arXiv subjects

Junpeng Zhang

Publications and source records attributed to Junpeng Zhang.

24 records · Page 2Linked to original sources

arXiv2022

Inferring cell-specific lncRNA regulation with single-cell RNA-sequencing data in the developing human neocortex

Long non-coding RNAs (lncRNAs) are important regulators to modulate gene expression and cell proliferation in the developing human brain. Previous methods mainly use bulk lncRNA and mRNA expression data to study lncRNA regulation. However, to analyze lncRNA regulation regarding individual cells, we focus on single-cell RNA-sequencing (scRNA-seq) data instead of bulk data. Recent advance in scRNA-seq has provided a way to investigate lncRNA regulation at single-cell level. We will propose a novel computational method, CSlncR (cell-specific lncRNA regulation), which combines putative lncRNA-mRNA binding information with scRNA-seq data including lncRNAs and mRNAs to identify cell-specific lncRNA-mRNA regulation networks at individual cells. To understand lncRNA regulation at different development stages, we apply CSlncR to the scRNA-seq data of human neocortex. Network analysis shows that the lncRNA regulation is unique in each cell from the different human neocortex development stages. The comparison results indicate that CSlncR is also an effective tool for predicting cell-specific lncRNA targets and clustering single cells, which helps understand cell-cell communication.

q-bio.MN↗

arXiv2022

An Efficient Implementation for Spatial-Temporal Gaussian Process Regression and Its Applications

Spatial-temporal Gaussian process regression is a popular method for spatial-temporal data modeling. Its state-of-art implementation is based on the state-space model realization of the spatial-temporal Gaussian process and its corresponding Kalman filter and smoother, and has computational complexity $\mathcal{O}(NM^3)$, where $N$ and $M$ are the number of time instants and spatial input locations, respectively, and thus can only be applied to data with large $N$ but relatively small $M$. In this paper, our primary goal is to show that by exploring the Kronecker structure of the state-space model realization of the spatial-temporal Gaussian process, it is possible to further reduce the computational complexity to $\mathcal{O}(M^3+NM^2)$ and thus the proposed implementation can be applied to data with large $N$ and moderately large $M$. The proposed implementation is illustrated over applications in weather data prediction and spatially-distributed system identification. Our secondary goal is to design a kernel for both the Colorado precipitation data and the GHCN temperature data, such that while having more efficient implementation, better prediction performance can also be achieved than the state-of-art result.

eess.SY↗

arXiv2022

Knowledge Distillation for Oriented Object Detection on Aerial Images

Deep convolutional neural network with increased number of parameters has achieved improved precision in task of object detection on natural images, where objects of interests are annotated with horizontal boundary boxes. On aerial images captured from the bird-view perspective, these improvements on model architecture and deeper convolutional layers can also boost the performance on oriented object detection task. However, it is hard to directly apply those state-of-the-art object detectors on the devices with limited computation resources, which necessitates lightweight models through model compression. In order to address this issue, we present a model compression method for rotated object detection on aerial images by knowledge distillation, namely KD-RNet. With a well-trained teacher oriented object detector with a large number of parameters, the obtained object category and location information are both transferred to a compact student network in KD-RNet by collaborative training strategy. Transferring the category information is achieved by knowledge distillation on predicted probability distribution, and a soft regression loss is adopted for handling displacement in location information transfer. The experimental result on a large-scale aerial object detection dataset (DOTA) demonstrates that the proposed KD-RNet model can achieve improved mean-average precision (mAP) with reduced number of parameters, at the same time, KD-RNet boost the performance on providing high quality detections with higher overlap with groundtruth annotations.

cs.CV↗

arXiv2021

MidNet: An Anchor-and-Angle-Free Detector for Oriented Ship Detection in Aerial Images

Ship detection in aerial images remains an active yet challenging task due to arbitrary object orientation and complex background from a bird's-eye perspective. Most of the existing methods rely on angular prediction or predefined anchor boxes, making these methods highly sensitive to unstable angular regression and excessive hyper-parameter setting. To address these issues, we replace the angular-based object encoding with an anchor-and-angle-free paradigm, and propose a novel detector deploying a center and four midpoints for encoding each oriented object, namely MidNet. MidNet designs a symmetrical deformable convolution customized for enhancing the midpoints of ships, then the center and midpoints for an identical ship are adaptively matched by predicting corresponding centripetal shift and matching radius. Finally, a concise analytical geometry algorithm is proposed to refine the centers and midpoints step-wisely for building precise oriented bounding boxes. On two public ship detection datasets, HRSC2016 and FGSD2021, MidNet outperforms the state-of-the-art detectors by achieving APs of 90.52% and 86.50%. Additionally, MidNet obtains competitive results in the ship detection of DOTA.

cs.CV↗

arXiv2019

Online Structured Sparsity-based Moving Object Detection from Satellite Videos

Inspired by the recent developments in computer vision, low-rank and structured sparse matrix decomposition can be potentially be used for extract moving objects in satellite videos. This set of approaches seeks for rank minimization on the background that typically requires batch-based optimization over a sequence of frames, which causes delays in processing and limits their applications. To remedy this delay, we propose an Online Low-rank and Structured Sparse Decomposition (O-LSD). O-LSD reformulates the batch-based low-rank matrix decomposition with the structured sparse penalty to its equivalent frame-wise separable counterpart, which then defines a stochastic optimization problem for online subspace basis estimation. In order to promote online processing, O-LSD conducts the foreground and background separation and the subspace basis update alternatingly for every frame in a video. We also show the convergence of O-LSD theoretically. Experimental results on two satellite videos demonstrate the performance of O-LSD in term of accuracy and time consumption is comparable with the batch-based approaches with significantly reduced delay in processing.

cs.CV↗

arXiv2019

Error Bounded Foreground and Background Modeling for Moving Object Detection in Satellite Videos

Detecting moving objects from ground-based videos is commonly achieved by using background subtraction techniques. Low-rank matrix decomposition inspires a set of state-of-the-art approaches for this task. It is integrated with structured sparsity regularization to achieve background subtraction in the developed method of Low-rank and Structured Sparse Decomposition (LSD). However, when this method is applied to satellite videos where spatial resolution is poor and targets' contrast to the background is low, its performance is limited as the data no longer fits adequately either the foreground structure or the background model. In this paper, we handle these unexplained data explicitly and address the moving target detection from space as one of the pioneer studies. We propose a technique by extending the decomposition formulation with bounded errors, named Extended Low-rank and Structured Sparse Decomposition (E-LSD). This formulation integrates low-rank background, structured sparse foreground and their residuals in a matrix decomposition problem. We provide an effective solution by introducing an alternative treatment and adopting the direct extension of Alternating Direction Method of Multipliers (ADMM). The proposed E-LSD was validated on two satellite videos, and experimental results demonstrate the improvement in background modeling with boosted moving object detection precision over state-of-the-art methods.

cs.CV↗