Depth-wise Decomposition for Accelerating Separable Convolutions in Efficient Convolutional Neural Networks

Very deep convolutional neural networks (CNNs) have been firmly established as the primary methods for many computer vision tasks. However, most state-of-the-art CNNs are large, which results in high inference latency. Recently, depth-wise separable convolution has been proposed for image recognition tasks on computationally limited platforms such as robotics and self-driving cars. Though it is much faster than its counterpart, regular convolution, accuracy is sacrificed. In this paper, we propose a novel decomposition approach based on SVD, namely depth-wise decomposition, for expanding regular convolutions into depthwise separable convolutions while maintaining high accuracy. We show our approach can be further generalized to the multi-channel and multi-layer cases, based on Generalized Singular Value Decomposition (GSVD) [59]. We conduct thorough experiments with the latest ShuffleNet V2 model [47] on both random synthesized dataset and a large-scale image recognition dataset: ImageNet [10]. Our approach outperforms channel decomposition [73] on all datasets. More importantly, our approach improves the Top-1 accuracy of ShuffleNet V2 by ~2%.Comment: CVPR 2019 workshop, Efficient Deep Learning for Computer Visio

A surgical system for automatic registration, stiffness mapping and dynamic image overlay

In this paper we develop a surgical system using the da Vinci research kit (dVRK) that is capable of autonomously searching for tumors and dynamically displaying the tumor location using augmented reality. Such a system has the potential to quickly reveal the location and shape of tumors and visually overlay that information to reduce the cognitive overload of the surgeon. We believe that our approach is one of the first to incorporate state-of-the-art methods in registration, force sensing and tumor localization into a unified surgical system. First, the preoperative model is registered to the intra-operative scene using a Bingham distribution-based filtering approach. An active level set estimation is then used to find the location and the shape of the tumors. We use a recently developed miniature force sensor to perform the palpation. The estimated stiffness map is then dynamically overlaid onto the registered preoperative model of the organ. We demonstrate the efficacy of our system by performing experiments on phantom prostate models with embedded stiff inclusions.Comment: International Symposium on Medical Robotics (ISMR 2018

Integrating multi-type aberrations from DNA and RNA through dynamic mapping gene space for subtype-specific breast cancer driver discovery

Driver event discovery is a crucial demand for breast cancer diagnosis and therapy. Especially, discovering subtype-specificity of drivers can prompt the personalized biomarker discovery and precision treatment of cancer patients. still, most of the existing computational driver discovery studies mainly exploit the information from DNA aberrations and gene interactions. Notably, cancer driver events would occur due to not only DNA aberrations but also RNA alternations, but integrating multi-type aberrations from both DNA and RNA is still a challenging task for breast cancer drivers. On the one hand, the data formats of different aberration types also differ from each other, known as data format incompatibility. One the other hand, different types of aberrations demonstrate distinct patterns across samples, known as aberration type heterogeneity. To promote the integrated analysis of subtype-specific breast cancer drivers, we design a "splicing-and-fusing" framework to address the issues of data format incompatibility and aberration type heterogeneity respectively. To overcome the data format incompatibility, the "splicing-step" employs a knowledge graph structure to connect multi-type aberrations from the DNA and RNA data into a unified formation. To tackle the aberration type heterogeneity, the "fusing-step" adopts a dynamic mapping gene space integration approach to represent the multi-type information by vectorized profiles. The experiments also demonstrate the advantages of our approach in both the integration of multi-type aberrations from DNA and RNA and the discovery of subtype-specific breast cancer drivers. In summary, our "splicing-and-fusing" framework with knowledge graph connection and dynamic mapping gene space fusion of multi-type aberrations data from DNA and RNA can successfully discover potential breast cancer drivers with subtype-specificity indication.Comment: 14 pages, 5 figures, 1 tabl

Prompting Large Language Models with Chain-of-Thought for Few-Shot Knowledge Base Question Generation

The task of Question Generation over Knowledge Bases (KBQG) aims to convert a logical form into a natural language question. For the sake of expensive cost of large-scale question annotation, the methods of KBQG under low-resource scenarios urgently need to be developed. However, current methods heavily rely on annotated data for fine-tuning, which is not well-suited for few-shot question generation. The emergence of Large Language Models (LLMs) has shown their impressive generalization ability in few-shot tasks. Inspired by Chain-of-Thought (CoT) prompting, which is an in-context learning strategy for reasoning, we formulate KBQG task as a reasoning problem, where the generation of a complete question is splitted into a series of sub-question generation. Our proposed prompting method KQG-CoT first retrieves supportive logical forms from the unlabeled data pool taking account of the characteristics of the logical form. Then, we write a prompt to explicit the reasoning chain of generating complicated questions based on the selected demonstrations. To further ensure prompt quality, we extend KQG-CoT into KQG-CoT+ via sorting the logical forms by their complexity. We conduct extensive experiments over three public KBQG datasets. The results demonstrate that our prompting method consistently outperforms other prompting baselines on the evaluated datasets. Remarkably, our KQG-CoT+ method could surpass existing few-shot SoTA results of the PathQuestions dataset by 18.25, 10.72, and 10.18 absolute points on BLEU-4, METEOR, and ROUGE-L, respectively.Comment: Accepted by EMNLP 2023 main conferenc

Nanoroughened adhesion-based capture of circulating tumor cells with heterogeneous expression and metastatic characteristics

Abstract Background Circulating tumor cells (CTCs) have shown prognostic relevance in many cancer types. However, the majority of current CTC capture methods rely on positive selection techniques that require a priori knowledge about the surface protein expression of disseminated CTCs, which are known to be a dynamic population. Methods We developed a microfluidic CTC capture chip that incorporated a nanoroughened glass substrate for capturing CTCs from blood samples. Our CTC capture chip utilized the differential adhesion preference of cancer cells to nanoroughened etched glass surfaces as compared to normal blood cells and thus did not depend on the physical size or surface protein expression of CTCs. Results The microfluidic CTC capture chip was able to achieve a superior capture yield for both epithelial cell adhesion molecule positive (EpCAM+) and EpCAM- cancer cells in blood samples. Additionally, the microfluidic CTC chip captured CTCs undergoing transforming growth factor beta-induced epithelial-to-mesenchymal transition (TGF-β-induced EMT) with dynamically down-regulated EpCAM expression. In a mouse model of human breast cancer using EpCAM positive and negative cell lines, the number of CTCs captured correlated positively with the size of the primary tumor and was independent of their EpCAM expression. Furthermore, in a syngeneic mouse model of lung cancer using cell lines with differential metastasis capability, CTCs were captured from all mice with detectable primary tumors independent of the cell lines’ metastatic ability. Conclusions The microfluidic CTC capture chip using a novel nanoroughened glass substrate is broadly applicable to capturing heterogeneous CTC populations of clinical interest independent of their surface marker expression and metastatic propensity. We were able to capture CTCs from a non-metastatic lung cancer model, demonstrating the potential of the chip to collect the entirety of CTC populations including subgroups of distinct biological and phenotypical properties. Further exploration of the biological potential of metastatic and presumably non-metastatic CTCs captured using the microfluidic chip will yield insights into their relevant differences and their effects on tumor progression and cancer outcomes.http://deepblue.lib.umich.edu/bitstream/2027.42/134622/1/12885_2016_Article_2638.pd

Findings of a videofluoroscopic swallowing study in patients with dysphagia

ObjectiveSwallowing examination is crucial in patients with dysphagia. We aimed to compare qualitative and quantitative videofluoroscopic swallowing study (VFSS) results to provide reference for standardizing quantitative parameters.Materials and methodsIn total, 117 patients with dysphagia were included, 38 with Parkinson’s disease and 39 and 40 in convalescence following cerebral hemorrhage and infarction. VFSS was both qualitatively and quantitatively analyzed.ResultsA significant difference of Oral transit time was found between the oral motor function grades (p < 0.001), also was swallowing reaction times found between swallowing reaction duration grades (p < 0.001), and soft palate lift duration between the soft palate lift grades (p < 0.001). Superior hyoid bone movement (p < 0.001), anterior hyoid bone movement (p < 0.001), hyoid pause time (p < 0.001), and hyoid movement duration (p = 0.032) had significant differences between the hyoid laryngeal complex movement grades, as did the pharyngeal cavity transit time among the cricopharyngeal muscle opening duration grades (p < 0.001). The laryngeal vestibule closure duration differed among the glottic closure grades (p < 0.001). No statistically significant difference in upper esophageal sphincter opening diameter (p = 0.682) or duration (p = 0.682) among the cyclopharyngeal muscle opening duration grades. The pharyngeal area at rest did not significantly differ among the different vallecular residue (p = 0.202) and pyriform sinus residue (p = 0.116) grades.ConclusionSeveral quantitative parameters can reflect the swallowing assessment process well. Further optimization of quantitative parameters is recommended

Long Noncoding RNA Expression Signatures of Metastatic Nasopharyngeal Carcinoma and Their Prognostic Value

Long noncoding RNAs (lncRNAs) have recently been found to play important roles in various cancer types. The elucidation of genome-wide lncRNA expression patterns in metastatic nasopharyngeal carcinoma (NPC) could reveal novel mechanisms underlying NPC carcinogenesis and progression. In this study, lncRNA expression profiling was performed on metastatic and primary NPC tumors, and the differentially expressed lncRNAs between these samples were identified. A total of 33,045 lncRNA probes were generated for our microarray based on authoritative data sources, including RefSeq, UCSC Knowngenes, Ensembl, and related literature. Using these probes, 8,088 lncRNAs were found to be significantly differentially expressed (2-fold). To identify the prognostic value of these differentially expressed lncRNAs, four lncRNAs (LOC84740, ENST00000498296, AL359062, and ENST00000438550) were selected; their expression levels were measured in an independent panel of 106 primary NPC samples via QPCR. Among these lncRNAs, ENST00000438550 expression was demonstrated to be significantly correlated with NPC disease progression. A survival analysis showed that a high expression level of ENST00000438550 was an independent indicator of disease progression in NPC patients (). In summary, this study may provide novel diagnostic and prognostic biomarkers for NPC, as well as a novel understanding of the mechanism underlying NPC metastasis and potential targets for future treatment