arXiv subjects

Hongyi Pan

Publications and source records attributed to Hongyi Pan.

At least 37 records · Page 2Linked to original sources

arXiv2024

Sparse Mamba: Introducing Controllability, Observability, And Stability To Structural State Space Models

Structured state space models' (SSMs) development in recent studies, such as Mamba and Mamba2, outperformed and solved the computational inefficiency of transformers and large language models at small to medium scale. In this work, we introduce the concept of controllability and observability to the original Mamba SSM's architecture in our Sparse-Mamba (S-Mamba) for natural language processing (NLP) applications. Moreover, we reinforce stability on the $nxn$ $A$ matrix on Mmaba2. The Mamba SSMs architecture drops the need for attention layers or multilayer perception blocks in transformers. However, current Mamba models lack reinforcement of controllability in state-space equations for computing the $A$, $B$, $C$, and $D$ matrices at each time step, leading to increased complexity and computational costs. Furthermore, the $A$ matrix in Mamba2 is not always stable. We demonstrate a reduction of parameters compared to the first published Mamba and Mamba2. We showcase an improvement in perplexity by 5\% and a decrease in training time by 3\% after reinforcing controllability and observability on the original Mamba architecture in our proposed S-Mamba. We further enforce stability on the $A$ matrix in Mamba2 to improve the loss and perplexity of the model. The controllable and stable $n \times n$ state matrix $A$ is sparse, and it has only $n$ free parameters. Our novel approach will ensure controllable/observable and stable SSMs, which will be the gate key for Mamba3.

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arXiv2024

A Probabilistic Hadamard U-Net for MRI Bias Field Correction

Magnetic field inhomogeneity correction remains a challenging task in MRI analysis. Most established techniques are designed for brain MRI by supposing that image intensities in the identical tissue follow a uniform distribution. Such an assumption cannot be easily applied to other organs, especially those that are small in size and heterogeneous in texture (large variations in intensity), such as the prostate. To address this problem, this paper proposes a probabilistic Hadamard U-Net (PHU-Net) for prostate MRI bias field correction. First, a novel Hadamard U-Net (HU-Net) is introduced to extract the low-frequency scalar field, multiplied by the original input to obtain the prototypical corrected image. HU-Net converts the input image from the time domain into the frequency domain via Hadamard transform. In the frequency domain, high-frequency components are eliminated using the trainable filter (scaling layer), hard-thresholding layer, and sparsity penalty. Next, a conditional variational autoencoder is used to encode possible bias field-corrected variants into a low-dimensional latent space. Random samples drawn from latent space are then incorporated with a prototypical corrected image to generate multiple plausible images. Experimental results demonstrate the effectiveness of PHU-Net in correcting bias-field in prostate MRI with a fast inference speed. It has also been shown that prostate MRI segmentation accuracy improves with the high-quality corrected images from PHU-Net. The code will be available in the final version of this manuscript.

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arXiv2024

Large-Scale Multi-Center CT and MRI Segmentation of Pancreas with Deep Learning

Automated volumetric segmentation of the pancreas on cross-sectional imaging is needed for diagnosis and follow-up of pancreatic diseases. While CT-based pancreatic segmentation is more established, MRI-based segmentation methods are understudied, largely due to a lack of publicly available datasets, benchmarking research efforts, and domain-specific deep learning methods. In this retrospective study, we collected a large dataset (767 scans from 499 participants) of T1-weighted (T1W) and T2-weighted (T2W) abdominal MRI series from five centers between March 2004 and November 2022. We also collected CT scans of 1,350 patients from publicly available sources for benchmarking purposes. We developed a new pancreas segmentation method, called PanSegNet, combining the strengths of nnUNet and a Transformer network with a new linear attention module enabling volumetric computation. We tested PanSegNet's accuracy in cross-modality (a total of 2,117 scans) and cross-center settings with Dice and Hausdorff distance (HD95) evaluation metrics. We used Cohen's kappa statistics for intra and inter-rater agreement evaluation and paired t-tests for volume and Dice comparisons, respectively. For segmentation accuracy, we achieved Dice coefficients of 88.3% (std: 7.2%, at case level) with CT, 85.0% (std: 7.9%) with T1W MRI, and 86.3% (std: 6.4%) with T2W MRI. There was a high correlation for pancreas volume prediction with R^2 of 0.91, 0.84, and 0.85 for CT, T1W, and T2W, respectively. We found moderate inter-observer (0.624 and 0.638 for T1W and T2W MRI, respectively) and high intra-observer agreement scores. All MRI data is made available at https://osf.io/kysnj/. Our source code is available at https://github.com/NUBagciLab/PaNSegNet.

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arXiv2024

MDNet: Multi-Decoder Network for Abdominal CT Organs Segmentation

Accurate segmentation of organs from abdominal CT scans is essential for clinical applications such as diagnosis, treatment planning, and patient monitoring. To handle challenges of heterogeneity in organ shapes, sizes, and complex anatomical relationships, we propose a \textbf{\textit{\ac{MDNet}}}, an encoder-decoder network that uses the pre-trained \textit{MiT-B2} as the encoder and multiple different decoder networks. Each decoder network is connected to a different part of the encoder via a multi-scale feature enhancement dilated block. With each decoder, we increase the depth of the network iteratively and refine segmentation masks, enriching feature maps by integrating previous decoders' feature maps. To refine the feature map further, we also utilize the predicted masks from the previous decoder to the current decoder to provide spatial attention across foreground and background regions. MDNet effectively refines the segmentation mask with a high dice similarity coefficient (DSC) of 0.9013 and 0.9169 on the Liver Tumor segmentation (LiTS) and MSD Spleen datasets. Additionally, it reduces Hausdorff distance (HD) to 3.79 for the LiTS dataset and 2.26 for the spleen segmentation dataset, underscoring the precision of MDNet in capturing the complex contours. Moreover, \textit{\ac{MDNet}} is more interpretable and robust compared to the other baseline models.

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arXiv2024

PAM-UNet: Shifting Attention on Region of Interest in Medical Images

Computer-aided segmentation methods can assist medical personnel in improving diagnostic outcomes. While recent advancements like UNet and its variants have shown promise, they face a critical challenge: balancing accuracy with computational efficiency. Shallow encoder architectures in UNets often struggle to capture crucial spatial features, leading in inaccurate and sparse segmentation. To address this limitation, we propose a novel \underline{P}rogressive \underline{A}ttention based \underline{M}obile \underline{UNet} (\underline{PAM-UNet}) architecture. The inverted residual (IR) blocks in PAM-UNet help maintain a lightweight framework, while layerwise \textit{Progressive Luong Attention} ($\mathcal{PLA}$) promotes precise segmentation by directing attention toward regions of interest during synthesis. Our approach prioritizes both accuracy and speed, achieving a commendable balance with a mean IoU of 74.65 and a dice score of 82.87, while requiring only 1.32 floating-point operations per second (FLOPS) on the Liver Tumor Segmentation Benchmark (LiTS) 2017 dataset. These results highlight the importance of developing efficient segmentation models to accelerate the adoption of AI in clinical practice.

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arXiv2024

Multichannel Orthogonal Transform-Based Perceptron Layers for Efficient ResNets

In this paper, we propose a set of transform-based neural network layers as an alternative to the $3\times3$ Conv2D layers in Convolutional Neural Networks (CNNs). The proposed layers can be implemented based on orthogonal transforms such as the Discrete Cosine Transform (DCT), Hadamard transform (HT), and biorthogonal Block Wavelet Transform (BWT). Furthermore, by taking advantage of the convolution theorems, convolutional filtering operations are performed in the transform domain using element-wise multiplications. Trainable soft-thresholding layers, that remove noise in the transform domain, bring nonlinearity to the transform domain layers. Compared to the Conv2D layer, which is spatial-agnostic and channel-specific, the proposed layers are location-specific and channel-specific. Moreover, these proposed layers reduce the number of parameters and multiplications significantly while improving the accuracy results of regular ResNets on the ImageNet-1K classification task. Furthermore, they can be inserted with a batch normalization layer before the global average pooling layer in the conventional ResNets as an additional layer to improve classification accuracy.

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arXiv2024

A Hybrid Quantum-Classical Approach based on the Hadamard Transform for the Convolutional Layer

In this paper, we propose a novel Hadamard Transform (HT)-based neural network layer for hybrid quantum-classical computing. It implements the regular convolutional layers in the Hadamard transform domain. The idea is based on the HT convolution theorem which states that the dyadic convolution between two vectors is equivalent to the element-wise multiplication of their HT representation. Computing the HT is simply the application of a Hadamard gate to each qubit individually, so the HT computations of our proposed layer can be implemented on a quantum computer. Compared to the regular Conv2D layer, the proposed HT-perceptron layer is computationally more efficient. Compared to a CNN with the same number of trainable parameters and 99.26\% test accuracy, our HT network reaches 99.31\% test accuracy with 57.1\% MACs reduced in the MNIST dataset; and in our ImageNet-1K experiments, our HT-based ResNet-50 exceeds the accuracy of the baseline ResNet-50 by 0.59\% center-crop top-1 accuracy using 11.5\% fewer parameters with 12.6\% fewer MACs.

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arXiv2023

Domain Generalization with Fourier Transform and Soft Thresholding

Domain generalization aims to train models on multiple source domains so that they can generalize well to unseen target domains. Among many domain generalization methods, Fourier-transform-based domain generalization methods have gained popularity primarily because they exploit the power of Fourier transformation to capture essential patterns and regularities in the data, making the model more robust to domain shifts. The mainstream Fourier-transform-based domain generalization swaps the Fourier amplitude spectrum while preserving the phase spectrum between the source and the target images. However, it neglects background interference in the amplitude spectrum. To overcome this limitation, we introduce a soft-thresholding function in the Fourier domain. We apply this newly designed algorithm to retinal fundus image segmentation, which is important for diagnosing ocular diseases but the neural network's performance can degrade across different sources due to domain shifts. The proposed technique basically enhances fundus image augmentation by eliminating small values in the Fourier domain and providing better generalization. The innovative nature of the soft thresholding fused with Fourier-transform-based domain generalization improves neural network models' performance by reducing the target images' background interference significantly. Experiments on public data validate our approach's effectiveness over conventional and state-of-the-art methods with superior segmentation metrics.

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arXiv2023

A novel asymmetrical autoencoder with a sparsifying discrete cosine Stockwell transform layer for gearbox sensor data compression

The lack of an efficient compression model remains a challenge for the wireless transmission of gearbox data in non-contact gear fault diagnosis problems. In this paper, we present a signal-adaptive asymmetrical autoencoder with a transform domain layer to compress sensor signals. First, a new discrete cosine Stockwell transform (DCST) layer is introduced to replace linear layers in a multi-layer autoencoder. A trainable filter is implemented in the DCST domain by utilizing the multiplication property of the convolution. A trainable hard-thresholding layer is applied to reduce redundant data in the DCST layer to make the feature map sparse. In comparison to the linear layer, the DCST layer reduces the number of trainable parameters and improves the accuracy of data reconstruction. Second, training the autoencoder with a sparsifying DCST layer only requires a small number of datasets. The proposed method is superior to other autoencoder-based methods on the University of Connecticut (UoC) and Southeast University (SEU) gearbox datasets, as the average quality score is improved by 2.00% at the lowest and 32.35% at the highest with a limited number of training samples

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arXiv2023

Electroencephalogram Sensor Data Compression Using An Asymmetrical Sparse Autoencoder With A Discrete Cosine Transform Layer

Electroencephalogram (EEG) data compression is necessary for wireless recording applications to reduce the amount of data that needs to be transmitted. In this paper, an asymmetrical sparse autoencoder with a discrete cosine transform (DCT) layer is proposed to compress EEG signals. The encoder module of the autoencoder has a combination of a fully connected linear layer and the DCT layer to reduce redundant data using hard-thresholding nonlinearity. Furthermore, the DCT layer includes trainable hard-thresholding parameters and scaling layers to give emphasis or de-emphasis on individual DCT coefficients. Finally, the one-by-one convolutional layer generates the latent space. The sparsity penalty-based cost function is employed to keep the feature map as sparse as possible in the latent space. The latent space data is transmitted to the receiver. The decoder module of the autoencoder is designed using the inverse DCT and two fully connected linear layers to improve the accuracy of data reconstruction. In comparison to other state-of-the-art methods, the proposed method significantly improves the average quality score in various data compression experiments.

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arXiv2023

ADC/DAC-Free Analog Acceleration of Deep Neural Networks with Frequency Transformation

The edge processing of deep neural networks (DNNs) is becoming increasingly important due to its ability to extract valuable information directly at the data source to minimize latency and energy consumption. Frequency-domain model compression, such as with the Walsh-Hadamard transform (WHT), has been identified as an efficient alternative. However, the benefits of frequency-domain processing are often offset by the increased multiply-accumulate (MAC) operations required. This paper proposes a novel approach to an energy-efficient acceleration of frequency-domain neural networks by utilizing analog-domain frequency-based tensor transformations. Our approach offers unique opportunities to enhance computational efficiency, resulting in several high-level advantages, including array micro-architecture with parallelism, ADC/DAC-free analog computations, and increased output sparsity. Our approach achieves more compact cells by eliminating the need for trainable parameters in the transformation matrix. Moreover, our novel array micro-architecture enables adaptive stitching of cells column-wise and row-wise, thereby facilitating perfect parallelism in computations. Additionally, our scheme enables ADC/DAC-free computations by training against highly quantized matrix-vector products, leveraging the parameter-free nature of matrix multiplications. Another crucial aspect of our design is its ability to handle signed-bit processing for frequency-based transformations. This leads to increased output sparsity and reduced digitization workload. On a 16$\times$16 crossbars, for 8-bit input processing, the proposed approach achieves the energy efficiency of 1602 tera operations per second per Watt (TOPS/W) without early termination strategy and 5311 TOPS/W with early termination strategy at VDD = 0.8 V.

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arXiv2023

GazeGNN: A Gaze-Guided Graph Neural Network for Chest X-ray Classification

Eye tracking research is important in computer vision because it can help us understand how humans interact with the visual world. Specifically for high-risk applications, such as in medical imaging, eye tracking can help us to comprehend how radiologists and other medical professionals search, analyze, and interpret images for diagnostic and clinical purposes. Hence, the application of eye tracking techniques in disease classification has become increasingly popular in recent years. Contemporary works usually transform gaze information collected by eye tracking devices into visual attention maps (VAMs) to supervise the learning process. However, this is a time-consuming preprocessing step, which stops us from applying eye tracking to radiologists' daily work. To solve this problem, we propose a novel gaze-guided graph neural network (GNN), GazeGNN, to leverage raw eye-gaze data without being converted into VAMs. In GazeGNN, to directly integrate eye gaze into image classification, we create a unified representation graph that models both images and gaze pattern information. With this benefit, we develop a real-time, real-world, end-to-end disease classification algorithm for the first time in the literature. This achievement demonstrates the practicality and feasibility of integrating real-time eye tracking techniques into the daily work of radiologists. To our best knowledge, GazeGNN is the first work that adopts GNN to integrate image and eye-gaze data. Our experiments on the public chest X-ray dataset show that our proposed method exhibits the best classification performance compared to existing methods. The code is available at https://github.com/ukaukaaaa/GazeGNN.

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arXiv2023

Input Normalized Stochastic Gradient Descent Training of Deep Neural Networks

In this paper, we propose a novel optimization algorithm for training machine learning models called Input Normalized Stochastic Gradient Descent (INSGD), inspired by the Normalized Least Mean Squares (NLMS) algorithm used in adaptive filtering. When training complex models on large datasets, the choice of optimizer parameters, particularly the learning rate, is crucial to avoid divergence. Our algorithm updates the network weights using stochastic gradient descent with $\ell_1$ and $\ell_2$-based normalizations applied to the learning rate, similar to NLMS. However, unlike existing normalization methods, we exclude the error term from the normalization process and instead normalize the update term using the input vector to the neuron. Our experiments demonstrate that our optimization algorithm achieves higher accuracy levels compared to different initialization settings. We evaluate the efficiency of our training algorithm on benchmark datasets using ResNet-18, WResNet-20, ResNet-50, and a toy neural network. Our INSGD algorithm improves the accuracy of ResNet-18 on CIFAR-10 from 92.42\% to 92.71\%, WResNet-20 on CIFAR-100 from 76.20\% to 77.39\%, and ResNet-50 on ImageNet-1K from 75.52\% to 75.67\%.

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arXiv2023

Wildfire Detection Via Transfer Learning: A Survey

This paper surveys different publicly available neural network models used for detecting wildfires using regular visible-range cameras which are placed on hilltops or forest lookout towers. The neural network models are pre-trained on ImageNet-1K and fine-tuned on a custom wildfire dataset. The performance of these models is evaluated on a diverse set of wildfire images, and the survey provides useful information for those interested in using transfer learning for wildfire detection. Swin Transformer-tiny has the highest AUC value but ConvNext-tiny detects all the wildfire events and has the lowest false alarm rate in our dataset.

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arXiv2023

Real-time Wireless ECG-derived Respiration Rate Estimation Using an Autoencoder with a DCT Layer

In this paper, we present a wireless ECG-derived Respiration Rate (RR) estimation using an autoencoder with a DCT Layer. The wireless wearable system records the ECG data of the subject and the respiration rate is determined from the variations in the baseline level of the ECG data. A straightforward Fourier analysis of the ECG data obtained using the wireless wearable system may lead to incorrect results due to uneven breathing. To improve the estimation precision, we propose a neural network that uses a novel Discrete Cosine Transform (DCT) layer to denoise and decorrelates the data. The DCT layer has trainable weights and soft-thresholds in the transform domain. In our dataset, we improve the Mean Squared Error (MSE) and Mean Absolute Error (MAE) of the Fourier analysis-based approach using our novel neural network with the DCT layer.

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arXiv2022

Classification of the Cervical Vertebrae Maturation (CVM) stages Using the Tripod Network

We present a novel deep learning method for fully automated detection and classification of the Cervical Vertebrae Maturation (CVM) stages. The deep convolutional neural network consists of three parallel networks (TriPodNet) independently trained with different initialization parameters. They also have a built-in set of novel directional filters that highlight the Cervical Verte edges in X-ray images. Outputs of the three parallel networks are combined using a fully connected layer. 1018 cephalometric radiographs were labeled, divided by gender, and classified according to the CVM stages. Resulting images, using different training techniques and patches, were used to train TripodNet together with a set of tunable directional edge enhancers. Data augmentation is implemented to avoid overfitting. TripodNet achieves the state-of-the-art accuracy of 81.18\% in female patients and 75.32\% in male patients. The proposed TripodNet achieves a higher accuracy in our dataset than the Swin Transformers and the previous network models that we investigated for CVM stage estimation.

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arXiv2022

DCT Perceptron Layer: A Transform Domain Approach for Convolution Layer

In this paper, we propose a novel Discrete Cosine Transform (DCT)-based neural network layer which we call DCT-perceptron to replace the $3\times3$ Conv2D layers in the Residual neural Network (ResNet). Convolutional filtering operations are performed in the DCT domain using element-wise multiplications by taking advantage of the Fourier and DCT Convolution theorems. A trainable soft-thresholding layer is used as the nonlinearity in the DCT perceptron. Compared to ResNet's Conv2D layer which is spatial-agnostic and channel-specific, the proposed layer is location-specific and channel-specific. The DCT-perceptron layer reduces the number of parameters and multiplications significantly while maintaining comparable accuracy results of regular ResNets in CIFAR-10 and ImageNet-1K. Moreover, the DCT-perceptron layer can be inserted with a batch normalization layer before the global average pooling layer in the conventional ResNets as an additional layer to improve classification accuracy.

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arXiv2022

Multipod Convolutional Network

In this paper, we introduce a convolutional network which we call MultiPodNet consisting of a combination of two or more convolutional networks which process the input image in parallel to achieve the same goal. Output feature maps of parallel convolutional networks are fused at the fully connected layer of the network. We experimentally observed that three parallel pod networks (TripodNet) produce the best results in commonly used object recognition datasets. Baseline pod networks can be of any type. In this paper, we use ResNets as baseline networks and their inputs are augmented image patches. The number of parameters of the TripodNet is about three times that of a single ResNet. We train the TripodNet using the standard backpropagation type algorithms. In each individual ResNet, parameters are initialized with different random numbers during training. The TripodNet achieved state-of-the-art performance on CIFAR-10 and ImageNet datasets. For example, it improved the accuracy of a single ResNet from 91.66% to 92.47% under the same training process on the CIFAR-10 dataset.

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