Recovering frequency-localized functions from pointwise data is a fundamental task in signal processing. We examine this problem from an approximation-theoretic perspective, focusing on least squares and deep learning-based methods. First, we establish a novel recovery theorem for least squares approximations using the Slepian basis from uniform random samples in low dimensions, explicitly tracking the dependence of the bandwidth on the sampling complexity. Building on these results, we then present a recovery guarantee for approximating bandlimited functions via deep learning from pointwise data. This result, framed as a practical existence theorem, provides conditions on the network architecture, training procedure, and data acquisition sufficient for accurate approximation. To complement our theoretical findings, we perform numerical comparisons between least squares and deep learning for approximating one- and two-dimensional functions. We conclude with a discussion of the theoretical limitations and the practical gaps between theory and implementation.
Efficient and accurate object detection is an important topic in the development of computer vision systems. With the advent of deep learning techniques, the accuracy of object detection has increased significantly. The project aims to integrate a modern technique for object detection with the aim of achieving high accuracy with real-time performance. The reliance on other computer vision algorithms in many object identification systems, which results in poor and ineffective performance, is a significant obstacle. In this research, we solve the end-to-end object detection problem entirely using deep learning techniques. The network is trained using the most difficult publicly available dataset, which is used for an annual item detection challenge. Applications that need object detection can benefit the system's quick and precise finding.
Fine-tuned large language models (LLMs) often exhibit overconfidence, particularly when trained on small datasets, resulting in poor calibration and inaccurate uncertainty estimates. Evidential Deep Learning (EDL), an uncertainty-aware approach, enables uncertainty estimation in a single forward pass, making it a promising method for calibrating fine-tuned LLMs. However, despite its computational efficiency, EDL is prone to overfitting, as its training objective can result in overly concentrated probability distributions. To mitigate this, we propose regularizing EDL by incorporating an information bottleneck (IB). Our approach IB-EDL suppresses spurious information in the evidence generated by the model and encourages truly predictive information to influence both the predictions and uncertainty estimates. Extensive experiments across various fine-tuned LLMs and tasks demonstrate that IB-EDL outperforms both existing EDL and non-EDL approaches. By improving the trustworthiness of LLMs, IB-EDL facilitates their broader adoption in domains requiring high levels of confidence calibration. Code is available at https://github.com/sandylaker/ib-edl.
In this work, we study optimization methods that leverage the linear minimization oracle (LMO) over a norm-ball. We propose a new stochastic family of algorithms that uses the LMO to adapt to the geometry of the problem and, perhaps surprisingly, show that they can be applied to unconstrained problems. The resulting update rule unifies several existing optimization methods under a single framework. Furthermore, we propose an explicit choice of norm for deep architectures, which, as a side benefit, leads to the transferability of hyperparameters across model sizes. Experimentally, we demonstrate significant speedups on nanoGPT training using our algorithm, Scion, without any reliance on Adam. The proposed method is memory-efficient, requiring only one set of model weights and one set of gradients, which can be stored in half-precision. The code is available at https://github.com/LIONS-EPFL/scion .
Predictive tasks on relational databases are critical in real-world applications spanning e-commerce, healthcare, and social media. To address these tasks effectively, Relational Deep Learning (RDL) encodes relational data as graphs, enabling Graph Neural Networks (GNNs) to exploit relational structures for improved predictions. However, existing RDL methods often overlook the intrinsic structural properties of the graphs built from relational databases, leading to modeling inefficiencies, particularly in handling many-to-many relationships. Here we introduce RelGNN, a novel GNN framework specifically designed to leverage the unique structural characteristics of the graphs built from relational databases. At the core of our approach is the introduction of atomic routes, which are simple paths that enable direct single-hop interactions between the source and destination nodes. Building upon these atomic routes, RelGNN designs new composite message passing and graph attention mechanisms that reduce redundancy, highlight key signals, and enhance predictive accuracy. RelGNN is evaluated on 30 diverse real-world tasks from Relbench (Fey et al., 2024), and achieves state-of-the-art performance on the vast majority of tasks, with improvements of up to 25%. Code is available at https://github.com/snap-stanford/RelGNN.
Diffusion MRI (dMRI) provides unique insights into fetal brain microstructure in utero. Longitudinal and cross-sectional fetal dMRI studies can reveal crucial neurodevelopmental changes but require precise spatial alignment across scans and subjects. This is challenging due to low data quality, rapid brain development, and limited anatomical landmarks. Existing registration methods, designed for high-quality adult data, struggle with these complexities. To address this, we introduce FetDTIAlign, a deep learning approach for fetal brain dMRI registration, enabling accurate affine and deformable alignment. FetDTIAlign features a dual-encoder architecture and iterative feature-based inference, reducing the impact of noise and low resolution. It optimizes network configurations and domain-specific features at each registration stage, enhancing both robustness and accuracy. We validated FetDTIAlign on data from 23 to 36 weeks gestation, covering 60 white matter tracts. It consistently outperformed two classical optimization-based methods and a deep learning pipeline, achieving superior anatomical correspondence. Further validation on external data from the Developing Human Connectome Project confirmed its generalizability across acquisition protocols. Our results demonstrate the feasibility of deep learning for fetal brain dMRI registration, providing a more accurate and reliable alternative to classical techniques. By enabling precise cross-subject and tract-specific analyses, FetDTIAlign supports new discoveries in early brain development.
We propose a novel deep learning method which combines classical regularization with data augmentation for estimating myelin water fraction (MWF) in the brain via biexponential analysis. Our aim is to design an accurate deep learning technique for analysis of signals arising in magnetic resonance relaxometry. In particular, we study the biexponential model, one of the signal models used for MWF estimation. We greatly extend our previous work on \emph{input layer regularization (ILR)} in several ways. We now incorporate optimal regularization parameter selection via a dedicated neural network or generalized cross validation (GCV) on a signal-by-signal, or pixel-by-pixel, basis to form the augmented input signal, and now incorporate estimation of MWF, rather than just exponential time constants, into the analysis. On synthetically generated data, our proposed deep learning architecture outperformed both classical methods and a conventional multi-layer perceptron. On in vivo brain data, our architecture again outperformed other comparison methods, with GCV proving to be somewhat superior to a NN for regularization parameter selection. Thus, ILR improves estimation of MWF within the biexponential model. In addition, classical methods such as GCV may be combined with deep learning to optimize MWF imaging in the human brain.
Functional brain connectome is crucial for deciphering the neural mechanisms underlying cognitive functions and neurological disorders. Graph deep learning models have recently gained tremendous popularity in this field. However, their actual effectiveness in modeling the brain connectome remains unclear. In this study, we re-examine graph deep learning models based on four large-scale neuroimaging studies encompassing diverse cognitive and clinical outcomes. Surprisingly, we find that the message aggregation mechanism, a hallmark of graph deep learning models, does not help with predictive performance as typically assumed, but rather consistently degrades it. To address this issue, we propose a hybrid model combining a linear model with a graph attention network through dual pathways, achieving robust predictions and enhanced interpretability by revealing both localized and global neural connectivity patterns. Our findings urge caution in adopting complex deep learning models for functional brain connectome analysis, emphasizing the need for rigorous experimental designs to establish tangible performance gains and perhaps more importantly, to pursue improvements in model interpretability.
Cryo-electron tomography (cryo-ET) enables 3D visualization of cellular environments. Accurate reconstruction of high-resolution volumes is complicated by the very low signal-to-noise ratio and a restricted range of sample tilts, creating a missing wedge of Fourier information. Recent self-supervised deep learning approaches, which post-process initial reconstructions done by filtered backprojection (FBP), have significantly improved reconstruction quality, but they are computationally expensive, demand large memory, and require retraining for each new dataset. End-to-end supervised learning is an appealing alternative but is impeded by the lack of ground truth and the large memory demands of high-resolution volumetric data. Training on synthetic data often leads to overfitting and poor generalization to real data, and, to date, no general end-to-end deep learning reconstructors exist for cryo-ET. In this work, we introduce CryoLithe, a local, memory-efficient reconstruction network that directly estimates the volume from an aligned tilt-series, overcoming the suboptimal FBP. We demonstrate that leveraging transform-domain locality makes our network robust to distribution shifts, enabling effective supervised training and giving excellent results on real data -- without retraining or fine-tuning.
Transfer Learning (TL) is an emerging field in modeling building thermal dynamics. This method reduces the data required for a data-driven model of a target building by leveraging knowledge from a source building. Consequently, it enables the creation of data-efficient models that can be used for advanced control and fault detection & diagnosis. A major limitation of the TL approach is its inconsistent performance across different sources. Although accurate source-building selection for a target is crucial, it remains a persistent challenge. We present GenTL, a general transfer learning model for single-family houses in Central Europe. GenTL can be efficiently fine-tuned to a large variety of target buildings. It is pretrained on a Long Short-Term Memory (LSTM) network with data from 450 different buildings. The general transfer learning model eliminates the need for source-building selection by serving as a universal source for fine-tuning. Comparative analysis with conventional single-source to single-target TL demonstrates the efficacy and reliability of the general pretraining approach. Testing GenTL on 144 target buildings for fine-tuning reveals an average prediction error (RMSE) reduction of 42.1 % compared to fine-tuning single-source models.
Quantification, or prevalence estimation, is the task of predicting the prevalence of each class within an unknown bag of examples. Most existing quantification methods in the literature rely on prior probability shift assumptions to create a quantification model that uses the predictions of an underlying classifier to make optimal prevalence estimates. In this work, we present an end-to-end neural network that uses Gaussian distributions in latent spaces to obtain invariant representations of bags of examples. This approach addresses the quantification problem using deep learning, enabling the optimization of specific loss functions relevant to the problem and avoiding the need for an intermediate classifier, tackling the quantification problem as a direct optimization problem. Our method achieves state-of-the-art results, both against traditional quantification methods and other deep learning approaches for quantification. The code needed to reproduce all our experiments is publicly available at https://github.com/AICGijon/gmnet.
Multi-objective optimization (MOO) in deep learning aims to simultaneously optimize multiple conflicting objectives, a challenge frequently encountered in areas like multi-task learning and multi-criteria learning. Recent advancements in gradient-based MOO methods have enabled the discovery of diverse types of solutions, ranging from a single balanced solution to finite or even infinite Pareto sets, tailored to user needs. These developments have broad applications across domains such as reinforcement learning, computer vision, recommendation systems, and large language models. This survey provides the first comprehensive review of gradient-based MOO in deep learning, covering algorithms, theories, and practical applications. By unifying various approaches and identifying critical challenges, it serves as a foundational resource for driving innovation in this evolving field. A comprehensive list of MOO algorithms in deep learning is available at \url{https://github.com/Baijiong-Lin/Awesome-Multi-Objective-Deep-Learning}.
Recent work [ 14 ] has introduced a method for prior elicitation that utilizes records of expert decisions to infer a prior distribution. While this method provides a promising approach to eliciting expert uncertainty, it has only been demonstrated using tabular data, which may not entirely represent the information used by experts to make decisions. In this paper, we demonstrate how analysts can adopt a deep learning approach to utilize the method proposed in [14 ] with the actual information experts use. We provide an overview of deep learning models that can effectively model expert decision-making to elicit distributions that capture expert uncertainty and present an example examining the risk of colon cancer to show in detail how these models can be used.
Alzheimer's Disease is a neurodegenerative condition characterized by dementia and impairment in neurological function. The study primarily focuses on the individuals above age 40, affecting their memory, behavior, and cognitive processes of the brain. Alzheimer's disease requires diagnosis by a detailed assessment of MRI scans and neuropsychological tests of the patients. This project compares existing deep learning models in the pursuit of enhancing the accuracy and efficiency of AD diagnosis, specifically focusing on the Convolutional Neural Network, Bayesian Convolutional Neural Network, and the U-net model with the Open Access Series of Imaging Studies brain MRI dataset. Besides, to ensure robustness and reliability in the model evaluations, we address the challenge of imbalance in data. We then perform rigorous evaluation to determine strengths and weaknesses for each model by considering sensitivity, specificity, and computational efficiency. This comparative analysis would shed light on the future role of AI in revolutionizing AD diagnostics but also paved ways for future innovation in medical imaging and the management of neurodegenerative diseases.
This study presents a comprehensive review of the potential of multimodal deep learning (DL) in medical diagnosis, using COVID-19 as a case example. Motivated by the success of artificial intelligence applications during the COVID-19 pandemic, this research aims to uncover the capabilities of DL in disease screening, prediction, and classification, and to derive insights that enhance the resilience, sustainability, and inclusiveness of science, technology, and innovation systems. Adopting a systematic approach, we investigate the fundamental methodologies, data sources, preprocessing steps, and challenges encountered in various studies and implementations. We explore the architecture of deep learning models, emphasising their data-specific structures and underlying algorithms. Subsequently, we compare different deep learning strategies utilised in COVID-19 analysis, evaluating them based on methodology, data, performance, and prerequisites for future research. By examining diverse data types and diagnostic modalities, this research contributes to scientific understanding and knowledge of the multimodal application of DL and its effectiveness in diagnosis. We have implemented and analysed 11 deep learning models using COVID-19 image, text, and speech (ie, cough) data. Our analysis revealed that the MobileNet model achieved the highest accuracy of 99.97% for COVID-19 image data and 93.73% for speech data (i.e., cough). However, the BiGRU model demonstrated superior performance in COVID-19 text classification with an accuracy of 99.89%. The broader implications of this research suggest potential benefits for other domains and disciplines that could leverage deep learning techniques for image, text, and speech analysis.
4D Flow Magnetic Resonance Imaging (4D Flow MRI) is a non-invasive technique for volumetric, time-resolved blood flow quantification. However, apparent trade-offs between acquisition time, image noise, and resolution limit clinical applicability. In particular, in regions of highly transient flow, coarse temporal resolution can hinder accurate capture of physiologically relevant flow variations. To overcome these issues, post-processing techniques using deep learning have shown promising results to enhance resolution post-scan using so-called super-resolution networks. However, while super-resolution has been focusing on spatial upsampling, temporal super-resolution remains largely unexplored. The aim of this study was therefore to implement and evaluate a residual network for temporal super-resolution 4D Flow MRI. To achieve this, an existing spatial network (4DFlowNet) was re-designed for temporal upsampling, adapting input dimensions, and optimizing internal layer structures. Training and testing were performed using synthetic 4D Flow MRI data originating from patient-specific in-silico models, as well as using in-vivo datasets. Overall, excellent performance was achieved with input velocities effectively denoised and temporally upsampled, with a mean absolute error (MAE) of 1.0 cm/s in an unseen in-silico setting, outperforming deterministic alternatives (linear interpolation MAE = 2.3 cm/s, sinc interpolation MAE = 2.6 cm/s). Further, the network synthesized high-resolution temporal information from unseen low-resolution in-vivo data, with strong correlation observed at peak flow frames. As such, our results highlight the potential of utilizing data-driven neural networks for temporal super-resolution 4D Flow MRI, enabling high-frame-rate flow quantification without extending acquisition times beyond clinically acceptable limits.
Glioblastoma, a highly aggressive brain tumor, poses major challenges due to its poor prognosis and high morbidity rates. Partial differential equation-based models offer promising potential to enhance therapeutic outcomes by simulating patient-specific tumor behavior for improved radiotherapy planning. However, model calibration remains a bottleneck due to the high computational demands of optimization methods like Monte Carlo sampling and evolutionary algorithms. To address this, we recently introduced an approach leveraging a neural forward solver with gradient-based optimization to significantly reduce calibration time. This approach requires a highly accurate and fully differentiable forward model. We investigate multiple architectures, including (i) an enhanced TumorSurrogate, (ii) a modified nnU-Net, and (iii) a 3D Vision Transformer (ViT). The optimized TumorSurrogate achieved the best overall results, excelling in both tumor outline matching and voxel-level prediction of tumor cell concentration. It halved the MSE relative to the baseline model and achieved the highest Dice score across all tumor cell concentration thresholds. Our study demonstrates significant enhancement in forward solver performance and outlines important future research directions.
Facial expressions play a crucial role in human communication serving as a powerful and impactful means to express a wide range of emotions. With advancements in artificial intelligence and computer vision, deep neural networks have emerged as effective tools for facial emotion recognition. In this paper, we propose EmoNeXt, a novel deep learning framework for facial expression recognition based on an adapted ConvNeXt architecture network. We integrate a Spatial Transformer Network (STN) to focus on feature-rich regions of the face and Squeeze-and-Excitation blocks to capture channel-wise dependencies. Moreover, we introduce a self-attention regularization term, encouraging the model to generate compact feature vectors. We demonstrate the superiority of our model over existing state-of-the-art deep learning models on the FER2013 dataset regarding emotion classification accuracy.
Physics-based numerical models have been the bedrock of atmospheric sciences for decades, offering robust solutions but often at the cost of significant computational resources. Deep learning (DL) models have emerged as powerful tools in meteorology, capable of analyzing complex weather and climate data by learning intricate dependencies and providing rapid predictions once trained. While these models demonstrate promising performance in weather prediction, often surpassing traditional physics-based methods, they still face critical challenges. This paper presents a comprehensive survey of recent deep learning and foundation models for weather prediction. We propose a taxonomy to classify existing models based on their training paradigms: deterministic predictive learning, probabilistic generative learning, and pre-training and fine-tuning. For each paradigm, we delve into the underlying model architectures, address major challenges, offer key insights, and propose targeted directions for future research. Furthermore, we explore real-world applications of these methods and provide a curated summary of open-source code repositories and widely used datasets, aiming to bridge research advancements with practical implementations while fostering open and trustworthy scientific practices in adopting cutting-edge artificial intelligence for weather prediction. The related sources are available at https://github.com/JimengShi/ DL-Foundation-Models-Weather.
Prognostic task is of great importance as it closely related to the survival analysis of patients, the optimization of treatment plans and the allocation of resources. The existing prognostic models have shown promising results on specific datasets, but there are limitations in two aspects. On the one hand, they merely explore certain types of modal data, such as patient histopathology WSI and gene expression analysis. On the other hand, they adopt the per-cancer-per-model paradigm, which means the trained models can only predict the prognostic effect of a single type of cancer, resulting in weak generalization ability. In this paper, a deep-learning based model, named UMPSNet, is proposed. Specifically, to comprehensively understand the condition of patients, in addition to constructing encoders for histopathology images and genomic expression profiles respectively, UMPSNet further integrates four types of important meta data (demographic information, cancer type information, treatment protocols, and diagnosis results) into text templates, and then introduces a text encoder to extract textual features. In addition, the optimal transport OT-based attention mechanism is utilized to align and fuse features of different modalities. Furthermore, a guided soft mixture of experts (GMoE) mechanism is introduced to effectively address the issue of distribution differences among multiple cancer datasets. By incorporating the multi-modality of patient data and joint training, UMPSNet outperforms all SOTA approaches, and moreover, it demonstrates the effectiveness and generalization ability of the proposed learning paradigm of a single model for multiple cancer types. The code of UMPSNet is available at https://github.com/binging512/UMPSNet.