arXiv subjects

Mohammad Javad Shafiee

Publications and source records attributed to Mohammad Javad Shafiee.

At least 55 records · Page 3Linked to original sources

arXiv2017

Discovery Radiomics via Evolutionary Deep Radiomic Sequencer Discovery for Pathologically-Proven Lung Cancer Detection

While lung cancer is the second most diagnosed form of cancer in men and women, a sufficiently early diagnosis can be pivotal in patient survival rates. Imaging-based, or radiomics-driven, detection methods have been developed to aid diagnosticians, but largely rely on hand-crafted features which may not fully encapsulate the differences between cancerous and healthy tissue. Recently, the concept of discovery radiomics was introduced, where custom abstract features are discovered from readily available imaging data. We propose a novel evolutionary deep radiomic sequencer discovery approach based on evolutionary deep intelligence. Motivated by patient privacy concerns and the idea of operational artificial intelligence, the evolutionary deep radiomic sequencer discovery approach organically evolves increasingly more efficient deep radiomic sequencers that produce significantly more compact yet similarly descriptive radiomic sequences over multiple generations. As a result, this framework improves operational efficiency and enables diagnosis to be run locally at the radiologist's computer while maintaining detection accuracy. We evaluated the evolved deep radiomic sequencer (EDRS) discovered via the proposed evolutionary deep radiomic sequencer discovery framework against state-of-the-art radiomics-driven and discovery radiomics methods using clinical lung CT data with pathologically-proven diagnostic data from the LIDC-IDRI dataset. The evolved deep radiomic sequencer shows improved sensitivity (93.42%), specificity (82.39%), and diagnostic accuracy (88.78%) relative to previous radiomics approaches.

cs.NE↗

arXiv2017

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

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.

cs.CV↗

arXiv2017

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

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.

cs.CV↗

arXiv2017

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

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%.

cs.NE↗

arXiv2017

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

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.

cs.NE↗

arXiv2017

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

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.

cs.NE↗

arXiv2017

Discovery Radiomics for Pathologically-Proven Computed Tomography Lung Cancer Prediction

Lung cancer is the leading cause for cancer related deaths. As such, there is an urgent need for a streamlined process that can allow radiologists to provide diagnosis with greater efficiency and accuracy. A powerful tool to do this is radiomics: a high-dimension imaging feature set. In this study, we take the idea of radiomics one step further by introducing the concept of discovery radiomics for lung cancer prediction using CT imaging data. In this study, we realize these custom radiomic sequencers as deep convolutional sequencers using a deep convolutional neural network learning architecture. To illustrate the prognostic power and effectiveness of the radiomic sequences produced by the discovered sequencer, we perform cancer prediction between malignant and benign lesions from 97 patients using the pathologically-proven diagnostic data from the LIDC-IDRI dataset. Using the clinically provided pathologically-proven data as ground truth, the proposed framework provided an average accuracy of 77.52% via 10-fold cross-validation with a sensitivity of 79.06% and specificity of 76.11%, surpassing the state-of-the art method.

cs.CV↗

arXiv2017

Deep Learning with Darwin: Evolutionary Synthesis of Deep Neural Networks

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.

cs.CV↗

arXiv2016

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

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.

cs.LG↗

arXiv2016

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

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.

stat.ME↗

arXiv2016

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

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.

cs.CV↗

arXiv2015

Sparse Reconstruction of Compressive Sensing MRI using Cross-Domain Stochastically Fully Connected Conditional Random Fields

Magnetic Resonance Imaging (MRI) is a crucial medical imaging technology for the screening and diagnosis of frequently occurring cancers. However image quality may suffer by long acquisition times for MRIs due to patient motion, as well as result in great patient discomfort. Reducing MRI acquisition time can reduce patient discomfort and as a result reduces motion artifacts from the acquisition process. Compressive sensing strategies, when applied to MRI, have been demonstrated to be effective at decreasing acquisition times significantly by sparsely sampling the \emph{k}-space during the acquisition process. However, such a strategy requires advanced reconstruction algorithms to produce high quality and reliable images from compressive sensing MRI. This paper proposes a new reconstruction approach based on cross-domain stochastically fully connected conditional random fields (CD-SFCRF) for compressive sensing MRI. The CD-SFCRF introduces constraints in both \emph{k}-space and spatial domains within a stochastically fully connected graphical model to produce improved MRI reconstruction. Experimental results using T2-weighted (T2w) imaging and diffusion-weighted imaging (DWI) of the prostate show strong performance in preserving fine details and tissue structures in the reconstructed images when compared to other tested methods even at low sampling rates.

cs.CV↗

arXiv2015

Domain Adaptation and Transfer Learning in StochasticNets

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.

cs.CV↗

arXiv2015

Efficient Deep Feature Learning and Extraction via StochasticNets

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.

cs.LG↗

arXiv2015

Discovery Radiomics via StochasticNet Sequencers for Cancer Detection

Radiomics has proven to be a powerful prognostic tool for cancer detection, and has previously been applied in lung, breast, prostate, and head-and-neck cancer studies with great success. However, these radiomics-driven methods rely on pre-defined, hand-crafted radiomic feature sets that can limit their ability to characterize unique cancer traits. In this study, we introduce a novel discovery radiomics framework where we directly discover custom radiomic features from the wealth of available medical imaging data. In particular, we leverage novel StochasticNet radiomic sequencers for extracting custom radiomic features tailored for characterizing unique cancer tissue phenotype. Using StochasticNet radiomic sequencers discovered using a wealth of lung CT data, we perform binary classification on 42,340 lung lesions obtained from the CT scans of 93 patients in the LIDC-IDRI dataset. Preliminary results show significant improvement over previous state-of-the-art methods, indicating the potential of the proposed discovery radiomics framework for improving cancer screening and diagnosis.

cs.CV↗

arXiv2015

StochasticNet: Forming Deep Neural Networks via Stochastic Connectivity

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.

cs.CV↗

arXiv2015

Discovery Radiomics for Multi-Parametric MRI Prostate Cancer Detection

Prostate cancer is the most diagnosed form of cancer in Canadian men, and is the third leading cause of cancer death. Despite these statistics, prognosis is relatively good with a sufficiently early diagnosis, making fast and reliable prostate cancer detection crucial. As imaging-based prostate cancer screening, such as magnetic resonance imaging (MRI), requires an experienced medical professional to extensively review the data and perform a diagnosis, radiomics-driven methods help streamline the process and has the potential to significantly improve diagnostic accuracy and efficiency, and thus improving patient survival rates. These radiomics-driven methods currently rely on hand-crafted sets of quantitative imaging-based features, which are selected manually and can limit their ability to fully characterize unique prostate cancer tumour phenotype. In this study, we propose a novel \textit{discovery radiomics} framework for generating custom radiomic sequences tailored for prostate cancer detection. Discovery radiomics aims to uncover abstract imaging-based features that capture highly unique tumour traits and characteristics beyond what can be captured using predefined feature models. In this paper, we discover new custom radiomic sequencers for generating new prostate radiomic sequences using multi-parametric MRI data. We evaluated the performance of the discovered radiomic sequencer against a state-of-the-art hand-crafted radiomic sequencer for computer-aided prostate cancer detection with a feedforward neural network using real clinical prostate multi-parametric MRI data. Results for the discovered radiomic sequencer demonstrate good performance in prostate cancer detection and clinical decision support relative to the hand-crafted radiomic sequencer. The use of discovery radiomics shows potential for more efficient and reliable automatic prostate cancer detection.

cs.CV↗

arXiv2015

Depth Compensated Spectral Domain Optical Coherence Tomography via Digital Compensation

Spectral Domain Optical Coherence Tomography (SD-OCT) is a well-known imaging modality which allows for \textit{in-vivo} visualization of the morphology of different biological tissues at cellular level resolutions. The overall SD-OCT imaging quality in terms of axial resolution and Signal-to-Noise Ratio (SNR) degrades with imaging depth, while the lateral resolution degrades with distance from the focal plane. This image quality degradation is due both to the design of the SD-OCT imaging system and the optical properties of the imaged object. Here, we present a novel Depth Compensated SD-OCT (DC-OCT) system that integrates a Depth Compensating Digital Signal Processing (DC-DSP) module to improve the overall imaging quality via digital compensation. The designed DC-DSP module can be integrated to any SD-OCT system and is able to simultaneously compensate for the depth-dependent loss of axial and lateral resolutions, depth-varying SNR, as well as sidelobe artifact for improved imaging quality. The integrated DC-DSP module is based on a unified Maximum a Posteriori (MAP) framework which incorporates a Stochastically Fully-connected Conditional Random Field (SF-CRF) model to produce tomograms with reduced speckle noise and artifact, as well as higher spatial resolution. The performance of our proposed DC-OCT system was tested on a USAF resolution target as well as different biological tissue samples, and the results demonstrate the potential of the proposed DC-OCT system for improving spatial resolution, contrast, and SNR.

physics.optics↗