Learning Spatially-Adaptive Squeeze-Excitation Networks for Image Synthesis and Image Recognition

Learning light-weight yet expressive deep networks in both image synthesis and image recognition remains a challenging problem. Inspired by a more recent observation that it is the data-specificity that makes the multi-head self-attention (MHSA) in the Transformer model so powerful, this paper proposes to extend the widely adopted light-weight Squeeze-Excitation (SE) module to be spatially-adaptive to reinforce its data specificity, as a convolutional alternative of the MHSA, while retaining the efficiency of SE and the inductive basis of convolution. It presents two designs of spatially-adaptive squeeze-excitation (SASE) modules for image synthesis and image recognition respectively. For image synthesis tasks, the proposed SASE is tested in both low-shot and one-shot learning tasks. It shows better performance than prior arts. For image recognition tasks, the proposed SASE is used as a drop-in replacement for convolution layers in ResNets and achieves much better accuracy than the vanilla ResNets, and slightly better than the MHSA counterparts such as the Swin-Transformer and Pyramid-Transformer in the ImageNet-1000 dataset, with significantly smaller models

Exploring city social interaction ties in the big data era: Evidence based on location-based social media data from China

Location-based social media data is, increasingly, an important facilitator of exploring the movement of goods and people in and between countries across the globe. Typical examples include Twitter, Facebook, Foursquare. As with all social media data outputs, the fundamental value of location-based social media data is for sensing users? space?time trajectories, and thus, makes social media data a new platform for understanding business and social interactions in the spatial context. In large developing and emerging economies with massive social media users via computers and mobile phones, real-time ?geo-tagged? human mobility information from social media data sources are clearly potentially large. In these settings, cyberspaces are often built and expanded with the explicit aim of stimulating digital socioeconomic activities and balancing regional disparities. However, despite intense policy and public enthusiasms, there is virtually no direct evidence on exploring the configuration of urban network patterns by using social media users? mobility flows within a large developing country context. The scarcity of empirical evidence is not surprising, given that mining location-based social media data faces serious identification challenges. First, location-based social media data, as a type of big data resource, are often featured by the dynamic, massive information generated by billions of users across space. In truth, despite of the recent development of intensive-computational geographic information system (GIS) modeling programs, social media data with precise individual-level location information is still extremely large to proceed by using the GIS techniques at multiple geographical scales. Furthermore, conventional GIS-based computational methods cannot directly read the unstructured social media datasets (e.g. words, pictures, videos). Additional big data mining methods are often needed to transform social media data information from unstructured data formats to structured, and ready-to-use spatial datasets. In this paper, we tackle these problems by analysing the configuration of intercity connection patterns in China to provide new evidence to the applications of location-based social media data in urban and regional studies. Our examination of changes in human mobility patterns by months by city-pairs throughout China by months involves many potential stages of big data mining analysis. We stratify cities by core-periphery urban systems, by regions and by calendar months, finding that human mobility flows are not distributed evenly over time and across space. We find larger human mobility flows around the Chinese New Year month and the summer months. Our evidence suggests the significantly heterogeneity patterns of core-periphery urban systems as reflected from real-time human mobility flows. As a baseline, this paper is?for the first time in the literature?to comprehensively measure urban network patterns at a detailed spatial degree (the city-pair level) based on location-based social media data from a large developing country context

The geography of city liveliness and consumption: evidence from location-based big data

Understanding the complexity in the connection between city liveliness and spatial configurationsfor consumptive amenities has been an important but understudied research field in fast urbanising countries like China. This paper presents the first step towards filling this gap though location-based big data perspectives. City liveliness is measured by aggregated spacetime human activity intensities using mobile phone positioning data.Consumptive amenities are identified by point-of-interest data from Chinese Yelp website (dian ping). The results provide the insights into the geographic contextual uncertainties of consumptive amenities in shaping the rise and fall in the vibrancy of city liveliness

MIS-FM: 3D Medical Image Segmentation using Foundation Models Pretrained on a Large-Scale Unannotated Dataset

Pretraining with large-scale 3D volumes has a potential for improving the segmentation performance on a target medical image dataset where the training images and annotations are limited. Due to the high cost of acquiring pixel-level segmentation annotations on the large-scale pretraining dataset, pretraining with unannotated images is highly desirable. In this work, we propose a novel self-supervised learning strategy named Volume Fusion (VF) for pretraining 3D segmentation models. It fuses several random patches from a foreground sub-volume to a background sub-volume based on a predefined set of discrete fusion coefficients, and forces the model to predict the fusion coefficient of each voxel, which is formulated as a self-supervised segmentation task without manual annotations. Additionally, we propose a novel network architecture based on parallel convolution and transformer blocks that is suitable to be transferred to different downstream segmentation tasks with various scales of organs and lesions. The proposed model was pretrained with 110k unannotated 3D CT volumes, and experiments with different downstream segmentation targets including head and neck organs, thoracic/abdominal organs showed that our pretrained model largely outperformed training from scratch and several state-of-the-art self-supervised training methods and segmentation models. The code and pretrained model are available at https://github.com/openmedlab/MIS-FM.Comment: 13 pages, 8 figure

TISS-net: Brain tumor image synthesis and segmentation using cascaded dual-task networks and error-prediction consistency

Accurate segmentation of brain tumors from medical images is important for diagnosis and treatment planning, and it often requires multi-modal or contrast-enhanced images. However, in practice some modalities of a patient may be absent. Synthesizing the missing modality has a potential for filling this gap and achieving high segmentation performance. Existing methods often treat the synthesis and segmentation tasks separately or consider them jointly but without effective regularization of the complex joint model, leading to limited performance. We propose a novel brain Tumor Image Synthesis and Segmentation network (TISS-Net) that obtains the synthesized target modality and segmentation of brain tumors end-to-end with high performance. First, we propose a dual-task-regularized generator that simultaneously obtains a synthesized target modality and a coarse segmentation, which leverages a tumor-aware synthesis loss with perceptibility regularization to minimize the high-level semantic domain gap between synthesized and real target modalities. Based on the synthesized image and the coarse segmentation, we further propose a dual-task segmentor that predicts a refined segmentation and error in the coarse segmentation simultaneously, where a consistency between these two predictions is introduced for regularization. Our TISS-Net was validated with two applications: synthesizing FLAIR images for whole glioma segmentation, and synthesizing contrast-enhanced T1 images for Vestibular Schwannoma segmentation. Experimental results showed that our TISS-Net largely improved the segmentation accuracy compared with direct segmentation from the available modalities, and it outperformed state-of-the-art image synthesis-based segmentation methods

Photoemission Evidence of a Novel Charge Order in Kagome Metal FeGe

A charge order has been discovered to emerge deep into the antiferromagnetic phase of the kagome metal FeGe. To study its origin, the evolution of the low-lying electronic structure across the charge order phase transition is investigated with angle-resolved photoemission spectroscopy. We do not find signatures of nesting between Fermi surface sections or van-Hove singularities in zero-frequency joint density of states, and there are no obvious energy gaps at the Fermi level, which exclude the nesting mechanism for the charge order formation in FeGe. However, two obvious changes in the band structure have been detected, i.e., one electron-like band around the K point and another one around the A point move upward in energy position when the charge order forms. These features can be well reproduced by our density-functional theory calculations, where the charge order is primarily driven by magnetic energy saving via large dimerizations of a quarter of Ge1-sites (in the kagome plane) along the c-axis. Our results provide strong support for this novel charge order formation mechanism in FeGe, in contrast to the conventional nesting mechanism.Comment: 6 pages, 4 figure

Detection and analysis of human papillomavirus (HPV) DNA in breast cancer patients by an effective method of HPV capture

Despite an increase in the number of molecular epidemiological studies conducted in recent years to evaluate the association between human papillomavirus (HPV) and the risk of breast carcinoma, these studies remain inconclusive. Here we aim to detect HPV DNA in various tissues from patients with breast carcinoma using the method of HPV capture combined with massive paralleled sequencing (MPS). To validate the confidence of our methods, 15 cervical cancer samples were tested by PCR and the new method. Results showed that there was 100% consistence between the two methods.DNA from peripheral blood, tumor tissue, adjacent lymph nodes and adjacent normal tissue were collected from seven malignant breast cancer patients, and HPV type 16(HPV16) was detected in 1/7, 1/7, 1/7and 1/7 of patients respectively. Peripheral blood, tumor tissue and adjacent normal tissue were also collected from two patients with benign breast tumor, and 1/2, 2/2 and 2/2 was detected to have HPV16 DNA respectively. MPS metrics including mapping ratio, coverage, depth and SNVs were provided to characterize HPV in samples. The average coverage was 69% and 61.2% for malignant and benign samples respectively. 126 SNVs were identified in all 9 samples. The maximum number of SNVs was located in the gene of E2 and E4 among all samples. Our study not only provided an efficient method to capture HPV DNA, but detected the SNVS, coverage, SNV type and depth. The finding has provided further clue of association between HPV16 and breast cancer

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

Background: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed. Results: We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2). Conclusions: Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level

Full-length single-cell RNA-seq applied to a viral human cancer:applications to HPV expression and splicing analysis in HeLa S3 cells

Background: Viral infection causes multiple forms of human cancer, and HPV infection is the primary factor in cervical carcinomas Recent single-cell RNA-seq studies highlight the tumor heterogeneity present in most cancers, but virally induced tumors have not been studied HeLa is a well characterized HPV+ cervical cancer cell line Result: We developed a new high throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells and 40 of them were randomly selected to perform single-cell RNA sequencing Based on these data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in gene expression, alternative splicing and fusions Furthermore, we identified a high diversity of HPV-18 expression and splicing at the single-cell level By co-expression analysis we identified 283 E6, E7 co-regulated genes, including CDC25, PCNA, PLK4, BUB1B and IRF1 known to interact with HPV viral proteins Conclusion: Our results reveal the heterogeneity of a virus-infected cell line It not only provides a transcriptome characterization of HeLa S3 cells at the single cell level, but is a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers