arXiv subjects

Pengfei Gu

Publications and source records attributed to Pengfei Gu.

32 records · Page 2Linked to original sources

arXiv2025

Hierarchical LoG Bayesian Neural Network for Enhanced Aorta Segmentation

Accurate segmentation of the aorta and its associated arch branches is crucial for diagnosing aortic diseases. While deep learning techniques have significantly improved aorta segmentation, they remain challenging due to the intricate multiscale structure and the complexity of the surrounding tissues. This paper presents a novel approach for enhancing aorta segmentation using a Bayesian neural network-based hierarchical Laplacian of Gaussian (LoG) model. Our model consists of a 3D U-Net stream and a hierarchical LoG stream: the former provides an initial aorta segmentation, and the latter enhances blood vessel detection across varying scales by learning suitable LoG kernels, enabling self-adaptive handling of different parts of the aorta vessels with significant scale differences. We employ a Bayesian method to parameterize the LoG stream and provide confidence intervals for the segmentation results, ensuring robustness and reliability of the prediction for vascular medical image analysts. Experimental results show that our model can accurately segment main and supra-aortic vessels, yielding at least a 3% gain in the Dice coefficient over state-of-the-art methods across multiple volumes drawn from two aorta datasets, and can provide reliable confidence intervals for different parts of the aorta. The code is available at https://github.com/adlsn/LoGBNet.

cs.CV↗

arXiv2024

Sli2Vol+: Segmenting 3D Medical Images Based on an Object Estimation Guided Correspondence Flow Network

Deep learning (DL) methods have shown remarkable successes in medical image segmentation, often using large amounts of annotated data for model training. However, acquiring a large number of diverse labeled 3D medical image datasets is highly difficult and expensive. Recently, mask propagation DL methods were developed to reduce the annotation burden on 3D medical images. For example, Sli2Vol~\cite{yeung2021sli2vol} proposed a self-supervised framework (SSF) to learn correspondences by matching neighboring slices via slice reconstruction in the training stage; the learned correspondences were then used to propagate a labeled slice to other slices in the test stage. But, these methods are still prone to error accumulation due to the inter-slice propagation of reconstruction errors. Also, they do not handle discontinuities well, which can occur between consecutive slices in 3D images, as they emphasize exploiting object continuity. To address these challenges, in this work, we propose a new SSF, called \proposed, {for segmenting any anatomical structures in 3D medical images using only a single annotated slice per training and testing volume.} Specifically, in the training stage, we first propagate an annotated 2D slice of a training volume to the other slices, generating pseudo-labels (PLs). Then, we develop a novel Object Estimation Guided Correspondence Flow Network to learn reliable correspondences between consecutive slices and corresponding PLs in a self-supervised manner. In the test stage, such correspondences are utilized to propagate a single annotated slice to the other slices of a test volume. We demonstrate the effectiveness of our method on various medical image segmentation tasks with different datasets, showing better generalizability across different organs, modalities, and modals. Code is available at \url{https://github.com/adlsn/Sli2Volplus}

cs.CV↗

arXiv2024

FCNR: Fast Compressive Neural Representation of Visualization Images

We present FCNR, a fast compressive neural representation for tens of thousands of visualization images under varying viewpoints and timesteps. The existing NeRVI solution, albeit enjoying a high compression ratio, incurs slow speeds in encoding and decoding. Built on the recent advances in stereo image compression, FCNR assimilates stereo context modules and joint context transfer modules to compress image pairs. Our solution significantly improves encoding and decoding speed while maintaining high reconstruction quality and satisfying compression ratio. To demonstrate its effectiveness, we compare FCNR with state-of-the-art neural compression methods, including E-NeRV, HNeRV, NeRVI, and ECSIC. The source code can be found at https://github.com/YunfeiLu0112/FCNR.

cs.CV↗

arXiv2024

Boosting Medical Image Classification with Segmentation Foundation Model

The Segment Anything Model (SAM) exhibits impressive capabilities in zero-shot segmentation for natural images. Recently, SAM has gained a great deal of attention for its applications in medical image segmentation. However, to our best knowledge, no studies have shown how to harness the power of SAM for medical image classification. To fill this gap and make SAM a true ``foundation model'' for medical image analysis, it is highly desirable to customize SAM specifically for medical image classification. In this paper, we introduce SAMAug-C, an innovative augmentation method based on SAM for augmenting classification datasets by generating variants of the original images. The augmented datasets can be used to train a deep learning classification model, thereby boosting the classification performance. Furthermore, we propose a novel framework that simultaneously processes raw and SAMAug-C augmented image input, capitalizing on the complementary information that is offered by both. Experiments on three public datasets validate the effectiveness of our new approach.

cs.CV↗

arXiv2024

Current and future directions in network biology

Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These challenges stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology and highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on the future directions of network biology. Additionally, we offer insights into scientific communities, educational initiatives, and the importance of fostering diversity within the field. This paper establishes a roadmap for an immediate and long-term vision for network biology.

q-bio.MN↗

arXiv2024

SwIPE: Efficient and Robust Medical Image Segmentation with Implicit Patch Embeddings

Modern medical image segmentation methods primarily use discrete representations in the form of rasterized masks to learn features and generate predictions. Although effective, this paradigm is spatially inflexible, scales poorly to higher-resolution images, and lacks direct understanding of object shapes. To address these limitations, some recent works utilized implicit neural representations (INRs) to learn continuous representations for segmentation. However, these methods often directly adopted components designed for 3D shape reconstruction. More importantly, these formulations were also constrained to either point-based or global contexts, lacking contextual understanding or local fine-grained details, respectively--both critical for accurate segmentation. To remedy this, we propose a novel approach, SwIPE (Segmentation with Implicit Patch Embeddings), that leverages the advantages of INRs and predicts shapes at the patch level--rather than at the point level or image level--to enable both accurate local boundary delineation and global shape coherence. Extensive evaluations on two tasks (2D polyp segmentation and 3D abdominal organ segmentation) show that SwIPE significantly improves over recent implicit approaches and outperforms state-of-the-art discrete methods with over 10x fewer parameters. Our method also demonstrates superior data efficiency and improved robustness to data shifts across image resolutions and datasets. Code is available on Github (https://github.com/charzharr/miccai23-swipe-implicit-segmentation).

cs.CV↗

arXiv2024

Path-GPTOmic: A Balanced Multi-modal Learning Framework for Survival Outcome Prediction

For predicting cancer survival outcomes, standard approaches in clinical research are often based on two main modalities: pathology images for observing cell morphology features, and genomic (e.g., bulk RNA-seq) for quantifying gene expressions. However, existing pathology-genomic multi-modal algorithms face significant challenges: (1) Valuable biological insights regarding genes and gene-gene interactions are frequently overlooked; (2) one modality often dominates the optimization process, causing inadequate training for the other modality. In this paper, we introduce a new multi-modal ``Path-GPTOmic" framework for cancer survival outcome prediction. First, to extract valuable biological insights, we regulate the embedding space of a foundation model, scGPT, initially trained on single-cell RNA-seq data, making it adaptable for bulk RNA-seq data. Second, to address the imbalance-between-modalities problem, we propose a gradient modulation mechanism tailored to the Cox partial likelihood loss for survival prediction. The contributions of the modalities are dynamically monitored and adjusted during the training process, encouraging that both modalities are sufficiently trained. Evaluated on two TCGA(The Cancer Genome Atlas) datasets, our model achieves substantially improved survival prediction accuracy.

cs.CV↗

arXiv2023

SamDSK: Combining Segment Anything Model with Domain-Specific Knowledge for Semi-Supervised Learning in Medical Image Segmentation

The Segment Anything Model (SAM) exhibits a capability to segment a wide array of objects in natural images, serving as a versatile perceptual tool for various downstream image segmentation tasks. In contrast, medical image segmentation tasks often rely on domain-specific knowledge (DSK). In this paper, we propose a novel method that combines the segmentation foundation model (i.e., SAM) with domain-specific knowledge for reliable utilization of unlabeled images in building a medical image segmentation model. Our new method is iterative and consists of two main stages: (1) segmentation model training; (2) expanding the labeled set by using the trained segmentation model, an unlabeled set, SAM, and domain-specific knowledge. These two stages are repeated until no more samples are added to the labeled set. A novel optimal-matching-based method is developed for combining the SAM-generated segmentation proposals and pixel-level and image-level DSK for constructing annotations of unlabeled images in the iterative stage (2). In experiments, we demonstrate the effectiveness of our proposed method for breast cancer segmentation in ultrasound images, polyp segmentation in endoscopic images, and skin lesion segmentation in dermoscopic images. Our work initiates a new direction of semi-supervised learning for medical image segmentation: the segmentation foundation model can be harnessed as a valuable tool for label-efficient segmentation learning in medical image segmentation.

cs.CV↗

arXiv2023

Graph-Free Learning in Graph-Structured Data: A More Efficient and Accurate Spatiotemporal Learning Perspective

Spatiotemporal learning, which aims at extracting spatiotemporal correlations from the collected spatiotemporal data, is a research hotspot in recent years. And considering the inherent graph structure of spatiotemporal data, recent works focus on capturing spatial dependencies by utilizing Graph Convolutional Networks (GCNs) to aggregate vertex features with the guidance of adjacency matrices. In this paper, with extensive and deep-going experiments, we comprehensively analyze existing spatiotemporal graph learning models and reveal that extracting adjacency matrices with carefully design strategies, which are viewed as the key of enhancing performance on graph learning, are largely ineffective. Meanwhile, based on these experiments, we also discover that the aggregation itself is more important than the way that how vertices are aggregated. With these preliminary, a novel efficient Graph-Free Spatial (GFS) learning module based on layer normalization for capturing spatial correlations in spatiotemporal graph learning. The proposed GFS module can be easily plugged into existing models for replacing all graph convolution components. Rigorous theoretical proof demonstrates that the time complexity of GFS is significantly better than that of graph convolution operation. Extensive experiments verify the superiority of GFS in both the perspectives of efficiency and learning effect in processing graph-structured data especially extreme large scale graph data.

cs.LG↗

arXiv2022

Keep Your Friends Close & Enemies Farther: Debiasing Contrastive Learning with Spatial Priors in 3D Radiology Images

Understanding of spatial attributes is central to effective 3D radiology image analysis where crop-based learning is the de facto standard. Given an image patch, its core spatial properties (e.g., position & orientation) provide helpful priors on expected object sizes, appearances, and structures through inherent anatomical consistencies. Spatial correspondences, in particular, can effectively gauge semantic similarities between inter-image regions, while their approximate extraction requires no annotations or overbearing computational costs. However, recent 3D contrastive learning approaches either neglect correspondences or fail to maximally capitalize on them. To this end, we propose an extensible 3D contrastive framework (Spade, for Spatial Debiasing) that leverages extracted correspondences to select more effective positive & negative samples for representation learning. Our method learns both globally invariant and locally equivariant representations with downstream segmentation in mind. We also propose separate selection strategies for global & local scopes that tailor to their respective representational requirements. Compared to recent state-of-the-art approaches, Spade shows notable improvements on three downstream segmentation tasks (CT Abdominal Organ, CT Heart, MR Heart).

cs.CV↗

arXiv2022

A Point in the Right Direction: Vector Prediction for Spatially-aware Self-supervised Volumetric Representation Learning

High annotation costs and limited labels for dense 3D medical imaging tasks have recently motivated an assortment of 3D self-supervised pretraining methods that improve transfer learning performance. However, these methods commonly lack spatial awareness despite its centrality in enabling effective 3D image analysis. More specifically, position, scale, and orientation are not only informative but also automatically available when generating image crops for training. Yet, to date, no work has proposed a pretext task that distills all key spatial features. To fulfill this need, we develop a new self-supervised method, VectorPOSE, which promotes better spatial understanding with two novel pretext tasks: Vector Prediction (VP) and Boundary-Focused Reconstruction (BFR). VP focuses on global spatial concepts (i.e., properties of 3D patches) while BFR addresses weaknesses of recent reconstruction methods to learn more effective local representations. We evaluate VectorPOSE on three 3D medical image segmentation tasks, showing that it often outperforms state-of-the-art methods, especially in limited annotation settings.

cs.CV↗

arXiv2022

ConvFormer: Combining CNN and Transformer for Medical Image Segmentation

Convolutional neural network (CNN) based methods have achieved great successes in medical image segmentation, but their capability to learn global representations is still limited due to using small effective receptive fields of convolution operations. Transformer based methods are capable of modelling long-range dependencies of information for capturing global representations, yet their ability to model local context is lacking. Integrating CNN and Transformer to learn both local and global representations while exploring multi-scale features is instrumental in further improving medical image segmentation. In this paper, we propose a hierarchical CNN and Transformer hybrid architecture, called ConvFormer, for medical image segmentation. ConvFormer is based on several simple yet effective designs. (1) A feed forward module of Deformable Transformer (DeTrans) is re-designed to introduce local information, called Enhanced DeTrans. (2) A residual-shaped hybrid stem based on a combination of convolutions and Enhanced DeTrans is developed to capture both local and global representations to enhance representation ability. (3) Our encoder utilizes the residual-shaped hybrid stem in a hierarchical manner to generate feature maps in different scales, and an additional Enhanced DeTrans encoder with residual connections is built to exploit multi-scale features with feature maps of different scales as input. Experiments on several datasets show that our ConvFormer, trained from scratch, outperforms various CNN- or Transformer-based architectures, achieving state-of-the-art performance.

cs.CV↗

arXiv2018

Approximate Set Union Via Approximate Randomization

We develop an randomized approximation algorithm for the size of set union problem $\arrowvert A_1\cup A_2\cup...\cup A_m\arrowvert$, which given a list of sets $A_1,...,A_m$ with approximate set size $m_i$ for $A_i$ with $m_i\in \left((1-β_L)|A_i|, (1+β_R)|A_i|\right)$, and biased random generators with $Prob(x=\randomElm(A_i))\in \left[{1-α_L\over |A_i|},{1+α_R\over |A_i|}\right]$ for each input set $A_i$ and element $x\in A_i,$ where $i=1, 2, ..., m$. The approximation ratio for $\arrowvert A_1\cup A_2\cup...\cup A_m\arrowvert$ is in the range $[(1-ε)(1-α_L)(1-β_L), (1+ε)(1+α_R)(1+β_R)]$ for any $ε\in (0,1)$, where $α_L, α_R, β_L,β_R\in (0,1)$. The complexity of the algorithm is measured by both time complexity, and round complexity. The algorithm is allowed to make multiple membership queries and get random elements from the input sets in one round. Our algorithm makes adaptive accesses to input sets with multiple rounds. Our algorithm gives an approximation scheme with $O(\setCount\cdot(\log \setCount)^{O(1)})$ running time and $O(\log m)$ rounds, where $m$ is the number of sets. Our algorithm can handle input sets that can generate random elements with bias, and its approximation ratio depends on the bias. Our algorithm gives a flexible tradeoff with time complexity $O\left(\setCount^{1+ξ}\right)$ and round complexity $O\left({1\over ξ}\right)$ for any $ξ\in(0,1)$.

cs.DS↗

arXiv2018

Polyhedra Circuits and Their Applications

We introduce polyhedra circuits. Each polyhedra circuit characterizes a geometric region in $\mathbb{R}^d$. They can be applied to represent a rich class of geometric objects, which include all polyhedra and the union of a finite number of polyhedra. They can be used to approximate a large class of $d$-dimensional manifolds in $\mathbb{R}^d$. Barvinok developed polynomial time algorithms to compute the volume of a rational polyhedra, and to count the number of lattice points in a rational polyhedra in a fixed dimensional space $\mathbb{R}^d$ with a fix $d$. Define $T_V(d,\, n)$ be the polynomial time in $n$ to compute the volume of one rational polyhedra, $T_L(d,\, n)$ be the polynomial time in $n$ to count the number of lattice points in one rational polyhedra with $d$ be a fixed dimensional number, $T_I(d,\, n)$ be the polynomial time in $n$ to solve integer linear programming time with $d$ be the fixed dimensional number, where $n$ is the total number of linear inequalities from input polyhedra. We develop algorithms to count the number of lattice points in the geometric region determined by a polyhedra circuit in $O\left(nd\cdot r_d(n)\cdot T_V(d,\, n)\right)$ time and to compute the volume of the geometric region determined by a polyhedra circuit in $O\left(n\cdot r_d(n)\cdot T_I(d,\, n)+r_d(n)T_L(d,\, n)\right)$ time, where $n$ is the number of input linear inequalities, $d$ is number of variables and $r_d(n)$ be the maximal number of regions that $n$ linear inequalities with $d$ variables partition $\mathbb{R}^d$.

cs.CG↗