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.
Neurosymbolic learning enables the integration of symbolic reasoning with deep learning but faces significant challenges in scaling to complex symbolic programs, large datasets, or both. We introduce Dolphin, a framework that tackles these challenges by supporting neurosymbolic programs in Python, executing complex symbolic reasoning on the CPU while vectorizing probabilistic computations and gradient propagation on the GPU. Across 13 benchmarks spanning tasks over text, image, and video data, with symbolic reasoning features like recursion and black-box functions, Dolphin converges to state-of-the-art accuracies on the more complex benchmarks while existing frameworks such as Scallop, ISED, and IndeCateR+ fail to converge within the time limit. On simpler benchmarks, Dolphin matches their performance, while achieving these results 1.71x to 62x faster than the baselines. Overall, Dolphin advances the scalability of neurosymbolic frameworks, achieving state-of-the-art efficiency and convergence on difficult benchmarks where existing frameworks struggle.
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.
In this proof-of-concept study, we conduct multivariate timeseries forecasting for the concentrations of nitrogen dioxide (NO2), ozone (O3), and (fine) particulate matter (PM10 & PM2.5) with meteorological covariates between two locations using various deep learning models, with a focus on long short-term memory (LSTM) and gated recurrent unit (GRU) architectures. In particular, we propose an integrated, hierarchical model architecture inspired by air pollution dynamics and atmospheric science that employs multi-task learning and is benchmarked by unidirectional and fully-connected models. Results demonstrate that, above all, the hierarchical GRU proves itself as a competitive and efficient method for forecasting the concentration of smog-related pollutants.
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.
Deep generative models that learn from the distribution of natural protein sequences and structures may enable the design of new proteins with valuable functions. While the majority of today's models focus on generating either sequences or structures, emerging co-generation methods promise more accurate and controllable protein design, ideally achieved by modeling both modalities simultaneously. Here we review recent advances in deep generative models for protein design, with a particular focus on sequence-structure co-generation methods. We describe the key methodological and evaluation principles underlying these methods, highlight recent advances from the literature, and discuss opportunities for continued development of sequence-structure co-generation approaches.
In contemporary economic society, credit scores are crucial for every participant. A robust credit evaluation system is essential for the profitability of core businesses such as credit cards, loans, and investments for commercial banks and the financial sector. This paper combines high-performance models like XGBoost and LightGBM, already widely used in modern banking systems, with the powerful TabNet model. We have developed a potent model capable of accurately determining credit score levels by integrating Random Forest, XGBoost, and TabNet, and through the stacking technique in ensemble modeling. This approach surpasses the limitations of single models and significantly advances the precise credit score prediction. In the following sections, we will explain the techniques we used and thoroughly validate our approach by comprehensively comparing a series of metrics such as Precision, Recall, F1, and AUC. By integrating Random Forest, XGBoost, and with the TabNet deep learning architecture, these models complement each other, demonstrating exceptionally strong overall performance.
The task of action spotting consists in both identifying actions and precisely localizing them in time with a single timestamp in long, untrimmed video streams. Automatically extracting those actions is crucial for many sports applications, including sports analytics to produce extended statistics on game actions, coaching to provide support to video analysts, or fan engagement to automatically overlay content in the broadcast when specific actions occur. However, before 2018, no large-scale datasets for action spotting in sports were publicly available, which impeded benchmarking action spotting methods. In response, our team built the largest dataset and the most comprehensive benchmarks for sports video understanding, under the umbrella of SoccerNet. Particularly, our dataset contains a subset specifically dedicated to action spotting, called SoccerNet Action Spotting, containing more than 550 complete broadcast games annotated with almost all types of actions that can occur in a football game. This dataset is tailored to develop methods for automatic spotting of actions of interest, including deep learning approaches, by providing a large amount of manually annotated actions. To engage with the scientific community, the SoccerNet initiative organizes yearly challenges, during which participants from all around the world compete to achieve state-of-the-art performances. Thanks to our dataset and challenges, more than 60 methods were developed or published over the past five years, improving on the first baselines and making action spotting a viable option for the sports industry. This paper traces the history of action spotting in sports, from the creation of the task back in 2018, to the role it plays today in research and the sports industry.
This research focuses on the development of a drone equipped with pruning tools and a stereo vision camera to accurately detect and measure the spatial positions of tree branches. YOLO is employed for branch segmentation, while two depth estimation approaches, monocular and stereo, are investigated. In comparison to SGBM, deep learning techniques produce more refined and accurate depth maps. In the absence of ground-truth data, a fine-tuning process using deep neural networks is applied to approximate optimal depth values. This methodology facilitates precise branch detection and distance measurement, addressing critical challenges in the automation of pruning operations. The results demonstrate notable advancements in both accuracy and efficiency, underscoring the potential of deep learning to drive innovation and enhance automation in the agricultural sector.
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.
Credit card is one of the most extensive methods of instalment for both online and offline mode of payment for electronic transactions in recent times. credit cards invention has provided significant ease in electronic transactions. However, it has also provided new fraud opportunities for criminals, which results in increased fraud rates. Substantial amount of money has been lost by many institutions and individuals due to fraudulent credit card transactions. Adapting improved and dynamic fraud recognition frameworks thus became essential for all credit card distributing banks to mitigate their losses. In fact, the problem of fraudulent credit card transactions implicates a number of relevant real-time challenges, namely: Concept drift, Class imbalance, and Verification latency. However, the vast majority of current systems are based on artificial intelligence (AI), Fuzzy logic, Machine Learning, Data mining, Genetic Algorithms, and so on, rely on assumptions that hardly address all the relevant challenges of fraud-detection system (FDS). This paper aims to understand & implement Deep Learning algorithms in order to obtain a high fraud coverage with very low false positive rate. Also, it aims to implement an auto-encoder as an unsupervised (semi-supervised) method of learning common patterns. Keywords: Credit card fraud, Fraud-detection system (FDS), Electronic transactions, Concept drift, Class imbalance, Verification latency, Machine Learning, Deep Learning
This research proposal discusses two challenges in the field of medical image analysis: the multi-parametric investigation on microstructural and macrostructural characteristics of the cervical spinal cord and deep learning-based medical image segmentation. First, we conduct a thorough analysis of the cervical spinal cord within a healthy population. Unlike most previous studies, which required medical professionals to perform functional examinations using metrics like the modified Japanese Orthopaedic Association (mJOA) score or the American Spinal Injury Association (ASIA) impairment scale, this research focuses solely on Magnetic Resonance (MR) images of the cervical spinal cord. Second, we employ cutting-edge deep learning-based segmentation methods to achieve highly accurate macrostructural measurements from MR images. To this end, we propose an enhanced UNet-like Transformer-based framework with attentive skip connections. This paper reports on the problem domain, proposed solutions, current status of research, and expected contributions.
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.
Recent advances in deep learning-based image reconstruction techniques have led to significant progress in phase retrieval using digital in-line holographic microscopy (DIHM). However, existing deep learning-based phase retrieval methods have technical limitations in generalization performance and three-dimensional (3D) morphology reconstruction from a single-shot hologram of biological cells. In this study, we propose a novel deep learning model, named MorpHoloNet, for single-shot reconstruction of 3D morphology by integrating physics-driven and coordinate-based neural networks. By simulating the optical diffraction of coherent light through a 3D phase shift distribution, the proposed MorpHoloNet is optimized by minimizing the loss between the simulated and input holograms on the sensor plane. Compared to existing DIHM methods that face challenges with twin image and phase retrieval problems, MorpHoloNet enables direct reconstruction of 3D complex light field and 3D morphology of a test sample from its single-shot hologram without requiring multiple phase-shifted holograms or angle scanning. The performance of the proposed MorpHoloNet is validated by reconstructing 3D morphologies and refractive index distributions from synthetic holograms of ellipsoids and experimental holograms of biological cells. The proposed deep learning model is utilized to reconstruct spatiotemporal variations in 3D translational and rotational behaviors and morphological deformations of biological cells from consecutive single-shot holograms captured using DIHM. MorpHoloNet would pave the way for advancing label-free, real-time 3D imaging and dynamic analysis of biological cells under various cellular microenvironments in biomedical and engineering fields.
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.
Training deep learning models is a repetitive and resource-intensive process. Data scientists often train several models before landing on set of parameters (e.g., hyper-parameter tuning), model architecture (e.g., neural architecture search), among other things that yields the highest accuracy. The computational efficiency of these training tasks depends highly on how well we can supply the training process with training data. The repetitive nature of these tasks results in the same data processing pipelines running over and over exacerbating the need for and costs of computational resources. In this paper, we present Tensorsocket to reduce the computational needs of deep learning training by enabling simultaneous training processes to share the same data loader. Tensorsocket mitigates CPU-side bottlenecks in cases where the collocated training workloads have high throughput on GPU, but are held back by lower data-loading throughput on CPU. Tensorsocket achieves this by reducing redundant computations across collocated training processes and leveraging modern GPU-GPU interconnects. We demonstrate the hardware- and pipeline-agnostic nature of Tensorsocket and evaluate it using a variety of training scenarios. Our evaluation shows that Tensorsocket enables scenarios that are infeasible without data sharing, increases training throughput by up to $100\%$, and when utilizing cloud instances, Tensorsocket achieves cost savings of $50\%$ by reducing the hardware resource needs on the CPU side. Furthermore, Tensorsocket outperforms the state-of-the-art solutions for shared data loading such as CoorDL and Joader. It is easier to use, maintain, and deploy, and either achieves higher or matches the throughput of other solutions while requiring less CPU resources.
Scientific machine learning (SciML) is an interdisciplinary research field that integrates machine learning, particularly deep learning, with physics theory to understand and predict complex natural phenomena. By incorporating physical knowledge, SciML reduces the dependency on observational data, which is often limited in the natural sciences. In this article, the fundamental concepts of SciML, its applications in seismology, and prospects are described. Specifically, two popular methods are mainly discussed: physics-informed neural networks (PINNs) and neural operators (NOs). PINNs can address both forward and inverse problems by incorporating governing laws into the loss functions. The use of PINNs is expanding into areas such as simultaneous solutions of differential equations, inference in underdetermined systems, and regularization based on physics. These research directions would broaden the scope of deep learning in natural sciences. NOs are models designed for operator learning, which deals with relationships between infinite-dimensional spaces. NOs show promise in modeling the time evolution of complex systems based on observational or simulation data. Since large amounts of data are often required, combining NOs with physics-informed learning holds significant potential. Finally, SciML is considered from a broader perspective beyond deep learning: statistical (or mathematical) frameworks that integrate observational data with physical principles to model natural phenomena. In seismology, mathematically rigorous Bayesian statistics has been developed over the past decades, whereas more flexible and scalable deep learning has only emerged recently. Both approaches can be considered as part of SciML in a broad sense. Theoretical and practical insights in both directions would advance SciML methodologies and thereby deepen our understanding of earthquake phenomena.