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At least 25 kinds of detector-like devices need to be integrated in Phase I of the High Energy Photon Source (HEPS), and the work needs to be carefully planned to maximise productivity with highly limited human resources. After a systematic analysis on the actual work involved in detector integration, a separation of concerns between collaborating groups of personnel is established to minimise the duplication of efforts. To facilitate software development for detector integration, the ADGenICam library, which abstracts repeated code in EPICS modules for cameras, is extended to support a much wider range of detectors. An increasingly considerable fraction of detectors, both inside and outside HEPS, offer performance that exceed capabilities of the areaDetector framework in EPICS. Given this background, areaDetector's limitations in performance and architecture are analysed, and a QueueIOC -based framework that overcomes these limitations is introduced. A simple, flexible ZeroMQ-based protocol is used for data transport in this framework, while RDMA transport and multi-node readout will be explored for higher data throughputs. By calling C/C++ libraries from within Python, the performance of the former and the expressiveness of the latter can coexist nicely; the expressiveness allows for much higher efficiency in the implementation and use of integration modules functionally comparable to their EPICS counterparts., Comment: 11 pages, 3 figures

For predicting cancer survival outcomes, standard approaches in clinical research are often based on two main modalities: pathology images for observing cell morphology features, and genomic (e.g., bulk RNA-seq) for quantifying gene expressions. However, existing pathology-genomic multi-modal algorithms face significant challenges: (1) Valuable biological insights regarding genes and gene-gene interactions are frequently overlooked; (2) one modality often dominates the optimization process, causing inadequate training for the other modality. In this paper, we introduce a new multi-modal ``Path-GPTOmic" framework for cancer survival outcome prediction. First, to extract valuable biological insights, we regulate the embedding space of a foundation model, scGPT, initially trained on single-cell RNA-seq data, making it adaptable for bulk RNA-seq data. Second, to address the imbalance-between-modalities problem, we propose a gradient modulation mechanism tailored to the Cox partial likelihood loss for survival prediction. The contributions of the modalities are dynamically monitored and adjusted during the training process, encouraging that both modalities are sufficiently trained. Evaluated on two TCGA(The Cancer Genome Atlas) datasets, our model achieves substantially improved survival prediction accuracy., Comment: Accepted by IEEE International Symposium on Biomedical Imaging (ISBI 2024)

Male infertility accounts for about one-third of global infertility cases. Manual assessment of sperm abnormalities through head morphology analysis encounters issues of observer variability and diagnostic discrepancies among experts. Its alternative, Computer-Assisted Semen Analysis (CASA), suffers from low-quality sperm images, small datasets, and noisy class labels. We propose a new approach for sperm head morphology classification, called SHMC-Net, which uses segmentation masks of sperm heads to guide the morphology classification of sperm images. SHMC-Net generates reliable segmentation masks using image priors, refines object boundaries with an efficient graph-based method, and trains an image network with sperm head crops and a mask network with the corresponding masks. In the intermediate stages of the networks, image and mask features are fused with a fusion scheme to better learn morphological features. To handle noisy class labels and regularize training on small datasets, SHMC-Net applies Soft Mixup to combine mixup augmentation and a loss function. We achieve state-of-the-art results on SCIAN and HuSHeM datasets, outperforming methods that use additional pre-training or costly ensembling techniques., Comment: Published on ISBI 2024

Image reconstruction-based anomaly detection models are widely explored in industrial visual inspection. However, existing models usually suffer from the trade-off between normal reconstruction fidelity and abnormal reconstruction distinguishability, which damages the performance. In this paper, we find that the above trade-off can be better mitigated by leveraging the distinct frequency biases between normal and abnormal reconstruction errors. To this end, we propose Frequency-aware Image Restoration (FAIR), a novel self-supervised image restoration task that restores images from their high-frequency components. It enables precise reconstruction of normal patterns while mitigating unfavorable generalization to anomalies. Using only a simple vanilla UNet, FAIR achieves state-of-the-art performance with higher efficiency on various defect detection datasets. Code: https://github.com/liutongkun/FAIR., Comment: 12 pages, 10 figures

Industrial visual inspection aims at detecting surface defects in products during the manufacturing process. Although existing anomaly detection models have shown great performance on many public benchmarks, their limited adjustability and ability to detect logical anomalies hinder their broader use in real-world settings. To this end, in this paper, we propose a novel component-aware anomaly detection framework (ComAD) which can simultaneously achieve adjustable and logical anomaly detection for industrial scenarios. Specifically, we propose to segment images into multiple components based on a lightweight and nearly training-free unsupervised semantic segmentation model. Then, we design an interpretable logical anomaly detection model through modeling the metrological features of each component and their relationships. Despite its simplicity, our framework achieves state-of-the-art performance on image-level logical anomaly detection. Meanwhile, segmenting a product image into multiple components provides a novel perspective for industrial visual inspection, demonstrating great potential in model customization, noise resistance, and anomaly classification. The code will be available at https://github.com/liutongkun/ComAD., Comment: 13 pages, 15 figures

Machine learning currently plays an increasingly important role in people's lives in areas such as credit scoring, auto-driving, disease diagnosing, and insurance quoting. However, in many of these areas, machine learning models have performed unfair behaviors against some sub-populations, such as some particular groups of race, sex, and age. These unfair behaviors can be on account of the pre-existing bias in the training dataset due to historical and social factors. In this paper, we focus on a real-world application of credit scoring and construct a fair prediction model by introducing latent variables to remove the correlation between protected attributes, such as sex and age, with the observable feature inputs, including house and job. For detailed implementation, we apply Bayesian approaches, including the Markov Chain Monte Carlo simulation, to estimate our proposed fair model.

Reconstruction-based methods are widely explored in industrial visual anomaly detection. Such methods commonly require the model to well reconstruct the normal patterns but fail in the anomalies, and thus the anomalies can be detected by evaluating the reconstruction errors. However, in practice, it's usually difficult to control the generalization boundary of the model. The model with an overly strong generalization capability can even well reconstruct the abnormal regions, making them less distinguishable, while the model with a poor generalization capability can not reconstruct those changeable high-frequency components in the normal regions, which ultimately leads to false positives. To tackle the above issue, we propose a new reconstruction network where we reconstruct the original RGB image from its gray value edges (EdgRec). Specifically, this is achieved by an UNet-type denoising autoencoder with skip connections. The input edge and skip connections can well preserve the high-frequency information in the original image. Meanwhile, the proposed restoration task can force the network to memorize the normal low-frequency and color information. Besides, the denoising design can prevent the model from directly copying the original high-frequent components. To evaluate the anomalies, we further propose a new interpretable hand-crafted evaluation function that considers both the color and gradient differences. Our method achieves competitive results on the challenging benchmark MVTec AD (97.8\% for detection and 97.7\% for localization, AUROC). In addition, we conduct experiments on the MVTec 3D-AD dataset and show convincing results using RGB images only. Our code will be available at https://github.com/liutongkun/EdgRec., Comment: 11 pages, 8 figures

One of the key problems in valleytronics is to realize valley polarization. Ferrovalley (FV) semiconductor and half-valley-metal (HVM) have been proposed, which possess intrinsic spontaneous valley polarization. Here, we propose the concept of quasi-half-valley-metal (QHVM), including electron and hole carriers with only a type of carriers being valley polarized. The QHVM may realize separation function of electron and hole. A concrete example of $\mathrm{VGe_2P_4}$ monolayer is used to illustrate our proposal through the first-principle calculations. To better realize QHVM, the electric field is applied to tune related valley properties of $\mathrm{VGe_2P_4}$. Within considered electric field range, $\mathrm{VGe_2P_4}$ is always ferromagnetic (FM) ground state, which possesses out-of-plane magnetization by calculating magnetic anisotropy energy (MAE) including magnetic shape anisotropy (MSA) and magnetocrystalline anisotropy (MCA) energies. These out-of-plane FM properties guarantee intrinsic spontaneous valley polarization in $\mathrm{VGe_2P_4}$. Within a certain range of electric field, the QHVM can be maintained, and the related polarization properties can be effectively tuned. Our works pave the way toward two-dimensional (2D) functional materials design of valleytronics., Comment: 8 pages, 10 figures. arXiv admin note: text overlap with arXiv:2208.02425

A large labeled dataset is a key to the success of supervised deep learning, but for medical image segmentation, it is highly challenging to obtain sufficient annotated images for model training. In many scenarios, unannotated images are abundant and easy to acquire. Self-supervised learning (SSL) has shown great potentials in exploiting raw data information and representation learning. In this paper, we propose Hierarchical Self-Supervised Learning (HSSL), a new self-supervised framework that boosts medical image segmentation by making good use of unannotated data. Unlike the current literature on task-specific self-supervised pretraining followed by supervised fine-tuning, we utilize SSL to learn task-agnostic knowledge from heterogeneous data for various medical image segmentation tasks. Specifically, we first aggregate a dataset from several medical challenges, then pre-train the network in a self-supervised manner, and finally fine-tune on labeled data. We develop a new loss function by combining contrastive loss and classification loss and pretrain an encoder-decoder architecture for segmentation tasks. Our extensive experiments show that multi-domain joint pre-training benefits downstream segmentation tasks and outperforms single-domain pre-training significantly. Compared to learning from scratch, our new method yields better performance on various tasks (e.g., +0.69% to +18.60% in Dice scores with 5% of annotated data). With limited amounts of training data, our method can substantially bridge the performance gap w.r.t. denser annotations (e.g., 10% vs.~100% of annotated data)., Comment: Accepted to MICCAI 2021