arXiv subjects

Yinan Chen

Publications and source records attributed to Yinan Chen.

33 records · Page 2Linked to original sources

arXiv2024

A Sentiment Analysis of Medical Text Based on Deep Learning

The field of natural language processing (NLP) has made significant progress with the rapid development of deep learning technologies. One of the research directions in text sentiment analysis is sentiment analysis of medical texts, which holds great potential for application in clinical diagnosis. However, the medical field currently lacks sufficient text datasets, and the effectiveness of sentiment analysis is greatly impacted by different model design approaches, which presents challenges. Therefore, this paper focuses on the medical domain, using bidirectional encoder representations from transformers (BERT) as the basic pre-trained model and experimenting with modules such as convolutional neural network (CNN), fully connected network (FCN), and graph convolutional networks (GCN) at the output layer. Experiments and analyses were conducted on the METS-CoV dataset to explore the training performance after integrating different deep learning networks. The results indicate that CNN models outperform other networks when trained on smaller medical text datasets in combination with pre-trained models like BERT. This study highlights the significance of model selection in achieving effective sentiment analysis in the medical domain and provides a reference for future research to develop more efficient model architectures.

cs.CL↗

arXiv2024

Generative Software Engineering

The rapid development of deep learning techniques, improved computational power, and the availability of vast training data have led to significant advancements in pre-trained models and large language models (LLMs). Pre-trained models based on architectures such as BERT and Transformer, as well as LLMs like ChatGPT, have demonstrated remarkable language capabilities and found applications in Software engineering. Software engineering tasks can be divided into many categories, among which generative tasks are the most concern by researchers, where pre-trained models and LLMs possess powerful language representation and contextual awareness capabilities, enabling them to leverage diverse training data and adapt to generative tasks through fine-tuning, transfer learning, and prompt engineering. These advantages make them effective tools in generative tasks and have demonstrated excellent performance. In this paper, we present a comprehensive literature review of generative tasks in SE using pre-trained models and LLMs. We accurately categorize SE generative tasks based on software engineering methodologies and summarize the advanced pre-trained models and LLMs involved, as well as the datasets and evaluation metrics used. Additionally, we identify key strengths, weaknesses, and gaps in existing approaches, and propose potential research directions. This review aims to provide researchers and practitioners with an in-depth analysis and guidance on the application of pre-trained models and LLMs in generative tasks within SE.

cs.SE↗

arXiv2024

Are your comments outdated? Towards automatically detecting code-comment consistency

In software development and maintenance, code comments can help developers understand source code, and improve communication among developers. However, developers sometimes neglect to update the corresponding comment when changing the code, resulting in outdated comments (i.e., inconsistent codes and comments). Outdated comments are dangerous and harmful and may mislead subsequent developers. More seriously, the outdated comments may lead to a fatal flaw sometime in the future. To automatically identify the outdated comments in source code, we proposed a learning-based method, called CoCC, to detect the consistency between code and comment. To efficiently identify outdated comments, we extract multiple features from both codes and comments before and after they change. Besides, we also consider the relation between code and comment in our model. Experiment results show that CoCC can effectively detect outdated comments with precision over 90%. In addition, we have identified the 15 most important factors that cause outdated comments, and verified the applicability of CoCC in different programming languages. We also used CoCC to find outdated comments in the latest commits of open source projects, which further proves the effectiveness of the proposed method.

cs.SE↗

arXiv2024

Phonon and defect mediated quantum anomalous Hall insulator to metal transition in magnetically doped topological insulators

Quantum Anomalous Hall (QAH) state in six quintuple layer Cr$_{0.1}$(Bi$_{0.2}$Sb$_{0.8}$)$_{1.9}$Te$_3$ thin films were studied through scanning tunneling spectroscopy (STS) and electrical transport measurements. While the surface state is gapless above the Curie temperature ($T_\mathrm{C} \approx 30$ K), scanning tunneling spectroscopy (STS) of the sample reveals a topologically non-trivial gap with an average value of $\approx 13.5$ meV at 4.2 K below the ferromagnetic transition. Nonetheless, areal STS scans of the magnetic topological insulator exhibit energy modulations on the order of several meV's in the surface bands which result in the valence band maximum in some regions becoming higher than the energy of the conduction band minimum of some other regions that are spatially separated by no more than 3 nm. First principle calculations demonstrate that the origin of the observed inhomogeneous energy band alignment is an outcome of many-body interactions, namely electron-defect interactions and electron-phonon interactions. Defects play the role of locally modifying the energy landscape of surface bands while electron-phonon interactions renormalize the surface bands such that the surface gap becomes reduced by more than 1 meV as temperature is raised from 0 to 4.2 K. These many-body interactions at a finite temperature result in substantial increase of electron tunneling across the spatially separated conduction band pockets even for finite temperatures well below $T_\mathrm{C}$ , thus driving the magnetic topological insulator out of its QAH insulating phase into a metallic phase at a relatively low temperature.

cond-mat.str-el↗

arXiv2023

UPL-SFDA: Uncertainty-aware Pseudo Label Guided Source-Free Domain Adaptation for Medical Image Segmentation

Domain Adaptation (DA) is important for deep learning-based medical image segmentation models to deal with testing images from a new target domain. As the source-domain data are usually unavailable when a trained model is deployed at a new center, Source-Free Domain Adaptation (SFDA) is appealing for data and annotation-efficient adaptation to the target domain. However, existing SFDA methods have a limited performance due to lack of sufficient supervision with source-domain images unavailable and target-domain images unlabeled. We propose a novel Uncertainty-aware Pseudo Label guided (UPL) SFDA method for medical image segmentation. Specifically, we propose Target Domain Growing (TDG) to enhance the diversity of predictions in the target domain by duplicating the pre-trained model's prediction head multiple times with perturbations. The different predictions in these duplicated heads are used to obtain pseudo labels for unlabeled target-domain images and their uncertainty to identify reliable pseudo labels. We also propose a Twice Forward pass Supervision (TFS) strategy that uses reliable pseudo labels obtained in one forward pass to supervise predictions in the next forward pass. The adaptation is further regularized by a mean prediction-based entropy minimization term that encourages confident and consistent results in different prediction heads. UPL-SFDA was validated with a multi-site heart MRI segmentation dataset, a cross-modality fetal brain segmentation dataset, and a 3D fetal tissue segmentation dataset. It improved the average Dice by 5.54, 5.01 and 6.89 percentage points for the three tasks compared with the baseline, respectively, and outperformed several state-of-the-art SFDA methods.

cs.CV↗

arXiv2023

Chemical Mapping of Excitons in Halide Double Perovskites

Halide double perovskites are an emerging class of semiconductors with tremendous chemical and electronic diversity. While their bandstructure features can be understood from frontier-orbital models, chemical intuition for optical excitations remains incomplete. Here, we use \textit{ab initio} many-body perturbation theory within the $GW$ and the Bethe-Salpeter Equation approach to calculate excited-state properties of a representative range of Cs$_2$BB$'$Cl$_6$ double perovskites. Our calculations reveal that double perovskites with different combinations of B and B$'$ cations display a broad variety of electronic bandstructures and dielectric properties, and form excitons with binding energies ranging over several orders of magnitude. We correlate these properties with the orbital-induced anisotropy of charge-carrier effective masses and the long-range behavior of the dielectric function, by comparing with the canonical conditions of the Wannier-Mott model. Furthermore, we derive chemically intuitive rules for predicting the nature of excitons in halide double perovskites using electronic structure information obtained from computationally inexpensive DFT calculations.

cond-mat.mtrl-sci↗

arXiv2023

Transforming Graphs for Enhanced Attribute Clustering: An Innovative Graph Transformer-Based Method

Graph Representation Learning (GRL) is an influential methodology, enabling a more profound understanding of graph-structured data and aiding graph clustering, a critical task across various domains. The recent incursion of attention mechanisms, originally an artifact of Natural Language Processing (NLP), into the realm of graph learning has spearheaded a notable shift in research trends. Consequently, Graph Attention Networks (GATs) and Graph Attention Auto-Encoders have emerged as preferred tools for graph clustering tasks. Yet, these methods primarily employ a local attention mechanism, thereby curbing their capacity to apprehend the intricate global dependencies between nodes within graphs. Addressing these impediments, this study introduces an innovative method known as the Graph Transformer Auto-Encoder for Graph Clustering (GTAGC). By melding the Graph Auto-Encoder with the Graph Transformer, GTAGC is adept at capturing global dependencies between nodes. This integration amplifies the graph representation and surmounts the constraints posed by the local attention mechanism. The architecture of GTAGC encompasses graph embedding, integration of the Graph Transformer within the autoencoder structure, and a clustering component. It strategically alternates between graph embedding and clustering, thereby tailoring the Graph Transformer for clustering tasks, whilst preserving the graph's global structural information. Through extensive experimentation on diverse benchmark datasets, GTAGC has exhibited superior performance against existing state-of-the-art graph clustering methodologies.

cs.LG↗

arXiv2023

Automatic lobe segmentation using attentive cross entropy and end-to-end fissure generation

The automatic lung lobe segmentation algorithm is of great significance for the diagnosis and treatment of lung diseases, however, which has great challenges due to the incompleteness of pulmonary fissures in lung CT images and the large variability of pathological features. Therefore, we propose a new automatic lung lobe segmentation framework, in which we urge the model to pay attention to the area around the pulmonary fissure during the training process, which is realized by a task-specific loss function. In addition, we introduce an end-to-end pulmonary fissure generation method in the auxiliary pulmonary fissure segmentation task, without any additional network branch. Finally, we propose a registration-based loss function to alleviate the convergence difficulty of the Dice loss supervised pulmonary fissure segmentation task. We achieve 97.83% and 94.75% dice scores on our private dataset STLB and public LUNA16 dataset respectively.

eess.IV↗

arXiv2023

Optimizing Investment Strategies with Lazy Factor and Probability Weighting: A Price Portfolio Forecasting and Mean-Variance Model with Transaction Costs Approach

Market traders often engage in the frequent transaction of volatile assets to optimize their total return. In this study, we introduce a novel investment strategy model, anchored on the 'lazy factor.' Our approach bifurcates into a Price Portfolio Forecasting Model and a Mean-Variance Model with Transaction Costs, utilizing probability weights as the coefficients of laziness factors. The Price Portfolio Forecasting Model, leveraging the EXPMA Mean Method, plots the long-term price trend line and forecasts future price movements, incorporating the tangent slope and rate of change. For short-term investments, we apply the ARIMA Model to predict ensuing prices. The Mean-Variance Model with Transaction Costs employs the Monte Carlo Method to formulate the feasible region. To strike an optimal balance between risk and return, equal probability weights are incorporated as coefficients of the laziness factor. To assess the efficacy of this combined strategy, we executed extensive experiments on a specified dataset. Our findings underscore the model's adaptability and generalizability, indicating its potential to transform investment strategies.

q-fin.PM↗

arXiv2023

Semi-supervised Medical Image Segmentation through Dual-task Consistency

Deep learning-based semi-supervised learning (SSL) algorithms have led to promising results in medical images segmentation and can alleviate doctors' expensive annotations by leveraging unlabeled data. However, most of the existing SSL algorithms in literature tend to regularize the model training by perturbing networks and/or data. Observing that multi/dual-task learning attends to various levels of information which have inherent prediction perturbation, we ask the question in this work: can we explicitly build task-level regularization rather than implicitly constructing networks- and/or data-level perturbation-and-transformation for SSL? To answer this question, we propose a novel dual-task-consistency semi-supervised framework for the first time. Concretely, we use a dual-task deep network that jointly predicts a pixel-wise segmentation map and a geometry-aware level set representation of the target. The level set representation is converted to an approximated segmentation map through a differentiable task transform layer. Simultaneously, we introduce a dual-task consistency regularization between the level set-derived segmentation maps and directly predicted segmentation maps for both labeled and unlabeled data. Extensive experiments on two public datasets show that our method can largely improve the performance by incorporating the unlabeled data. Meanwhile, our framework outperforms the state-of-the-art semi-supervised medical image segmentation methods. Code is available at: https://github.com/Luoxd1996/DTC

cs.CV↗

arXiv2022

CDDSA: Contrastive Domain Disentanglement and Style Augmentation for Generalizable Medical Image Segmentation

Generalization to previously unseen images with potential domain shifts and different styles is essential for clinically applicable medical image segmentation, and the ability to disentangle domain-specific and domain-invariant features is key for achieving Domain Generalization (DG). However, existing DG methods can hardly achieve effective disentanglement to get high generalizability. To deal with this problem, we propose an efficient Contrastive Domain Disentanglement and Style Augmentation (CDDSA) framework for generalizable medical image segmentation. First, a disentangle network is proposed to decompose an image into a domain-invariant anatomical representation and a domain-specific style code, where the former is sent to a segmentation model that is not affected by the domain shift, and the disentangle network is regularized by a decoder that combines the anatomical and style codes to reconstruct the input image. Second, to achieve better disentanglement, a contrastive loss is proposed to encourage the style codes from the same domain and different domains to be compact and divergent, respectively. Thirdly, to further improve generalizability, we propose a style augmentation method based on the disentanglement representation to synthesize images in various unseen styles with shared anatomical structures. Our method was validated on a public multi-site fundus image dataset for optic cup and disc segmentation and an in-house multi-site Nasopharyngeal Carcinoma Magnetic Resonance Image (NPC-MRI) dataset for nasopharynx Gross Tumor Volume (GTVnx) segmentation. Experimental results showed that the proposed CDDSA achieved remarkable generalizability across different domains, and it outperformed several state-of-the-art methods in domain-generalizable segmentation.

cs.CV↗

arXiv2022

SenseCare: A Research Platform for Medical Image Informatics and Interactive 3D Visualization

Clinical research on smart health has an increasing demand for intelligent and clinic-oriented medical image computing algorithms and platforms that support various applications. To this end, we have developed SenseCare research platform, which is designed to facilitate translational research on intelligent diagnosis and treatment planning in various clinical scenarios. To enable clinical research with Artificial Intelligence (AI), SenseCare provides a range of AI toolkits for different tasks, including image segmentation, registration, lesion and landmark detection from various image modalities ranging from radiology to pathology. In addition, SenseCare is clinic-oriented and supports a wide range of clinical applications such as diagnosis and surgical planning for lung cancer, pelvic tumor, coronary artery disease, etc. SenseCare provides several appealing functions and features such as advanced 3D visualization, concurrent and efficient web-based access, fast data synchronization and high data security, multi-center deployment, support for collaborative research, etc. In this report, we present an overview of SenseCare as an efficient platform providing comprehensive toolkits and high extensibility for intelligent image analysis and clinical research in different application scenarios. We also summarize the research outcome through the collaboration with multiple hospitals.

cs.HC↗

arXiv2022

SCPM-Net: An Anchor-free 3D Lung Nodule Detection Network using Sphere Representation and Center Points Matching

Lung nodule detection from 3D Computed Tomography scans plays a vital role in efficient lung cancer screening. Despite the SOTA performance obtained by recent anchor-based detectors using CNNs for this task, they require predetermined anchor parameters such as the size, number, and aspect ratio of anchors, and have limited robustness when dealing with lung nodules with a massive variety of sizes. To overcome these problems, we propose a 3D sphere representation-based center-points matching detection network that is anchor-free and automatically predicts the position, radius, and offset of nodules without the manual design of nodule/anchor parameters. The SCPM-Net consists of two novel components: sphere representation and center points matching. First, to match the nodule annotation in clinical practice, we replace the commonly used bounding box with our proposed bounding sphere to represent nodules with the centroid, radius, and local offset in 3D space. A compatible sphere-based intersection over-union loss function is introduced to train the lung nodule detection network stably and efficiently. Second, we empower the network anchor-free by designing a positive center-points selection and matching process, which naturally discards pre-determined anchor boxes. An online hard example mining and re-focal loss subsequently enable the CPM process to be more robust, resulting in more accurate point assignment and mitigation of class imbalance. In addition, to better capture spatial information and 3D context for the detection, we propose to fuse multi-level spatial coordinate maps with the feature extractor and combine them with 3D squeeze-and-excitation attention modules. Experimental results on the LUNA16 dataset showed that our proposed framework achieves superior performance compared with existing anchor-based and anchor-free methods for lung nodule detection.

cs.CV↗

arXiv2021

Efficient Semi-Supervised Gross Target Volume of Nasopharyngeal Carcinoma Segmentation via Uncertainty Rectified Pyramid Consistency

Gross Target Volume (GTV) segmentation plays an irreplaceable role in radiotherapy planning for Nasopharyngeal Carcinoma (NPC). Despite that Convolutional Neural Networks (CNN) have achieved good performance for this task, they rely on a large set of labeled images for training, which is expensive and time-consuming to acquire. In this paper, we propose a novel framework with Uncertainty Rectified Pyramid Consistency (URPC) regularization for semi-supervised NPC GTV segmentation. Concretely, we extend a backbone segmentation network to produce pyramid predictions at different scales. The pyramid predictions network (PPNet) is supervised by the ground truth of labeled images and a multi-scale consistency loss for unlabeled images, motivated by the fact that prediction at different scales for the same input should be similar and consistent. However, due to the different resolution of these predictions, encouraging them to be consistent at each pixel directly has low robustness and may lose some fine details. To address this problem, we further design a novel uncertainty rectifying module to enable the framework to gradually learn from meaningful and reliable consensual regions at different scales. Experimental results on a dataset with 258 NPC MR images showed that with only 10% or 20% images labeled, our method largely improved the segmentation performance by leveraging the unlabeled images, and it also outperformed five state-of-the-art semi-supervised segmentation methods. Moreover, when only 50% images labeled, URPC achieved an average Dice score of 82.74% that was close to fully supervised learning.

cs.CV↗

arXiv2020

KLDivNet: An unsupervised neural network for multi-modality image registration

Multi-modality image registration is one of the most underlined processes in medical image analysis. Recently, convolutional neural networks (CNNs) have shown significant potential in deformable registration. However, the lack of voxel-wise ground truth challenges the training of CNNs for an accurate registration. In this work, we propose a cross-modality similarity metric, based on the KL-divergence of image variables, and implement an efficient estimation method using a CNN. This estimation network, referred to as KLDivNet, can be trained unsupervisedly. We then embed the KLDivNet into a registration network to achieve the unsupervised deformable registration for multi-modality images. We employed three datasets, i.e., AAL Brain, LiTS Liver and Hospital Liver, with both the intra- and inter-modality image registration tasks for validation. Results showed that our similarity metric was effective, and the proposed registration network delivered superior performance compared to the state-of-the-art methods.

cs.CV↗