Time-of-flight (TOF) information provides more accurate location data for annihilation photons, thereby enhancing the quality of PET reconstruction images and reducing noise. List-mode reconstruction has a significant advantage in handling TOF information. However, current advanced TOF PET list-mode reconstruction algorithms still require improvements when dealing with low-count data. Deep learning algorithms have shown promising results in PET image reconstruction. Nevertheless, the incorporation of TOF information poses significant challenges related to the storage space required by deep learning methods, particularly for the advanced deep unrolled methods. In this study, we propose a deep unrolled primal dual network for TOF-PET list-mode reconstruction. The network is unrolled into multiple phases, with each phase comprising a dual network for list-mode domain updates and a primal network for image domain updates. We utilize CUDA for parallel acceleration and computation of the system matrix for TOF list-mode data, and we adopt a dynamic access strategy to mitigate memory consumption. Reconstructed images of different TOF resolutions and different count levels show that the proposed method outperforms the LM-OSEM, LM-EMTV, LM-SPDHG,LM-SPDHG-TV and FastPET method in both visually and quantitative analysis. These results demonstrate the potential application of deep unrolled methods for TOF-PET list-mode data and show better performance than current mainstream TOF-PET list-mode reconstruction algorithms, providing new insights for the application of deep learning methods in TOF list-mode data. The codes for this work are available at https://github.com/RickHH/LMPDnet
Computational wave imaging (CWI) extracts hidden structure and physical properties of a volume of material by analyzing wave signals that traverse that volume. Applications include seismic exploration of the Earth's subsurface, acoustic imaging and non-destructive testing in material science, and ultrasound computed tomography in medicine. Current approaches for solving CWI problems can be divided into two categories: those rooted in traditional physics, and those based on deep learning. Physics-based methods stand out for their ability to provide high-resolution and quantitatively accurate estimates of acoustic properties within the medium. However, they can be computationally intensive and are susceptible to ill-posedness and nonconvexity typical of CWI problems. Machine learning-based computational methods have recently emerged, offering a different perspective to address these challenges. Diverse scientific communities have independently pursued the integration of deep learning in CWI. This review delves into how contemporary scientific machine-learning (ML) techniques, and deep neural networks in particular, have been harnessed to tackle CWI problems. We present a structured framework that consolidates existing research spanning multiple domains, including computational imaging, wave physics, and data science. This study concludes with important lessons learned from existing ML-based methods and identifies technical hurdles and emerging trends through a systematic analysis of the extensive literature on this topic.
Under extreme operating conditions, characterized by high particle multiplicity and heavily overlapping shower energy deposits, classical particle flow algorithms encounter pronounced limitations in resolution, efficiency, and accuracy. To address this challenge, this paper proposes and systematically evaluates a deep learning reconstruction framework: For multichannel sparse features, we design a hybrid loss function combining weighted mean squared error with structural similarity index, effectively balancing pixel-level accuracy and structural fidelity. By integrating 3D convolutions, Squeeze-and-Excitation channel attention, and Offset self-attention modules into baseline convolutional neural networks, we enhance the model's capability to capture cross-modal spatiotemporal correlations and energy-displacement nonlinearities. Validated on custom-constructed simulation data and Pythia jet datasets, the framework's 90K-parameter lightweight variant approaches the performance of 5M-parameter baselines, while the 25M-parameter 3D model achieves state-of-the-art results in both interpolation and extrapolation tasks. Comprehensive experiments quantitatively evaluate component contributions and provide performance-parameter trade-off guidelines. All core code and data processing scripts are open-sourced on a GitHub repository to facilitate community reproducibility and extension.
Prior research has demonstrated the effectiveness of end-to-end deep learning for robotic navigation, where the control signals are directly derived from raw sensory data. However, the majority of existing end-to-end navigation solutions are predominantly camera-based. In this paper, we introduce TinyLidarNet, a lightweight 2D LiDAR-based end-to-end deep learning model for autonomous racing. An F1TENTH vehicle using TinyLidarNet won 3rd place in the 12th F1TENTH Autonomous Grand Prix competition, demonstrating its competitive performance. We systematically analyze its performance on untrained tracks and computing requirements for real-time processing. We find that TinyLidarNet's 1D Convolutional Neural Network (CNN) based architecture significantly outperforms widely used Multi-Layer Perceptron (MLP) based architecture. In addition, we show that it can be processed in real-time on low-end micro-controller units (MCUs).
We consider the portfolio optimisation problem where the terminal function is an S-shaped utility applied at the difference between the wealth and a random benchmark process. We develop several numerical methods for solving the problem using deep learning and duality methods. We use deep learning methods to solve the associated Hamilton-Jacobi-Bellman equation for both the primal and dual problems, and the adjoint equation arising from the stochastic maximum principle. We compare the solution of this non-concave problem to that of concavified utility, a random function depending on the benchmark, in both complete and incomplete markets. We give some numerical results for power and log utilities to show the accuracy of the suggested algorithms.
The Cold Posterior Effect (CPE) is a phenomenon in Bayesian Deep Learning (BDL), where tempering the posterior to a cold temperature often improves the predictive performance of the posterior predictive distribution (PPD). Although the term `CPE' suggests colder temperatures are inherently better, the BDL community increasingly recognizes that this is not always the case. Despite this, there remains no systematic method for finding the optimal temperature beyond grid search. In this work, we propose a data-driven approach to select the temperature that maximizes test log-predictive density, treating the temperature as a model parameter and estimating it directly from the data. We empirically demonstrate that our method performs comparably to grid search, at a fraction of the cost, across both regression and classification tasks. Finally, we highlight the differing perspectives on CPE between the BDL and Generalized Bayes communities: while the former primarily emphasizes the predictive performance of the PPD, the latter prioritizes the utility of the posterior under model misspecification; these distinct objectives lead to different temperature preferences.
Despite the strong performance in many computer vision tasks, Convolutional Neural Networks (CNNs) can sometimes struggle to efficiently capture long-range, complex non-linear dependencies in deeper layers of the network. We address this limitation by introducing Residual KAN, which incorporates the Kolmogorov-Arnold Network (KAN) within the CNN framework as a residual component. Our approach uses Chebyshev polynomials as the basis for KAN convolutions that enables more expressive and adaptive feature representations while maintaining computational efficiency. The proposed RKAN blocks, when integrated into established architectures such as ResNet and DenseNet, offer consistent improvements over the baseline models on various well-known benchmarks. Our results demonstrate the potential of RKAN to enhance the capabilities of deep CNNs in visual data.
Mangroves are dynamic coastal ecosystems that are crucial to environmental health, economic stability, and climate resilience. The monitoring and preservation of mangroves are of global importance, with remote sensing technologies playing a pivotal role in these efforts. The integration of cutting-edge artificial intelligence with satellite data opens new avenues for ecological monitoring, potentially revolutionizing conservation strategies at a time when the protection of natural resources is more crucial than ever. The objective of this work is to provide a comprehensive evaluation of recent deep-learning models on the task of mangrove segmentation. We first introduce and make available a novel open-source dataset, MagSet-2, incorporating mangrove annotations from the Global Mangrove Watch and satellite images from Sentinel-2, from mangrove positions all over the world. We then benchmark three architectural groups, namely convolutional, transformer, and mamba models, using the created dataset. The experimental outcomes further validate the deep learning community's interest in the Mamba model, which surpasses other architectures in all metrics.
Although it is traditionally believed that lossy image compression, such as JPEG compression, has a negative impact on the performance of deep neural networks (DNNs), it is shown by recent works that well-crafted JPEG compression can actually improve the performance of deep learning (DL). Inspired by this, we propose JPEG-DL, a novel DL framework that prepends any underlying DNN architecture with a trainable JPEG compression layer. To make the quantization operation in JPEG compression trainable, a new differentiable soft quantizer is employed at the JPEG layer, and then the quantization operation and underlying DNN are jointly trained. Extensive experiments show that in comparison with the standard DL, JPEG-DL delivers significant accuracy improvements across various datasets and model architectures while enhancing robustness against adversarial attacks. Particularly, on some fine-grained image classification datasets, JPEG-DL can increase prediction accuracy by as much as 20.9%. Our code is available on https://github.com/JpegInspiredDl/JPEG-Inspired-DL.git.
Precision agriculture relies heavily on effective weed management to ensure robust crop yields. This study presents RoWeeder, an innovative framework for unsupervised weed mapping that combines crop-row detection with a noise-resilient deep learning model. By leveraging crop-row information to create a pseudo-ground truth, our method trains a lightweight deep learning model capable of distinguishing between crops and weeds, even in the presence of noisy data. Evaluated on the WeedMap dataset, RoWeeder achieves an F1 score of 75.3, outperforming several baselines. Comprehensive ablation studies further validated the model's performance. By integrating RoWeeder with drone technology, farmers can conduct real-time aerial surveys, enabling precise weed management across large fields. The code is available at: \url{https://github.com/pasqualedem/RoWeeder}.
With the widespread deployment of deep learning models, they influence their environment in various ways. The induced distribution shifts can lead to unexpected performance degradation in deployed models. Existing methods to anticipate performativity typically incorporate information about the deployed model into the feature vector when predicting future outcomes. While enjoying appealing theoretical properties, modifying the input dimension of the prediction task is often not practical. To address this, we propose a novel technique to adjust pretrained backbones for performativity in a modular way, achieving better sample efficiency and enabling the reuse of existing deep learning assets. Focusing on performative label shift, the key idea is to train a shallow adapter module to perform a Bayes-optimal label shift correction to the backbone's logits given a sufficient statistic of the model to be deployed. As such, our framework decouples the construction of input-specific feature embeddings from the mechanism governing performativity. Motivated by dynamic benchmarking as a use-case, we evaluate our approach under adversarial sampling, for vision and language tasks. We show how it leads to smaller loss along the retraining trajectory and enables us to effectively select among candidate models to anticipate performance degradations. More broadly, our work provides a first baseline for addressing performativity in deep learning.
This paper explores alternative formulations of the Kolmogorov Superposition Theorem (KST) as a foundation for neural network design. The original KST formulation, while mathematically elegant, presents practical challenges due to its limited insight into the structure of inner and outer functions and the large number of unknown variables it introduces. Kolmogorov-Arnold Networks (KANs) leverage KST for function approximation, but they have faced scrutiny due to mixed results compared to traditional multilayer perceptrons (MLPs) and practical limitations imposed by the original KST formulation. To address these issues, we introduce ActNet, a scalable deep learning model that builds on the KST and overcomes many of the drawbacks of Kolmogorov's original formulation. We evaluate ActNet in the context of Physics-Informed Neural Networks (PINNs), a framework well-suited for leveraging KST's strengths in low-dimensional function approximation, particularly for simulating partial differential equations (PDEs). In this challenging setting, where models must learn latent functions without direct measurements, ActNet consistently outperforms KANs across multiple benchmarks and is competitive against the current best MLP-based approaches. These results present ActNet as a promising new direction for KST-based deep learning applications, particularly in scientific computing and PDE simulation tasks.
Immunogenicity prediction is a central topic in reverse vaccinology for finding candidate vaccines that can trigger protective immune responses. Existing approaches typically rely on highly compressed features and simple model architectures, leading to limited prediction accuracy and poor generalizability. To address these challenges, we introduce VenusVaccine, a novel deep learning solution with a dual attention mechanism that integrates pre-trained latent vector representations of protein sequences and structures. We also compile the most comprehensive immunogenicity dataset to date, encompassing over 7000 antigen sequences, structures, and immunogenicity labels from bacteria, virus, and tumor. Extensive experiments demonstrate that VenusVaccine outperforms existing methods across a wide range of evaluation metrics. Furthermore, we establish a post-hoc validation protocol to assess the practical significance of deep learning models in tackling vaccine design challenges. Our work provides an effective tool for vaccine design and sets valuable benchmarks for future research. The implementation is at https://github.com/songleee/VenusVaccine.
Despite the strong prediction power of deep learning models, their interpretability remains an important concern. Disentanglement models increase interpretability by decomposing the latent space into interpretable subspaces. In this paper, we propose the first disentanglement method for pathology images. We focus on the task of detecting tumor-infiltrating lymphocytes (TIL). We propose different ideas including cascading disentanglement, novel architecture, and reconstruction branches. We achieve superior performance on complex pathology images, thus improving the interpretability and even generalization power of TIL detection deep learning models. Our codes are available at https://github.com/Shauqi/SS-cVAE.
Deep learning has deeply influenced protein science, enabling breakthroughs in predicting protein properties, higher-order structures, and molecular interactions. This paper introduces DeepProtein, a comprehensive and user-friendly deep learning library tailored for protein-related tasks. It enables researchers to seamlessly address protein data with cutting-edge deep learning models. To assess model performance, we establish a benchmark evaluating different deep learning architectures across multiple protein-related tasks, including protein function prediction, subcellular localization prediction, protein-protein interaction prediction, and protein structure prediction. Furthermore, we introduce DeepProt-T5, a series of fine-tuned Prot-T5-based models that achieve state-of-the-art performance on four benchmark tasks, while demonstrating competitive results on six of others. Comprehensive documentation and tutorials are available which could ensure accessibility and support reproducibility. Built upon the widely used drug discovery library DeepPurpose, DeepProtein is publicly available at https://github.com/jiaqingxie/DeepProtein.
Single-molecule localization microscopy (SMLM) surpasses the diffraction limit, achieving subcellular resolution. Traditional SMLM analysis methods often rely on point spread function (PSF) model fitting, limiting the application of complex PSF models. In recent years, deep learning approaches have significantly improved SMLM algorithms, yielding promising results. However, limitations in inference speed and model size have restricted the widespread adoption of deep learning in practical applications. To address these challenges, this paper proposes an efficient model deployment framework and introduces a lightweight neural network, DilatedLoc, aimed at enhancing both image reconstruction quality and inference speed. Compared to leading network models, DilatedLoc reduces network parameters to under 100 MB and achieves a 50% improvement in inference speed, with superior GPU utilization through a novel deployment architecture compatible with various network models.
Evidential Deep Learning (EDL) is an emerging method for uncertainty estimation that provides reliable predictive uncertainty in a single forward pass, attracting significant attention. Grounded in subjective logic, EDL derives Dirichlet concentration parameters from neural networks to construct a Dirichlet probability density function (PDF), modeling the distribution of class probabilities. Despite its success, EDL incorporates several nonessential settings: In model construction, (1) a commonly ignored prior weight parameter is fixed to the number of classes, while its value actually impacts the balance between the proportion of evidence and its magnitude in deriving predictive scores. In model optimization, (2) the empirical risk features a variance-minimizing optimization term that biases the PDF towards a Dirac delta function, potentially exacerbating overconfidence. (3) Additionally, the structural risk typically includes a KL-divergence-minimizing regularization, whose optimization direction extends beyond the intended purpose and contradicts common sense, diminishing the information carried by the evidence magnitude. Therefore, we propose Re-EDL, a simplified yet more effective variant of EDL, by relaxing the nonessential settings and retaining the essential one, namely, the adoption of projected probability from subjective logic. Specifically, Re-EDL treats the prior weight as an adjustable hyperparameter rather than a fixed scalar, and directly optimizes the expectation of the Dirichlet PDF provided by deprecating both the variance-minimizing optimization term and the divergence regularization term. Extensive experiments and state-of-the-art performance validate the effectiveness of our method. The source code is available at https://github.com/MengyuanChen21/Re-EDL.
Periorbital segmentation and distance prediction using deep learning allows for the objective quantification of disease state, treatment monitoring, and remote medicine. However, there are currently no reports of segmentation datasets for the purposes of training deep learning models with sub mm accuracy on the regions around the eyes. All images (n=2842) had the iris, sclera, lid, caruncle, and brow segmented by five trained annotators. Here, we validate this dataset through intra and intergrader reliability tests and show the utility of the data in training periorbital segmentation networks. All the annotations are publicly available for free download. Having access to segmentation datasets designed specifically for oculoplastic surgery will permit more rapid development of clinically useful segmentation networks which can be leveraged for periorbital distance prediction and disease classification. In addition to the annotations, we also provide an open-source toolkit for periorbital distance prediction from segmentation masks. The weights of all models have also been open-sourced and are publicly available for use by the community.
The application of large deep learning models in weather forecasting has led to significant advancements in the field, including higher-resolution forecasting and extended prediction periods exemplified by models such as Pangu and Fuxi. Despite these successes, previous research has largely been characterized by the neglect of extreme weather events, and the availability of datasets specifically curated for such events remains limited. Given the critical importance of accurately forecasting extreme weather, this study introduces a comprehensive dataset that incorporates high-resolution extreme weather cases derived from the High-Resolution Rapid Refresh (HRRR) data, a 3-km real-time dataset provided by NOAA. We also evaluate the current state-of-the-art deep learning models and Numerical Weather Prediction (NWP) systems on HR-Extreme, and provide a improved baseline deep learning model called HR-Heim which has superior performance on both general loss and HR-Extreme compared to others. Our results reveal that the errors of extreme weather cases are significantly larger than overall forecast error, highlighting them as an crucial source of loss in weather prediction. These findings underscore the necessity for future research to focus on improving the accuracy of extreme weather forecasts to enhance their practical utility.
Convolutional neural networks (CNNs) learn abstract features to perform object classification, but understanding these features remains challenging due to difficult-to-interpret results or high computational costs. We propose an automatic method to visualize and systematically analyze learned features in CNNs. Specifically, we introduce a linking network that maps the penultimate layer of a pre-trained classifier to the latent space of a generative model (StyleGAN-XL), thereby enabling an interpretable, human-friendly visualization of the classifier's representations. Our findings indicate a congruent semantic order in both spaces, enabling a direct linear mapping between them. Training the linking network is computationally inexpensive and decoupled from training both the GAN and the classifier. We introduce an automatic pipeline that utilizes such GAN-based visualizations to quantify learned representations by analyzing activation changes in the classifier in the image domain. This quantification allows us to systematically study the learned representations in several thousand units simultaneously and to extract and visualize units selective for specific semantic concepts. Further, we illustrate how our method can be used to quantify and interpret the classifier's decision boundary using counterfactual examples. Overall, our method offers systematic and objective perspectives on learned abstract representations in CNNs. https://github.com/kaschube-lab/LinkingInStyle.git