Shiqi Xu

Lucas Kreiss, Shaowei Jiang, Xiang Li et al. · pku

Until recently, conventional biochemical staining had the undisputed status as well-established benchmark for most biomedical problems related to clinical diagnostics, fundamental research and biotechnology. Despite this role as gold-standard, staining protocols face several challenges, such as a need for extensive, manual processing of samples, substantial time delays, altered tissue homeostasis, limited choice of contrast agents for a given sample, 2D imaging instead of 3D tomography and many more. Label-free optical technologies, on the other hand, do not rely on exogenous and artificial markers, by exploiting intrinsic optical contrast mechanisms, where the specificity is typically less obvious to the human observer. Over the past few years, digital staining has emerged as a promising concept to use modern deep learning for the translation from optical contrast to established biochemical contrast of actual stainings. In this review article, we provide an in-depth analysis of the current state-of-the-art in this field, suggest methods of good practice, identify pitfalls and challenges and postulate promising advances towards potential future implementations and applications.

He Yan, Xinyao Hu, Xiangpeng Wan et al.

Despite the significant advancements in natural language processing capabilities demonstrated by large language models such as ChatGPT, their proficiency in comprehending and processing spatial information, especially within the domains of 2D and 3D route planning, remains notably underdeveloped. This paper investigates the inherent limitations of ChatGPT and similar models in spatial reasoning and navigation-related tasks, an area critical for applications ranging from autonomous vehicle guidance to assistive technologies for the visually impaired. In this paper, we introduce a novel evaluation framework complemented by a baseline dataset, meticulously crafted for this study. This dataset is structured around three key tasks: plotting spatial points, planning routes in two-dimensional (2D) spaces, and devising pathways in three-dimensional (3D) environments. We specifically developed this dataset to assess the spatial reasoning abilities of ChatGPT. Our evaluation reveals key insights into the model's capabilities and limitations in spatial understanding.

Xing Yao, Vinayak Pathak, Haoran Xi et al.

This work demonstrates a multi-lens microscopic imaging system that overlaps multiple independent fields of view on a single sensor for high-efficiency automated specimen analysis. Automatic detection, classification and counting of various morphological features of interest is now a crucial component of both biomedical research and disease diagnosis. While convolutional neural networks (CNNs) have dramatically improved the accuracy of counting cells and sub-cellular features from acquired digital image data, the overall throughput is still typically hindered by the limited space-bandwidth product (SBP) of conventional microscopes. Here, we show both in simulation and experiment that overlapped imaging and co-designed analysis software can achieve accurate detection of diagnostically-relevant features for several applications, including counting of white blood cells and the malaria parasite, leading to multi-fold increase in detection and processing throughput with minimal reduction in accuracy.

Jason Wei, Chengyu Huang, Shiqi Xu et al.

Traditional data augmentation aims to increase the coverage of the input distribution by generating augmented examples that strongly resemble original samples in an online fashion where augmented examples dominate training. In this paper, we propose an alternative perspective -- a multi-task view (MTV) of data augmentation -- in which the primary task trains on original examples and the auxiliary task trains on augmented examples. In MTV data augmentation, both original and augmented samples are weighted substantively during training, relaxing the constraint that augmented examples must resemble original data and thereby allowing us to apply stronger levels of augmentation. In empirical experiments using four common data augmentation techniques on three benchmark text classification datasets, we find that the MTV leads to higher and more robust performance improvements than traditional augmentation.

Yu Sun, Shiqi Xu, Yunzhe Li et al.

The plug-and-play priors (PnP) framework has been recently shown to achieve state-of-the-art results in regularized image reconstruction by leveraging a sophisticated denoiser within an iterative algorithm. In this paper, we propose a new online PnP algorithm for Fourier ptychographic microscopy (FPM) based on the fast iterative shrinkage/threshold algorithm (FISTA). Specifically, the proposed algorithm uses only a subset of measurements, which makes it scalable to a large set of measurements. We validate the algorithm by showing that it can lead to significant performance gains on both simulated and experimental data.