Journal Articles

Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915

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Author: search.filters.author.Liu BSubject: search.filters.subject.Deep Learning

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    Efficient Limb Range of Motion Analysis from a Monocular Camera for Edge Devices.
    (MDPI (Basel, Switzerland), 2025-01-22) Yan X; Zhang L; Liu B; Qu G; Amerini I; Russo P; Di Ciaccio F
    Traditional limb kinematic analysis relies on manual goniometer measurements. With computer vision advancements, integrating RGB cameras can minimize manual labor. Although deep learning-based cameras aim to offer the same ease as manual goniometers, previous approaches have prioritized accuracy over efficiency and cost on PC-based devices. Nevertheless, healthcare providers require a high-performance, low-cost, camera-based tool for assessing upper and lower limb range of motion (ROM). To address this, we propose a lightweight, fast, deep learning model to estimate a human pose and utilize predicted joints for limb ROM measurement. Furthermore, the proposed model is optimized for deployment on resource-constrained edge devices, balancing accuracy and the benefits of edge computing like cost-effectiveness and localized data processing. Our model uses a compact neural network architecture with 8-bit quantized parameters for enhanced memory efficiency and reduced latency. Evaluated on various upper and lower limb tasks, it runs 4.1 times faster and is 15.5 times smaller than a state-of-the-art model, achieving satisfactory ROM measurement accuracy and agreement with a goniometer. We also conduct an experiment on a Raspberry Pi, illustrating that the method can maintain accuracy while reducing equipment and energy costs. This result indicates the potential for deployment on other edge devices and provides the flexibility to adapt to various hardware environments, depending on diverse needs and resources.
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    Potential rapid intraoperative cancer diagnosis using dynamic full-field optical coherence tomography and deep learning: A prospective cohort study in breast cancer patients
    (Elsevier B V on behalf of the Science China Press, 2024-06-15) Zhang S; Yang B; Yang H; Zhao J; Zhang Y; Gao Y; Monteiro O; Zhang K; Liu B; Wang S
    An intraoperative diagnosis is critical for precise cancer surgery. However, traditional intraoperative assessments based on hematoxylin and eosin (H&E) histology, such as frozen section, are time-, resource-, and labor-intensive, and involve specimen-consuming concerns. Here, we report a near-real-time automated cancer diagnosis workflow for breast cancer that combines dynamic full-field optical coherence tomography (D-FFOCT), a label-free optical imaging method, and deep learning for bedside tumor diagnosis during surgery. To classify the benign and malignant breast tissues, we conducted a prospective cohort trial. In the modeling group (n = 182), D-FFOCT images were captured from April 26 to June 20, 2018, encompassing 48 benign lesions, 114 invasive ductal carcinoma (IDC), 10 invasive lobular carcinoma, 4 ductal carcinoma in situ (DCIS), and 6 rare tumors. Deep learning model was built up and fine-tuned in 10,357 D-FFOCT patches. Subsequently, from June 22 to August 17, 2018, independent tests (n = 42) were conducted on 10 benign lesions, 29 IDC, 1 DCIS, and 2 rare tumors. The model yielded excellent performance, with an accuracy of 97.62%, sensitivity of 96.88% and specificity of 100%; only one IDC was misclassified. Meanwhile, the acquisition of the D-FFOCT images was non-destructive and did not require any tissue preparation or staining procedures. In the simulated intraoperative margin evaluation procedure, the time required for our novel workflow (approximately 3 min) was significantly shorter than that required for traditional procedures (approximately 30 min). These findings indicate that the combination of D-FFOCT and deep learning algorithms can streamline intraoperative cancer diagnosis independently of traditional pathology laboratory procedures.
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    DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network
    (BioMed Central Ltd, 2023-09-18) Zhang J; Liu B; Wu J; Wang Z; Li J
    Understanding gene expression processes necessitates the accurate classification and identification of transcription factors, which is supported by high-throughput sequencing technologies. However, these techniques suffer from inherent limitations such as time consumption and high costs. To address these challenges, the field of bioinformatics has increasingly turned to deep learning technologies for analyzing gene sequences. Nevertheless, the pursuit of improved experimental results has led to the inclusion of numerous complex analysis function modules, resulting in models with a growing number of parameters. To overcome these limitations, it is proposed a novel approach for analyzing DNA transcription factor sequences, which is named as DeepCAC. This method leverages deep convolutional neural networks with a multi-head self-attention mechanism. By employing convolutional neural networks, it can effectively capture local hidden features in the sequences. Simultaneously, the multi-head self-attention mechanism enhances the identification of hidden features with long-distant dependencies. This approach reduces the overall number of parameters in the model while harnessing the computational power of sequence data from multi-head self-attention. Through training with labeled data, experiments demonstrate that this approach significantly improves performance while requiring fewer parameters compared to existing methods. Additionally, the effectiveness of our approach  is validated in accurately predicting DNA transcription factor sequences.
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    DL-PPI: a method on prediction of sequenced protein-protein interaction based on deep learning
    (BioMed Central Ltd, 2023-12) Wu J; Liu B; Zhang J; Wang Z; Li J
    PURPOSE: Sequenced Protein-Protein Interaction (PPI) prediction represents a pivotal area of study in biology, playing a crucial role in elucidating the mechanistic underpinnings of diseases and facilitating the design of novel therapeutic interventions. Conventional methods for extracting features through experimental processes have proven to be both costly and exceedingly complex. In light of these challenges, the scientific community has turned to computational approaches, particularly those grounded in deep learning methodologies. Despite the progress achieved by current deep learning technologies, their effectiveness diminishes when applied to larger, unfamiliar datasets. RESULTS: In this study, the paper introduces a novel deep learning framework, termed DL-PPI, for predicting PPIs based on sequence data. The proposed framework comprises two key components aimed at improving the accuracy of feature extraction from individual protein sequences and capturing relationships between proteins in unfamiliar datasets. 1. Protein Node Feature Extraction Module: To enhance the accuracy of feature extraction from individual protein sequences and facilitate the understanding of relationships between proteins in unknown datasets, the paper devised a novel protein node feature extraction module utilizing the Inception method. This module efficiently captures relevant patterns and representations within protein sequences, enabling more informative feature extraction. 2. Feature-Relational Reasoning Network (FRN): In the Global Feature Extraction module of our model, the paper developed a novel FRN that leveraged Graph Neural Networks to determine interactions between pairs of input proteins. The FRN effectively captures the underlying relational information between proteins, contributing to improved PPI predictions. DL-PPI framework demonstrates state-of-the-art performance in the realm of sequence-based PPI prediction.