Tensorial tomographic Fourier Ptychography with applications to muscle tissue imaging

We report Tensorial tomographic Fourier Ptychography (ToFu), a new non-scanning label-free tomographic microscopy method for simultaneous imaging of quantitative phase and anisotropic specimen information in 3D. Built upon Fourier Ptychography, a quantitative phase imaging technique, ToFu additionally highlights the vectorial nature of light. The imaging setup consists of a standard microscope equipped with an LED matrix, a polarization generator, and a polarization-sensitive camera. Permittivity tensors of anisotropic samples are computationally recovered from polarized intensity measurements across three dimensions. We demonstrate ToFu's efficiency through volumetric reconstructions of refractive index, birefringence, and orientation for various validation samples, as well as tissue samples from muscle fibers and diseased heart tissue. Our reconstructions of muscle fibers resolve their 3D fine-filament structure and yield consistent morphological measurements compared to gold-standard second harmonic generation scanning confocal microscope images found in the literature. Additionally, we demonstrate reconstructions of a heart tissue sample that carries important polarization information for detecting cardiac amyloidosis.

Multi-Granularity Archaeological Dating of Chinese Bronze Dings Based on a Knowledge-Guided Relation Graph

The archaeological dating of bronze dings has played a critical role in the study of ancient Chinese history. Current archaeology depends on trained experts to carry out bronze dating, which is time-consuming and labor-intensive. For such dating, in this study, we propose a learning-based approach to integrate advanced deep learning techniques and archaeological knowledge. To achieve this, we first collect a large-scale image dataset of bronze dings, which contains richer attribute information than other existing fine-grained datasets. Second, we introduce a multihead classifier and a knowledge-guided relation graph to mine the relationship between attributes and the ding era. Third, we conduct comparison experiments with various existing methods, the results of which show that our dating method achieves a state-of-the-art performance. We hope that our data and applied networks will enrich fine-grained classification research relevant to other interdisciplinary areas of expertise. The dataset and source code used are included in our supplementary materials, and will be open after submission owing to the anonymity policy. Source codes and data are available at: https://github.com/zhourixin/bronze-Ding.

Mixing Backward- with Forward-Chaining for Metacognitive Skill Acquisition and Transfer

Metacognitive skills have been commonly associated with preparation for future learning in deductive domains. Many researchers have regarded strategy- and time-awareness as two metacognitive skills that address how and when to use a problem-solving strategy, respectively. It was shown that students who are both strategy-and time-aware (StrTime) outperformed their nonStrTime peers across deductive domains. In this work, students were trained on a logic tutor that supports a default forward-chaining (FC) and a backward-chaining (BC) strategy. We investigated the impact of mixing BC with FC on teaching strategy- and time-awareness for nonStrTime students. During the logic instruction, the experimental students (Exp) were provided with two BC worked examples and some problems in BC to practice how and when to use BC. Meanwhile, their control (Ctrl) and StrTime peers received no such intervention. Six weeks later, all students went through a probability tutor that only supports BC to evaluate whether the acquired metacognitive skills are transferred from logic. Our results show that on both tutors, Exp outperformed Ctrl and caught up with StrTime.

Clinical Concept and Relation Extraction Using Prompt-based Machine Reading Comprehension

Objective: To develop a natural language processing system that solves both clinical concept extraction and relation extraction in a unified prompt-based machine reading comprehension (MRC) architecture with good generalizability for cross-institution applications. Methods: We formulate both clinical concept extraction and relation extraction using a unified prompt-based MRC architecture and explore state-of-the-art transformer models. We compare our MRC models with existing deep learning models for concept extraction and end-to-end relation extraction using two benchmark datasets developed by the 2018 National NLP Clinical Challenges (n2c2) challenge (medications and adverse drug events) and the 2022 n2c2 challenge (relations of social determinants of health [SDoH]). We also evaluate the transfer learning ability of the proposed MRC models in a cross-institution setting. We perform error analyses and examine how different prompting strategies affect the performance of MRC models. Results and Conclusion: The proposed MRC models achieve state-of-the-art performance for clinical concept and relation extraction on the two benchmark datasets, outperforming previous non-MRC transformer models. GatorTron-MRC achieves the best strict and lenient F1-scores for concept extraction, outperforming previous deep learning models on the two datasets by 1%~3% and 0.7%~1.3%, respectively. For end-to-end relation extraction, GatorTron-MRC and BERT-MIMIC-MRC achieve the best F1-scores, outperforming previous deep learning models by 0.9%~2.4% and 10%-11%, respectively. For cross-institution evaluation, GatorTron-MRC outperforms traditional GatorTron by 6.4% and 16% for the two datasets, respectively. The proposed method is better at handling nested/overlapped concepts, extracting relations, and has good portability for cross-institute applications.

Contextualized Medication Information Extraction Using Transformer-based Deep Learning Architectures

Objective: To develop a natural language processing (NLP) system to extract medications and contextual information that help understand drug changes. This project is part of the 2022 n2c2 challenge. Materials and methods: We developed NLP systems for medication mention extraction, event classification (indicating medication changes discussed or not), and context classification to classify medication changes context into 5 orthogonal dimensions related to drug changes. We explored 6 state-of-the-art pretrained transformer models for the three subtasks, including GatorTron, a large language model pretrained using >90 billion words of text (including >80 billion words from >290 million clinical notes identified at the University of Florida Health). We evaluated our NLP systems using annotated data and evaluation scripts provided by the 2022 n2c2 organizers. Results:Our GatorTron models achieved the best F1-scores of 0.9828 for medication extraction (ranked 3rd), 0.9379 for event classification (ranked 2nd), and the best micro-average accuracy of 0.9126 for context classification. GatorTron outperformed existing transformer models pretrained using smaller general English text and clinical text corpora, indicating the advantage of large language models. Conclusion: This study demonstrated the advantage of using large transformer models for contextual medication information extraction from clinical narratives.

OSIS: Efficient One-stage Network for 3D Instance Segmentation

Current 3D instance segmentation models generally use multi-stage methods to extract instance objects, including clustering, feature extraction, and post-processing processes. However, these multi-stage approaches rely on hyperparameter settings and hand-crafted processes, which restrict the inference speed of the model. In this paper, we propose a new 3D point cloud instance segmentation network, named OSIS. OSIS is a one-stage network, which directly segments instances from 3D point cloud data using neural network. To segment instances directly from the network, we propose an instance decoder, which decodes instance features from the network into instance segments. Our proposed OSIS realizes the end-to-end training by bipartite matching, therefore, our network does not require computationally expensive post-processing steps such as non maximum suppression (NMS) and clustering during inference. The results show that our network finally achieves excellent performance in the commonly used indoor scene instance segmentation dataset, and the inference speed of our network is only an average of 138ms per scene, which substantially exceeds the previous fastest method.

Reconfigurable Distributed Antennas and Reflecting Surface (RDARS): A New Architecture for Wireless Communications

Reconfigurable intelligent surfaces (RISs) have drawn much attention recently for their appealing advantages in shaping wireless channels to improve the spectral and energy efficiencies of wireless communications. However, conventional fully-passive RISs generally suffer from the so-called ``multiplicative fading'' effect which thereby limits RISs' practicability and manufacturability. In this paper, a novel architecture of ``Reconfigurable Distributed Antennas and Reflecting Surfaces (RDARS)'' is first proposed to overcome this limitation from the ``multiplicative fading'' effect. Specifically, unlike existing active RIS variants, RDARS inherits the low-cost and low-energy-consumption benefits of fully-passive RISs by default configuring all the elements as passive to perform the reflection mode. On the other hand, based on the design of the additional direct-through state, any element of the RDARS can be dynamically programmed to connect with the base station (BS) via fibers and perform the connected mode as remote distributed antennas of the BS to receive signals. Consequently, a controllable trade-off between the reflection gain and the distribution gain can be achieved via RDARS at the BS. To unveil the system behavior of the RDARS-aided system, we analyze the received signal-to-noise ratio (SNR) under maximum ratio combining (MRC) at BS. Closed-form outage probability and ergodic achievable rate are also provided and are verified through extensive simulations. To demonstrate the superiority of the proposed RDARS, experiments are carried out using a prototype of RDARS with a total number of 256 elements which revealed extra 76% throughput improvement could be achieved by deploying RDARS with only three elements performing connected mode. This thus confirms the effectiveness of the proposed RDARS and envisions it as a promising candidate for future 6G wireless systems.

Pay Less But Get More: A Dual-Attention-based Channel Estimation Network for Massive MIMO Systems with Low-Density Pilots

To reap the promising benefits of massive multiple-input multiple-output (MIMO) systems, accurate channel state information (CSI) is required through channel estimation. However, due to the complicated wireless propagation environment and large-scale antenna arrays, precise channel estimation for massive MIMO systems is significantly challenging and costs an enormous training overhead. Considerable time-frequency resources are consumed to acquire sufficient accuracy of CSI, which thus severely degrades systems' spectral and energy efficiencies. In this paper, we propose a dual-attention-based channel estimation network (DACEN) to realize accurate channel estimation via low-density pilots, by decoupling the spatial-temporal domain features of massive MIMO channels with the temporal attention module and the spatial attention module. To further improve the estimation accuracy, we propose a parameter-instance transfer learning approach based on the DACEN to transfer the channel knowledge learned from the high-density pilots pre-acquired during the training dataset collection period. Experimental results on a publicly available dataset reveal that the proposed DACEN-based method with low-density pilots ($\rho_L=6/52$) achieves better channel estimation performance than the existing methods even with higher-density pilots ($\rho_H=26/52$). Additionally, with the proposed transfer learning approach, the DACEN-based method with ultra-low-density pilots ($\rho_L^\prime=2/52$) achieves higher estimation accuracy than the existing methods with low-density pilots, thereby demonstrating the effectiveness and the superiority of the proposed method.

Large-scale single-photon imaging

Benefiting from its single-photon sensitivity, single-photon avalanche diode (SPAD) array has been widely applied in various fields such as fluorescence lifetime imaging and quantum computing. However, large-scale high-fidelity single-photon imaging remains a big challenge, due to the complex hardware manufacture craft and heavy noise disturbance of SPAD arrays. In this work, we introduce deep learning into SPAD, enabling super-resolution single-photon imaging over an order of magnitude, with significant enhancement of bit depth and imaging quality. We first studied the complex photon flow model of SPAD electronics to accurately characterize multiple physical noise sources, and collected a real SPAD image dataset (64 $\times$ 32 pixels, 90 scenes, 10 different bit depth, 3 different illumination flux, 2790 images in total) to calibrate noise model parameters. With this real-world physical noise model, we for the first time synthesized a large-scale realistic single-photon image dataset (image pairs of 5 different resolutions with maximum megapixels, 17250 scenes, 10 different bit depth, 3 different illumination flux, 2.6 million images in total) for subsequent network training. To tackle the severe super-resolution challenge of SPAD inputs with low bit depth, low resolution, and heavy noise, we further built a deep transformer network with a content-adaptive self-attention mechanism and gated fusion modules, which can dig global contextual features to remove multi-source noise and extract full-frequency details. We applied the technique on a series of experiments including macroscopic and microscopic imaging, microfluidic inspection, and Fourier ptychography. The experiments validate the technique's state-of-the-art super-resolution SPAD imaging performance, with more than 5 dB superiority on PSNR compared to the existing methods.

Towards Deeper and Better Multi-view Feature Fusion for 3D Semantic Segmentation

3D point clouds are rich in geometric structure information, while 2D images contain important and continuous texture information. Combining 2D information to achieve better 3D semantic segmentation has become mainstream in 3D scene understanding. Albeit the success, it still remains elusive how to fuse and process the cross-dimensional features from these two distinct spaces. Existing state-of-the-art usually exploit bidirectional projection methods to align the cross-dimensional features and realize both 2D & 3D semantic segmentation tasks. However, to enable bidirectional mapping, this framework often requires a symmetrical 2D-3D network structure, thus limiting the network's flexibility. Meanwhile, such dual-task settings may distract the network easily and lead to over-fitting in the 3D segmentation task. As limited by the network's inflexibility, fused features can only pass through a decoder network, which affects model performance due to insufficient depth. To alleviate these drawbacks, in this paper, we argue that despite its simplicity, projecting unidirectionally multi-view 2D deep semantic features into the 3D space aligned with 3D deep semantic features could lead to better feature fusion. On the one hand, the unidirectional projection enforces our model focused more on the core task, i.e., 3D segmentation; on the other hand, unlocking the bidirectional to unidirectional projection enables a deeper cross-domain semantic alignment and enjoys the flexibility to fuse better and complicated features from very different spaces. In joint 2D-3D approaches, our proposed method achieves superior performance on the ScanNetv2 benchmark for 3D semantic segmentation.