation when compared to existing fully-connected and principled deep random field frameworks.

* 8 pages 

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MicronNet: A Highly Compact Deep Convolutional Neural Network Architecture for Real-time Embedded Traffic Sign Classification

Oct 03, 2018
Alexander Wong, Mohammad Javad Shafiee, Michael St. Jules

Traffic sign recognition is a very important computer vision task for a number of real-world applications such as intelligent transportation surveillance and analysis. While deep neural networks have been demonstrated in recent years to provide state-of-the-art performance traffic sign recognition, a key challenge for enabling the widespread deployment of deep neural networks for embedded traffic sign recognition is the high computational and memory requirements of such networks. As a consequence, there are significant benefits in investigating compact deep neural network architectures for traffic sign recognition that are better suited for embedded devices. In this paper, we introduce MicronNet, a highly compact deep convolutional neural network for real-time embedded traffic sign recognition designed based on macroarchitecture design principles (e.g., spectral macroarchitecture augmentation, parameter precision optimization, etc.) as well as numerical microarchitecture optimization strategies. The resulting overall architecture of MicronNet is thus designed with as few parameters and computations as possible while maintaining recognition performance, leading to optimized information density of the proposed network. The resulting MicronNet possesses a model size of just ~1MB and ~510,000 parameters (~27x fewer parameters than state-of-the-art) while still achieving a human performance level top-1 accuracy of 98.9% on the German traffic sign recognition benchmark. Furthermore, MicronNet requires just ~10 million multiply-accumulate operations to perform inference, and has a time-to-compute of just 32.19 ms on a Cortex-A53 high efficiency processor. These experimental results show that highly compact, optimized deep neural network architectures can be designed for real-time traffic sign recognition that are well-suited for embedded scenarios.

* 11 pages 

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FermiNets: Learning generative machines to generate efficient neural networks via generative synthesis

Sep 17, 2018
Alexander Wong, Mohammad Javad Shafiee, Brendan Chwyl, Francis Li

The tremendous potential exhibited by deep learning is often offset by architectural and computational complexity, making widespread deployment a challenge for edge scenarios such as mobile and other consumer devices. To tackle this challenge, we explore the following idea: Can we learn generative machines to automatically generate deep neural networks with efficient network architectures? In this study, we introduce the idea of generative synthesis, which is premised on the intricate interplay between a generator-inquisitor pair that work in tandem to garner insights and learn to generate highly efficient deep neural networks that best satisfies operational requirements. What is most interesting is that, once a generator has been learned through generative synthesis, it can be used to generate not just one but a large variety of different, unique highly efficient deep neural networks that satisfy operational requirements. Experimental results for image classification, semantic segmentation, and object detection tasks illustrate the efficacy of generative synthesis in producing generators that automatically generate highly efficient deep neural networks (which we nickname FermiNets) with higher model efficiency and lower computational costs (reaching >10x more efficient and fewer multiply-accumulate operations than several tested state-of-the-art networks), as well as higher energy efficiency (reaching >4x improvements in image inferences per joule consumed on a Nvidia Tegra X2 mobile processor). As such, generative synthesis can be a powerful, generalized approach for accelerating and improving the building of deep neural networks for on-device edge scenarios.

* 4 pages 

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Unsupervised Feature Learning Toward a Real-time Vehicle Make and Model Recognition

Jun 08, 2018
Amir Nazemi, Mohammad Javad Shafiee, Zohreh Azimifar, Alexander Wong

Vehicle Make and Model Recognition (MMR) systems provide a fully automatic framework to recognize and classify different vehicle models. Several approaches have been proposed to address this challenge, however they can perform in restricted conditions. Here, we formulate the vehicle make and model recognition as a fine-grained classification problem and propose a new configurable on-road vehicle make and model recognition framework. We benefit from the unsupervised feature learning methods and in more details we employ Locality constraint Linear Coding (LLC) method as a fast feature encoder for encoding the input SIFT features. The proposed method can perform in real environments of different conditions. This framework can recognize fifty models of vehicles and has an advantage to classify every other vehicle not belonging to one of the specified fifty classes as an unknown vehicle. The proposed MMR framework can be configured to become faster or more accurate based on the application domain. The proposed approach is examined on two datasets including Iranian on-road vehicle dataset and CompuCar dataset. The Iranian on-road vehicle dataset contains images of 50 models of vehicles captured in real situations by traffic cameras in different weather and lighting conditions. Experimental results show superiority of the proposed framework over the state-of-the-art methods on Iranian on-road vehicle datatset and comparable results on CompuCar dataset with 97.5% and 98.4% accuracies, respectively.

* 15 pages include 14 figures and 5 tables 

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Tiny SSD: A Tiny Single-shot Detection Deep Convolutional Neural Network for Real-time Embedded Object Detection

Feb 19, 2018
Alexander Wong, Mohammad Javad Shafiee, Francis Li, Brendan Chwyl

Object detection is a major challenge in computer vision, involving both object classification and object localization within a scene. While deep neural networks have been shown in recent years to yield very powerful techniques for tackling the challenge of object detection, one of the biggest challenges with enabling such object detection networks for widespread deployment on embedded devices is high computational and memory requirements. Recently, there has been an increasing focus in exploring small deep neural network architectures for object detection that are more suitable for embedded devices, such as Tiny YOLO and SqueezeDet. Inspired by the efficiency of the Fire microarchitecture introduced in SqueezeNet and the object detection performance of the single-shot detection macroarchitecture introduced in SSD, this paper introduces Tiny SSD, a single-shot detection deep convolutional neural network for real-time embedded object detection that is composed of a highly optimized, non-uniform Fire sub-network stack and a non-uniform sub-network stack of highly optimized SSD-based auxiliary convolutional feature layers designed specifically to minimize model size while maintaining object detection performance. The resulting Tiny SSD possess a model size of 2.3MB (~26X smaller than Tiny YOLO) while still achieving an mAP of 61.3% on VOC 2007 (~4.2% higher than Tiny YOLO). These experimental results show that very small deep neural network architectures can be designed for real-time object detection that are well-suited for embedded scenarios.

* 7 pages 

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SquishedNets: Squishing SqueezeNet further for edge device scenarios via deep evolutionary synthesis

Nov 20, 2017
Mohammad Javad Shafiee, Francis Li, Brendan Chwyl, Alexander Wong

While deep neural networks have been shown in recent years to outperform other machine learning methods in a wide range of applications, one of the biggest challenges with enabling deep neural networks for widespread deployment on edge devices such as mobile and other consumer devices is high computational and memory requirements. Recently, there has been greater exploration into small deep neural network architectures that are more suitable for edge devices, with one of the most popular architectures being SqueezeNet, with an incredibly small model size of 4.8MB. Taking further advantage of the notion that many applications of machine learning on edge devices are often characterized by a low number of target classes, this study explores the utility of combining architectural modifications and an evolutionary synthesis strategy for synthesizing even smaller deep neural architectures based on the more recent SqueezeNet v1.1 macroarchitecture for applications with fewer target classes. In particular, architectural modifications are first made to SqueezeNet v1.1 to accommodate for a 10-class ImageNet-10 dataset, and then an evolutionary synthesis strategy is leveraged to synthesize more efficient deep neural networks based on this modified macroarchitecture. The resulting SquishedNets possess model sizes ranging from 2.4MB to 0.95MB (~5.17X smaller than SqueezeNet v1.1, or 253X smaller than AlexNet). Furthermore, the SquishedNets are still able to achieve accuracies ranging from 81.2% to 77%, and able to process at speeds of 156 images/sec to as much as 256 images/sec on a Nvidia Jetson TX1 embedded chip. These preliminary results show that a combination of architectural modifications and an evolutionary synthesis strategy can be a useful tool for producing very small deep neural network architectures that are well-suited for edge device scenarios.

* 4 pages 

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Fast YOLO: A Fast You Only Look Once System for Real-time Embedded Object Detection in Video

Sep 18, 2017
Mohammad Javad Shafiee, Brendan Chywl, Francis Li, Alexander Wong

Object detection is considered one of the most challenging problems in this field of computer vision, as it involves the combination of object classification and object localization within a scene. Recently, deep neural networks (DNNs) have been demonstrated to achieve superior object detection performance compared to other approaches, with YOLOv2 (an improved You Only Look Once model) being one of the state-of-the-art in DNN-based object detection methods in terms of both speed and accuracy. Although YOLOv2 can achieve real-time performance on a powerful GPU, it still remains very challenging for leveraging this approach for real-time object detection in video on embedded computing devices with limited computational power and limited memory. In this paper, we propose a new framework called Fast YOLO, a fast You Only Look Once framework which accelerates YOLOv2 to be able to perform object detection in video on embedded devices in a real-time manner. First, we leverage the evolutionary deep intelligence framework to evolve the YOLOv2 network architecture and produce an optimized architecture (referred to as O-YOLOv2 here) that has 2.8X fewer parameters with just a ~2% IOU drop. To further reduce power consumption on embedded devices while maintaining performance, a motion-adaptive inference method is introduced into the proposed Fast YOLO framework to reduce the frequency of deep inference with O-YOLOv2 based on temporal motion characteristics. Experimental results show that the proposed Fast YOLO framework can reduce the number of deep inferences by an average of 38.13%, and an average speedup of ~3.3X for objection detection in video compared to the original YOLOv2, leading Fast YOLO to run an average of ~18FPS on a Nvidia Jetson TX1 embedded system.


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The Mating Rituals of Deep Neural Networks: Learning Compact Feature Representations through Sexual Evolutionary Synthesis

Sep 07, 2017
Audrey Chung, Mohammad Javad Shafiee, Paul Fieguth, Alexander Wong

Evolutionary deep intelligence was recently proposed as a method for achieving highly efficient deep neural network architectures over successive generations. Drawing inspiration from nature, we propose the incorporation of sexual evolutionary synthesis. Rather than the current asexual synthesis of networks, we aim to produce more compact feature representations by synthesizing more diverse and generalizable offspring networks in subsequent generations via the combination of two parent networks. Experimental results were obtained using the MNIST and CIFAR-10 datasets, and showed improved architectural efficiency and comparable testing accuracy relative to the baseline asexual evolutionary neural networks. In particular, the network synthesized via sexual evolutionary synthesis for MNIST had approximately double the architectural efficiency (cluster efficiency of 34.29X and synaptic efficiency of 258.37X) in comparison to the network synthesized via asexual evolutionary synthesis, with both networks achieving a testing accuracy of ~97%.

* 8 pages 

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Scene Invariant Crowd Segmentation and Counting Using Scale-Normalized Histogram of Moving Gradients (HoMG)

Feb 01, 2016
Parthipan Siva, Mohammad Javad Shafiee, Mike Jamieson, Alexander Wong

The problem of automated crowd segmentation and counting has garnered significant interest in the field of video surveillance. This paper proposes a novel scene invariant crowd segmentation and counting algorithm designed with high accuracy yet low computational complexity in mind, which is key for widespread industrial adoption. A novel low-complexity, scale-normalized feature called Histogram of Moving Gradients (HoMG) is introduced for highly effective spatiotemporal representation of individuals and crowds within a video. Real-time crowd segmentation is achieved via boosted cascade of weak classifiers based on sliding-window HoMG features, while linear SVM regression of crowd-region HoMG features is employed for real-time crowd counting. Experimental results using multi-camera crowd datasets show that the proposed algorithm significantly outperform state-of-the-art crowd counting algorithms, as well as achieve very promising crowd segmentation results, thus demonstrating the efficacy of the proposed method for highly-accurate, real-time video-driven crowd analysis.

* 9 pages 

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Domain Adaptation and Transfer Learning in StochasticNets

Dec 18, 2015
Mohammad Javad Shafiee, Parthipan Siva, Paul Fieguth, Alexander Wong

Transfer learning is a recent field of machine learning research that aims to resolve the challenge of dealing with insufficient training data in the domain of interest. This is a particular issue with traditional deep neural networks where a large amount of training data is needed. Recently, StochasticNets was proposed to take advantage of sparse connectivity in order to decrease the number of parameters that needs to be learned, which in turn may relax training data size requirements. In this paper, we study the efficacy of transfer learning on StochasticNet frameworks. Experimental results show ~7% improvement on StochasticNet performance when the transfer learning is applied in training step.

* Vision Letters, Vol. 1, No. 1, pp. VL115, 2015 

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Efficient Deep Feature Learning and Extraction via StochasticNets

Dec 11, 2015
Mohammad Javad Shafiee, Parthipan Siva, Paul Fieguth, Alexander Wong

Deep neural networks are a powerful tool for feature learning and extraction given their ability to model high-level abstractions in highly complex data. One area worth exploring in feature learning and extraction using deep neural networks is efficient neural connectivity formation for faster feature learning and extraction. Motivated by findings of stochastic synaptic connectivity formation in the brain as well as the brain's uncanny ability to efficiently represent information, we propose the efficient learning and extraction of features via StochasticNets, where sparsely-connected deep neural networks can be formed via stochastic connectivity between neurons. To evaluate the feasibility of such a deep neural network architecture for feature learning and extraction, we train deep convolutional StochasticNets to learn abstract features using the CIFAR-10 dataset, and extract the learned features from images to perform classification on the SVHN and STL-10 datasets. Experimental results show that features learned using deep convolutional StochasticNets, with fewer neural connections than conventional deep convolutional neural networks, can allow for better or comparable classification accuracy than conventional deep neural networks: relative test error decrease of ~4.5% for classification on the STL-10 dataset and ~1% for classification on the SVHN dataset. Furthermore, it was shown that the deep features extracted using deep convolutional StochasticNets can provide comparable classification accuracy even when only 10% of the training data is used for feature learning. Finally, it was also shown that significant gains in feature extraction speed can be achieved in embedded applications using StochasticNets. As such, StochasticNets allow for faster feature learning and extraction performance while facilitate for better or comparable accuracy performances.

* 10 pages. arXiv admin note: substantial text overlap with arXiv:1508.05463 

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A deep-structured fully-connected random field model for structured inference

May 27, 2015
Alexander Wong, Mohammad Javad Shafiee, Parthipan Siva, Xiao Yu Wang

There has been significant interest in the use of fully-connected graphical models and deep-structured graphical models for the purpose of structured inference. However, fully-connected and deep-structured graphical models have been largely explored independently, leaving the unification of these two concepts ripe for exploration. A fundamental challenge with unifying these two types of models is in dealing with computational complexity. In this study, we investigate the feasibility of unifying fully-connected and deep-structured models in a computationally tractable manner for the purpose of structured inference. To accomplish this, we introduce a deep-structured fully-connected random field (DFRF) model that integrates a series of intermediate sparse auto-encoding layers placed between state layers to significantly reduce computational complexity. The problem of image segmentation was used to illustrate the feasibility of using the DFRF for structured inference in a computationally tractable manner. Results in this study show that it is feasible to unify fully-connected and deep-structured models in a computationally tractable manner for solving structured inference problems such as image segmentation.

* IEEE Access Journal, vol. 3, pp. 469-477, 2015 
* Accepted, 13 pages 

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Noise-Compensated, Bias-Corrected Diffusion Weighted Endorectal Magnetic Resonance Imaging via a Stochastically Fully-Connected Joint Conditional Random Field Model

Jul 05, 2016
Ameneh Boroomand, Mohammad Javad Shafiee, Farzad Khalvati, Masoom A. Haider, Alexander Wong

Diffusion weighted magnetic resonance imaging (DW-MR) is a powerful tool in imaging-based prostate cancer screening and detection. Endorectal coils are commonly used in DW-MR imaging to improve the signal-to-noise ratio (SNR) of the acquisition, at the expense of significant intensity inhomogeneities (bias field) that worsens as we move away from the endorectal coil. The presence of bias field can have a significant negative impact on the accuracy of different image analysis tasks, as well as prostate tumor localization, thus leading to increased inter- and intra-observer variability. Retrospective bias correction approaches are introduced as a more efficient way of bias correction compared to the prospective methods such that they correct for both of the scanner and anatomy-related bias fields in MR imaging. Previously proposed retrospective bias field correction methods suffer from undesired noise amplification that can reduce the quality of bias-corrected DW-MR image. Here, we propose a unified data reconstruction approach that enables joint compensation of bias field as well as data noise in DW-MR imaging. The proposed noise-compensated, bias-corrected (NCBC) data reconstruction method takes advantage of a novel stochastically fully connected joint conditional random field (SFC-JCRF) model to mitigate the effects of data noise and bias field in the reconstructed MR data. The proposed NCBC reconstruction method was tested on synthetic DW-MR data, physical DW-phantom as well as real DW-MR data all acquired using endorectal MR coil. Both qualitative and quantitative analysis illustrated that the proposed NCBC method can achieve improved image quality when compared to other tested bias correction methods. As such, the proposed NCBC method may have potential as a useful retrospective approach for improving the consistency of image interpretations.

* 11 pages 

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