pwc-archive/papers-with-abstracts huggingface dataset:
Computation-Efficient Era: A Comprehensive Survey of State Space Models in Medical Image Analysis
Authors: Moein Heidari, Sina Ghorbani Kolahi, Sanaz Karimijafarbigloo, Bobby Azad, Afshin Bozorgpour, Soheila Hatami, Reza Azad, Ali Diba, Ulas Bagci, Dorit Merhof, Ilker Hacihaliloglu
Date: 2024-06-05 00:00:00
Tasks: Mamba, Medical Image Analysis, Navigate, Representation Learning, State Space Models

Sequence modeling plays a vital role across various domains, with recurrent neural networks being historically the predominant method of performing these tasks. However, the emergence of transformers has altered this paradigm due to their superior performance. Built upon these advances, transformers have conjoined CNNs as two leading foundational models for learning visual representations. However, transformers are hindered by the $\mathcal{O}(N^2)$ complexity of their attention mechanisms, while CNNs lack global receptive fields and dynamic weight allocation. State Space Models (SSMs), specifically the \textit{\textbf{Mamba}} model with selection mechanisms and hardware-aware architecture, have garnered immense interest lately in sequential modeling and visual representation learning, challenging the dominance of transformers by providing infinite context lengths and offering substantial efficiency maintaining linear complexity in the input sequence. Capitalizing on the advances in computer vision, medical imaging has heralded a new epoch with Mamba models. Intending to help researchers navigate the surge, this survey seeks to offer an encyclopedic review of Mamba models in medical imaging. Specifically, we start with a comprehensive theoretical review forming the basis of SSMs, including Mamba architecture and its alternatives for sequence modeling paradigms in this context. Next, we offer a structured classification of Mamba models in the medical field and introduce a diverse categorization scheme based on their application, imaging modalities, and targeted organs. Finally, we summarize key challenges, discuss different future research directions of the SSMs in the medical domain, and propose several directions to fulfill the demands of this field. In addition, we have compiled the studies discussed in this paper along with their open-source implementations on our GitHub repository.
Post-hoc Part-prototype Networks
Authors: Andong Tan, Fengtao Zhou, Hao Chen
Date: 2024-06-05 00:00:00

Post-hoc explainability methods such as Grad-CAM are popular because they do not influence the performance of a trained model. However, they mainly reveal "where" a model looks at for a given input, fail to explain "what" the model looks for (e.g., what is important to classify a bird image to a Scott Oriole?). Existing part-prototype networks leverage part-prototypes (e.g., characteristic Scott Oriole's wing and head) to answer both "where" and "what", but often under-perform their black box counterparts in the accuracy. Therefore, a natural question is: can one construct a network that answers both "where" and "what" in a post-hoc manner to guarantee the model's performance? To this end, we propose the first post-hoc part-prototype network via decomposing the classification head of a trained model into a set of interpretable part-prototypes. Concretely, we propose an unsupervised prototype discovery and refining strategy to obtain prototypes that can precisely reconstruct the classification head, yet being interpretable. Besides guaranteeing the performance, we show that our network offers more faithful explanations qualitatively and yields even better part-prototypes quantitatively than prior part-prototype networks.
CoFie: Learning Compact Neural Surface Representations with Coordinate Fields
Authors: Hanwen Jiang, Haitao Yang, Georgios Pavlakos, QiXing Huang
Date: 2024-06-05 00:00:00

This paper introduces CoFie, a novel local geometry-aware neural surface representation. CoFie is motivated by the theoretical analysis of local SDFs with quadratic approximation. We find that local shapes are highly compressive in an aligned coordinate frame defined by the normal and tangent directions of local shapes. Accordingly, we introduce Coordinate Field, which is a composition of coordinate frames of all local shapes. The Coordinate Field is optimizable and is used to transform the local shapes from the world coordinate frame to the aligned shape coordinate frame. It largely reduces the complexity of local shapes and benefits the learning of MLP-based implicit representations. Moreover, we introduce quadratic layers into the MLP to enhance expressiveness concerning local shape geometry. CoFie is a generalizable surface representation. It is trained on a curated set of 3D shapes and works on novel shape instances during testing. When using the same amount of parameters with prior works, CoFie reduces the shape error by 48% and 56% on novel instances of both training and unseen shape categories. Moreover, CoFie demonstrates comparable performance to prior works when using only 70% fewer parameters.
UnWave-Net: Unrolled Wavelet Network for Compton Tomography Image Reconstruction
Authors: Ishak Ayad, Cécilia Tarpau, Javier Cebeiro, Maï K. Nguyen
Date: 2024-06-05 00:00:00
Tasks: Computational Efficiency, Computed Tomography (CT), Image Reconstruction, SSIM

Computed tomography (CT) is a widely used medical imaging technique to scan internal structures of a body, typically involving collimation and mechanical rotation. Compton scatter tomography (CST) presents an interesting alternative to conventional CT by leveraging Compton physics instead of collimation to gather information from multiple directions. While CST introduces new imaging opportunities with several advantages such as high sensitivity, compactness, and entirely fixed systems, image reconstruction remains an open problem due to the mathematical challenges of CST modeling. In contrast, deep unrolling networks have demonstrated potential in CT image reconstruction, despite their computationally intensive nature. In this study, we investigate the efficiency of unrolling networks for CST image reconstruction. To address the important computational cost required for training, we propose UnWave-Net, a novel unrolled wavelet-based reconstruction network. This architecture includes a non-local regularization term based on wavelets, which captures long-range dependencies within images and emphasizes the multi-scale components of the wavelet transform. We evaluate our approach using a CST of circular geometry which stays completely static during data acquisition, where UnWave-Net facilitates image reconstruction in the absence of a specific reconstruction formula. Our method outperforms existing approaches and achieves state-of-the-art performance in terms of SSIM and PSNR, and offers an improved computational efficiency compared to traditional unrolling networks.
Interactive Text-to-Image Retrieval with Large Language Models: A Plug-and-Play Approach
Authors: Saehyung Lee, Sangwon Yu, Junsung Park, Jihun Yi, Sungroh Yoon
Date: 2024-06-05 00:00:00
Tasks: Image Retrieval, Instruction Following, Retrieval

In this paper, we primarily address the issue of dialogue-form context query within the interactive text-to-image retrieval task. Our methodology, PlugIR, actively utilizes the general instruction-following capability of LLMs in two ways. First, by reformulating the dialogue-form context, we eliminate the necessity of fine-tuning a retrieval model on existing visual dialogue data, thereby enabling the use of any arbitrary black-box model. Second, we construct the LLM questioner to generate non-redundant questions about the attributes of the target image, based on the information of retrieval candidate images in the current context. This approach mitigates the issues of noisiness and redundancy in the generated questions. Beyond our methodology, we propose a novel evaluation metric, Best log Rank Integral (BRI), for a comprehensive assessment of the interactive retrieval system. PlugIR demonstrates superior performance compared to both zero-shot and fine-tuned baselines in various benchmarks. Additionally, the two methodologies comprising PlugIR can be flexibly applied together or separately in various situations. Our codes are available at https://github.com/Saehyung-Lee/PlugIR.
Gaussian Primitives for Deformable Image Registration
Authors: Jihe Li, Xiang Liu, Fabian Zhang, Xia Li, Xixin Cao, Ye Zhang, Joachim Buhmann
Date: 2024-06-05 00:00:00
Tasks: Computational Efficiency, Image Registration

Deformable Image Registration (DIR) is essential for aligning medical images that exhibit anatomical variations, facilitating applications such as disease tracking and radiotherapy planning. While classical iterative methods and deep learning approaches have achieved success in DIR, they are often hindered by computational inefficiency or poor generalization. In this paper, we introduce GaussianDIR, a novel, case-specific optimization DIR method inspired by 3D Gaussian splatting. In general, GaussianDIR represents image deformations using a sparse set of mobile and flexible Gaussian primitives, each defined by a center position, covariance, and local rigid transformation. This compact and explicit representation reduces noise and computational overhead while improving interpretability. Furthermore, the movement of individual voxel is derived via blending the local rigid transformation of the neighboring Gaussian primitives. By this, GaussianDIR captures both global smoothness and local rigidity as well as reduces the computational burden. To address varying levels of deformation complexity, GaussianDIR also integrates an adaptive density control mechanism that dynamically adjusts the density of Gaussian primitives. Additionally, we employ multi-scale Gaussian primitives to capture both coarse and fine deformations, reducing optimization to local minima. Experimental results on brain MRI, lung CT, and cardiac MRI datasets demonstrate that GaussianDIR outperforms existing DIR methods in both accuracy and efficiency, highlighting its potential for clinical applications. Finally, as a training-free approach, it challenges the stereotype that iterative methods are inherently slow and transcend the limitations of poor generalization.
SuperFormer: Volumetric Transformer Architectures for MRI Super-Resolution
Authors: Cristhian Forigua, Maria Escobar, Pablo Arbelaez
Date: 2024-06-05 00:00:00
Tasks: Super-Resolution

This paper presents a novel framework for processing volumetric medical information using Visual Transformers (ViTs). First, We extend the state-of-the-art Swin Transformer model to the 3D medical domain. Second, we propose a new approach for processing volumetric information and encoding position in ViTs for 3D applications. We instantiate the proposed framework and present SuperFormer, a volumetric transformer-based approach for Magnetic Resonance Imaging (MRI) Super-Resolution. Our method leverages the 3D information of the MRI domain and uses a local self-attention mechanism with a 3D relative positional encoding to recover anatomical details. In addition, our approach takes advantage of multi-domain information from volume and feature domains and fuses them to reconstruct the High-Resolution MRI. We perform an extensive validation on the Human Connectome Project dataset and demonstrate the superiority of volumetric transformers over 3D CNN-based methods. Our code and pretrained models are available at https://github.com/BCV-Uniandes/SuperFormer.
A Flexible Recursive Network for Video Stereo Matching Based on Residual Estimation
Authors: Youchen Zhao, Guorong Luo, Hua Zhong, Haixiong Li
Date: 2024-06-05 00:00:00
Tasks: GPU, Stereo Matching

Due to the high similarity of disparity between consecutive frames in video sequences, the area where disparity changes is defined as the residual map, which can be calculated. Based on this, we propose RecSM, a network based on residual estimation with a flexible recursive structure for video stereo matching. The RecSM network accelerates stereo matching using a Multi-scale Residual Estimation Module (MREM), which employs the temporal context as a reference and rapidly calculates the disparity for the current frame by computing only the residual values between the current and previous frames. To further reduce the error of estimated disparities, we use the Disparity Optimization Module (DOM) and Temporal Attention Module (TAM) to enforce constraints between each module, and together with MREM, form a flexible Stackable Computation Structure (SCS), which allows for the design of different numbers of SCS based on practical scenarios. Experimental results demonstrate that with a stack count of 3, RecSM achieves a 4x speed improvement compared to ACVNet, running at 0.054 seconds based on one NVIDIA RTX 2080TI GPU, with an accuracy decrease of only 0.7%. Code is available at https://github.com/Y0uchenZ/RecSM.
EngineBench: Flow Reconstruction in the Transparent Combustion Chamber III Optical Engine
Authors: Samuel J. Baker, Michael A. Hobley, Isabel Scherl, Xiaohang Fang, Felix C. P. Leach, Martin H. Davy
Date: 2024-06-05 00:00:00

We present EngineBench, the first machine learning (ML) oriented database to use high quality experimental data for the study of turbulent flows inside combustion machinery. Prior datasets for ML in fluid mechanics are synthetic or use overly simplistic geometries. EngineBench is comprised of real-world particle image velocimetry (PIV) data that captures the turbulent airflow patterns in a specially-designed optical engine. However, in PIV data from internal flows, such as from engines, it is often challenging to achieve a full field of view and large occlusions can be present. In order to design optimal combustion systems, insight into the turbulent flows in these obscured areas is needed, which can be provided via inpainting models. Here we propose a novel inpainting task using random edge gaps, a technique that emphasises realism by introducing occlusions at random sizes and orientations at the edges of the PIV images. We test five ML methods on random edge gaps using pixel-wise, vector-based, and multi-scale performance metrics. We find that UNet-based models are more accurate than the industry-norm non-parametric approach and the context encoder at this task on both small and large gap sizes. The dataset and inpainting task presented in this paper support the development of more general-purpose pre-trained ML models for engine design problems. The method comparisons allow for more informed selection of ML models for problems in experimental flow diagnostics. All data and code are publicly available at https://eng.ox.ac.uk/tpsrg/research/enginebench/.
Comparative Benchmarking of Failure Detection Methods in Medical Image Segmentation: Unveiling the Role of Confidence Aggregation
Authors: Maximilian Zenk, David Zimmerer, Fabian Isensee, Jeremias Traub, Tobias Norajitra, Paul F. Jäger, Klaus Maier-Hein
Date: 2024-06-05 00:00:00
Tasks: Benchmarking, Image Segmentation, Medical Image Analysis, Medical Image Segmentation, Segmentation, Semantic Segmentation

Semantic segmentation is an essential component of medical image analysis research, with recent deep learning algorithms offering out-of-the-box applicability across diverse datasets. Despite these advancements, segmentation failures remain a significant concern for real-world clinical applications, necessitating reliable detection mechanisms. This paper introduces a comprehensive benchmarking framework aimed at evaluating failure detection methodologies within medical image segmentation. Through our analysis, we identify the strengths and limitations of current failure detection metrics, advocating for the risk-coverage analysis as a holistic evaluation approach. Utilizing a collective dataset comprising five public 3D medical image collections, we assess the efficacy of various failure detection strategies under realistic test-time distribution shifts. Our findings highlight the importance of pixel confidence aggregation and we observe superior performance of the pairwise Dice score (Roy et al., 2019) between ensemble predictions, positioning it as a simple and robust baseline for failure detection in medical image segmentation. To promote ongoing research, we make the benchmarking framework available to the community.
Learning Visual Prompts for Guiding the Attention of Vision Transformers
Authors: Razieh Rezaei, Masoud Jalili Sabet, Jindong Gu, Daniel Rueckert, Philip Torr, Ashkan Khakzar
Date: 2024-06-05 00:00:00
Tasks: Visual Prompting

Visual prompting infuses visual information into the input image to adapt models toward specific predictions and tasks. Recently, manually crafted markers such as red circles are shown to guide the model to attend to a target region on the image. However, these markers only work on models trained with data containing those markers. Moreover, finding these prompts requires guesswork or prior knowledge of the domain on which the model is trained. This work circumvents manual design constraints by proposing to learn the visual prompts for guiding the attention of vision transformers. The learned visual prompt, added to any input image would redirect the attention of the pre-trained vision transformer to its spatial location on the image. Specifically, the prompt is learned in a self-supervised manner without requiring annotations and without fine-tuning the vision transformer. Our experiments demonstrate the effectiveness of the proposed optimization-based visual prompting strategy across various pre-trained vision encoders.
Text-to-Image Rectified Flow as Plug-and-Play Priors
Authors: Xiaofeng Yang, Cheng Chen, Xulei Yang, Fayao Liu, Guosheng Lin
Date: 2024-06-05 00:00:00
Tasks: 3D Generation, Text to 3D

Large-scale diffusion models have achieved remarkable performance in generative tasks. Beyond their initial training applications, these models have proven their ability to function as versatile plug-and-play priors. For instance, 2D diffusion models can serve as loss functions to optimize 3D implicit models. Rectified flow, a novel class of generative models, enforces a linear progression from the source to the target distribution and has demonstrated superior performance across various domains. Compared to diffusion-based methods, rectified flow approaches surpass in terms of generation quality and efficiency, requiring fewer inference steps. In this work, we present theoretical and experimental evidence demonstrating that rectified flow based methods offer similar functionalities to diffusion models - they can also serve as effective priors. Besides the generative capabilities of diffusion priors, motivated by the unique time-symmetry properties of rectified flow models, a variant of our method can additionally perform image inversion. Experimentally, our rectified flow-based priors outperform their diffusion counterparts - the SDS and VSD losses - in text-to-3D generation. Our method also displays competitive performance in image inversion and editing.
VWise: A novel benchmark for evaluating scene classification for vehicular applications
Authors: Pedro Azevedo, Emanuella Araújo, Gabriel Pierre, Willams de Lima Costa, João Marcelo Teixeira, Valter Ferreira, Roberto Jones, Veronica Teichrieb
Date: 2024-06-05 00:00:00
Tasks: Classification, Scene Classification

Current datasets for vehicular applications are mostly collected in North America or Europe. Models trained or evaluated on these datasets might suffer from geographical bias when deployed in other regions. Specifically, for scene classification, a highway in a Latin American country differs drastically from an Autobahn, for example, both in design and maintenance levels. We propose VWise, a novel benchmark for road-type classification and scene classification tasks, in addition to tasks focused on external contexts related to vehicular applications in LatAm. We collected over 520 video clips covering diverse urban and rural environments across Latin American countries, annotated with six classes of road types. We also evaluated several state-of-the-art classification models in baseline experiments, obtaining over 84% accuracy. With this dataset, we aim to enhance research on vehicular tasks in Latin America.
A Comprehensive Library for Benchmarking Multi-class Visual Anomaly Detection
Authors: Jiangning Zhang, Haoyang He, Zhenye Gan, Qingdong He, Yuxuan Cai, Zhucun Xue, Yabiao Wang, Chengjie Wang, Lei Xie, Yong liu
Date: 2024-06-05 00:00:00
Tasks: Anomaly Detection, Benchmarking, GPU, Lesion Detection, Multi-class Anomaly Detection

Visual anomaly detection aims to identify anomalous regions in images through unsupervised learning paradigms, with increasing application demand and value in fields such as industrial inspection and medical lesion detection. Despite significant progress in recent years, there is a lack of comprehensive benchmarks to adequately evaluate the performance of various mainstream methods across different datasets under the practical multi-class setting. The absence of standardized experimental setups can lead to potential biases in training epochs, resolution, and metric results, resulting in erroneous conclusions. This paper addresses this issue by proposing a comprehensive visual anomaly detection benchmark, ADer, which is a modular framework that is highly extensible for new methods. The benchmark includes multiple datasets from industrial and medical domains, implementing fifteen state-of-the-art methods and nine comprehensive metrics. Additionally, we have proposed the GPU-assisted ADEval package to address the slow evaluation problem of metrics like time-consuming mAU-PRO on large-scale data, significantly reducing evaluation time by more than \textit{1000-fold}. Through extensive experimental results, we objectively reveal the strengths and weaknesses of different methods and provide insights into the challenges and future directions of multi-class visual anomaly detection. We hope that ADer will become a valuable resource for researchers and practitioners in the field, promoting the development of more robust and generalizable anomaly detection systems. Full codes are open-sourced at https://github.com/zhangzjn/ader.
Generative Diffusion Models for Fast Simulations of Particle Collisions at CERN
Authors: Mikołaj Kita, Jan Dubiński, Przemysław Rokita, Kamil Deja
Date: 2024-06-05 00:00:00

In High Energy Physics simulations play a crucial role in unraveling the complexities of particle collision experiments within CERN's Large Hadron Collider. Machine learning simulation methods have garnered attention as promising alternatives to traditional approaches. While existing methods mainly employ Variational Autoencoders (VAEs) or Generative Adversarial Networks (GANs), recent advancements highlight the efficacy of diffusion models as state-of-the-art generative machine learning methods. We present the first simulation for Zero Degree Calorimeter (ZDC) at the ALICE experiment based on diffusion models, achieving the highest fidelity compared to existing baselines. We perform an analysis of trade-offs between generation times and the simulation quality. The results indicate a significant potential of latent diffusion model due to its rapid generation time.