Foundation models for computational pathology have shown great promise for specimen-level tasks and are increasingly accessible to researchers. However, specimen-level models built on these foundation models remain largely unavailable, hindering their broader utility and impact. To address this gap, we developed SpinPath, a toolkit designed to democratize specimen-level deep learning by providing a zoo of pretrained specimen-level models, a Python-based inference engine, and a JavaScript-based inference platform. We demonstrate the utility of SpinPath in metastasis detection tasks across nine foundation models. SpinPath may foster reproducibility, simplify experimentation, and accelerate the adoption of specimen-level deep learning in computational pathology research.
Objective: X-ray computed tomography employing sparse projection views has emerged as a contemporary technique to mitigate radiation dose. However, due to the inadequate number of projection views, an analytic reconstruction method utilizing filtered backprojection results in severe streaking artifacts. Recently, deep learning strategies employing image-domain networks have demonstrated remarkable performance in eliminating the streaking artifact caused by analytic reconstruction methods with sparse projection views. Nevertheless, it is difficult to clarify the theoretical justification for applying deep learning to sparse view CT reconstruction, and it has been understood as restoration by removing image artifacts, not reconstruction. Approach: By leveraging the theory of deep convolutional framelets and the hierarchical decomposition of measurement, this research reveals the constraints of conventional image- and projection-domain deep learning methodologies, subsequently, the research proposes a novel dual-domain deep learning framework utilizing hierarchical decomposed measurements. Specifically, the research elucidates how the performance of the projection-domain network can be enhanced through a low-rank property of deep convolutional framelets and a bowtie support of hierarchical decomposed measurement in the Fourier domain. Main Results: This study demonstrated performance improvement of the proposed framework based on the low-rank property, resulting in superior reconstruction performance compared to conventional analytic and deep learning methods. Significance: By providing a theoretically justified deep learning approach for sparse-view CT reconstruction, this study not only offers a superior alternative to existing methods but also opens new avenues for research in medical imaging.
Accurate load forecasting is crucial for predictive control in many energy domain applications, with significant economic and ecological implications. To address these implications, this study provides an extensive benchmark of state-of-the-art deep learning models for short-term load forecasting in energy communities. Namely, LSTM, xLSTM, and Transformers are compared with benchmarks such as KNNs, synthetic load models, and persistence forecasting models. This comparison considers different scales of aggregation (e.g., number of household loads) and varying training data availability (e.g., training data time spans). Further, the impact of transfer learning from synthetic (standard) load profiles and the deep learning model size (i.e., parameter count) is investigated in terms of forecasting error. Implementations are publicly available and other researchers are encouraged to benchmark models using this framework. Additionally, a comprehensive case study, comprising an energy community of 50 households and a battery storage demonstrates the beneficial financial implications of accurate predictions. Key findings of this research include: (1) Simple persistence benchmarks outperform deep learning models for short-term load forecasting when the available training data is limited to six months or less; (2) Pretraining with publicly available synthetic load profiles improves the normalized Mean Absolute Error (nMAE) by an average of 1.28%pt during the first nine months of training data; (3) Increased aggregation significantly enhances the performance of deep learning models relative to persistence benchmarks; (4) Improved load forecasting, with an nMAE reduction of 1.1%pt, translates to an economic benefit of approximately 600EUR per year in an energy community comprising 50 households.
The increasing reliance on Global Navigation Satellite Systems (GNSS), particularly the Global Positioning System (GPS), underscores the urgent need to safeguard these technologies against malicious threats such as spoofing and jamming. As the backbone for positioning, navigation, and timing (PNT) across various applications including transportation, telecommunications, and emergency services GNSS is vulnerable to deliberate interference that poses significant risks. Spoofing attacks, which involve transmitting counterfeit GNSS signals to mislead receivers into calculating incorrect positions, can result in serious consequences, from navigational errors in civilian aviation to security breaches in military operations. Furthermore, the lack of inherent security measures within GNSS systems makes them attractive targets for adversaries. While GNSS/GPS jamming and spoofing systems consist of numerous components, the ability to distinguish authentic signals from malicious ones is essential for maintaining system integrity. Recent advancements in machine learning and deep learning provide promising avenues for enhancing detection and mitigation strategies against these threats. This paper addresses both spoofing and jamming by tackling real-world challenges through machine learning, deep learning, and computer vision techniques. Through extensive experiments on two real-world datasets related to spoofing and jamming detection using advanced algorithms, we achieved state of the art results. In the GNSS/GPS jamming detection task, we attained approximately 99% accuracy, improving performance by around 5% compared to previous studies. Additionally, we addressed a challenging tasks related to spoofing detection, yielding results that underscore the potential of machine learning and deep learning in this domain.
We propose the Hyperbolic Tangent Exponential Linear Unit (TeLU), a neural network hidden activation function defined as TeLU(x)=xtanh(exp(x)). TeLU's design is grounded in the core principles of key activation functions, achieving strong convergence by closely approximating the identity function in its active region while effectively mitigating the vanishing gradient problem in its saturating region. Its simple formulation enhances computational efficiency, leading to improvements in scalability and convergence speed. Unlike many modern activation functions, TeLU seamlessly combines the simplicity and effectiveness of ReLU with the smoothness and analytic properties essential for learning stability in deep neural networks. TeLU's ability to mimic the behavior and optimal hyperparameter settings of ReLU, while introducing the benefits of smoothness and curvature, makes it an ideal drop-in replacement. Its analytic nature positions TeLU as a powerful universal approximator, enhancing both robustness and generalization across a multitude of experiments. We rigorously validate these claims through theoretical analysis and experimental validation, demonstrating TeLU's performance across challenging benchmarks; including ResNet18 on ImageNet, Dynamic-Pooling Transformers on Text8, and Recurrent Neural Networks (RNNs) on the Penn TreeBank dataset. These results highlight TeLU's potential to set a new standard in activation functions, driving more efficient and stable learning in deep neural networks, thereby accelerating scientific discoveries across various fields.
In this study, we focus on automated approaches to detect depression from clinical interviews using multi-modal machine learning (ML). Our approach differentiates from other successful ML methods such as context-aware analysis through feature engineering and end-to-end deep neural networks for depression detection utilizing the Distress Analysis Interview Corpus. We propose a novel method that incorporates: (1) pre-trained Transformer combined with data augmentation based on topic modelling for textual data; and (2) deep 1D convolutional neural network (CNN) for acoustic feature modeling. The simulation results demonstrate the effectiveness of the proposed method for training multi-modal deep learning models. Our deep 1D CNN and Transformer models achieved state-of-the-art performance for audio and text modalities respectively. Combining them in a multi-modal framework also outperforms state-of-the-art for the combined setting. Code available at https://github.com/genandlam/multi-modal-depression-detection
Test Input Generators (TIGs) are crucial to assess the ability of Deep Learning (DL) image classifiers to provide correct predictions for inputs beyond their training and test sets. Recent advancements in Generative AI (GenAI) models have made them a powerful tool for creating and manipulating synthetic images, although these advancements also imply increased complexity and resource demands for training. In this work, we benchmark and combine different GenAI models with TIGs, assessing their effectiveness, efficiency, and quality of the generated test images, in terms of domain validity and label preservation. We conduct an empirical study involving three different GenAI architectures (VAEs, GANs, Diffusion Models), five classification tasks of increasing complexity, and 364 human evaluations. Our results show that simpler architectures, such as VAEs, are sufficient for less complex datasets like MNIST. However, when dealing with feature-rich datasets, such as ImageNet, more sophisticated architectures like Diffusion Models achieve superior performance by generating a higher number of valid, misclassification-inducing inputs.
Detecting and tracking code clones can ease various software development and maintenance tasks when changes in a code fragment should be propagated over all its copies. Several deep learning-based clone detection models have appeared in the literature for detecting syntactic and semantic clones, widely evaluated with the BigCloneBench dataset. However, class imbalance and the small number of semantic clones make BigCloneBench less ideal for interpreting model performance. Researchers also use other datasets such as GoogleCodeJam, OJClone, and SemanticCloneBench to understand model generalizability. To overcome the limitations of existing datasets, the GPT-assisted semantic and cross-language clone dataset GPTCloneBench has been released. However, how these models compare across datasets remains unclear. In this paper, we propose a multi-step evaluation approach for five state-of-the-art clone detection models leveraging existing benchmark datasets, including GPTCloneBench, and using mutation operators to study model ability. Specifically, we examine three highly-performing single-language models (ASTNN, GMN, CodeBERT) on BigCloneBench, SemanticCloneBench, and GPTCloneBench, testing their robustness with mutation operations. Additionally, we compare them against cross-language models (C4, CLCDSA) known for detecting semantic clones. While single-language models show high F1 scores for BigCloneBench, their performance on SemanticCloneBench varies (up to 20%). Interestingly, the cross-language model (C4) shows superior performance (around 7%) on SemanticCloneBench over other models and performs similarly on BigCloneBench and GPTCloneBench. On mutation-based datasets, C4 has more robust performance (less than 1% difference) compared to single-language models, which show high variability.
Although Answer Set Programming (ASP) allows constraining neural-symbolic (NeSy) systems, its employment is hindered by the prohibitive costs of computing stable models and the CPU-bound nature of state-of-the-art solvers. To this end, we propose Answer Set Networks (ASN), a NeSy solver. Based on Graph Neural Networks (GNN), ASNs are a scalable approach to ASP-based Deep Probabilistic Logic Programming (DPPL). Specifically, we show how to translate ASPs into ASNs and demonstrate how ASNs can efficiently solve the encoded problem by leveraging GPU's batching and parallelization capabilities. Our experimental evaluations demonstrate that ASNs outperform state-of-the-art CPU-bound NeSy systems on multiple tasks. Simultaneously, we make the following two contributions based on the strengths of ASNs. Namely, we are the first to show the finetuning of Large Language Models (LLM) with DPPLs, employing ASNs to guide the training with logic. Further, we show the "constitutional navigation" of drones, i.e., encoding public aviation laws in an ASN for routing Unmanned Aerial Vehicles in uncertain environments.
Uncertainty quantification (UQ) methods play an important role in reducing errors in weather forecasting. Conventional approaches in UQ for weather forecasting rely on generating an ensemble of forecasts from physics-based simulations to estimate the uncertainty. However, it is computationally expensive to generate many forecasts to predict real-time extreme weather events. Evidential Deep Learning (EDL) is an uncertainty-aware deep learning approach designed to provide confidence about its predictions using only one forecast. It treats learning as an evidence acquisition process where more evidence is interpreted as increased predictive confidence. We apply EDL to storm forecasting using real-world weather datasets and compare its performance with traditional methods. Our findings indicate that EDL not only reduces computational overhead but also enhances predictive uncertainty. This method opens up novel opportunities in research areas such as climate risk assessment, where quantifying the uncertainty about future climate is crucial.
The discovery of novel superconducting materials is a longstanding challenge in materials science, with a wealth of potential for applications in energy, transportation, and computing. Recent advances in artificial intelligence (AI) have enabled expediting the search for new materials by efficiently utilizing vast materials databases. In this study, we developed an approach based on deep learning (DL) to predict new superconducting materials. We have synthesized a compound derived from our DL network and confirmed its superconducting properties in agreement with our prediction. Our approach is also compared to previous work based on random forests (RFs). In particular, RFs require knowledge of the chem-ical properties of the compound, while our neural net inputs depend solely on the chemical composition. With the help of hints from our network, we discover a new ternary compound $\textrm{Mo}_{20}\textrm{Re}_{6}\textrm{Si}_{4}$, which becomes superconducting below 5.4 K. We further discuss the existing limitations and challenges associated with using AI to predict and, along with potential future research directions.
Colloidal synthesis of nanocrystals usually includes complex chemical reactions and multi-step crystallization processes. Despite the great success in the past 30 years, it remains challenging to clarify the correlations between synthetic parameters of chemical reaction and physical properties of nanocrystals. Here, we developed a deep learning-based nanocrystal synthesis model that correlates synthetic parameters with the final size and shape of target nanocrystals, using a dataset of 3500 recipes covering 348 distinct nanocrystal compositions. The size and shape labels were obtained from transmission electron microscope images using a segmentation model trained with a semi-supervised algorithm on a dataset comprising 1.2 million nanocrystals. By applying the reaction intermediate-based data augmentation method and elaborated descriptors, the synthesis model was able to predict nanocrystal's size with a mean absolute error of 1.39 nm, while reaching an 89% average accuracy for shape classification. The synthesis model shows knowledge transfer capabilities across different nanocrystals with inputs of new recipes. With that, the influence of chemicals on the final size of nanocrystals was further evaluated, revealing the importance order of nanocrystal composition, precursor or ligand, and solvent. Overall, the deep learning-based nanocrystal synthesis model offers a powerful tool to expedite the development of high-quality nanocrystals.
Accurate anatomical labeling and analysis of the pulmonary structure and its surrounding anatomy from thoracic CT is getting increasingly important for understanding the etilogy of abnormalities or supporting targetted therapy and early interventions. Whilst lung and airway cell atlases have been attempted, there is a lack of fine-grained morphological atlases that are clinically deployable. In this work, we introduce AirMorph, a robust, end-to-end deep learning pipeline enabling fully automatic and comprehensive airway anatomical labeling at lobar, segmental, and subsegmental resolutions that can be used to create digital atlases of the lung. Evaluated across large-scale multi-center datasets comprising diverse pulmonary conditions, the AirMorph consistently outperformed existing segmentation and labeling methods in terms of accuracy, topological consistency, and completeness. To simplify clinical interpretation, we further introduce a compact anatomical signature quantifying critical morphological airway features, including stenosis, ectasia, tortuosity, divergence, length, and complexity. When applied to various pulmonary diseases such as pulmonary fibrosis, emphysema, atelectasis, consolidation, and reticular opacities, it demonstrates strong discriminative power, revealing disease-specific morphological patterns with high interpretability and explainability. Additionally, AirMorph supports efficient automated branching pattern analysis, potentially enhancing bronchoscopic navigation planning and procedural safety, offering a valuable clinical tool for improved diagnosis, targeted treatment, and personalized patient care.
Convolutional Neural Networks (CNNs) have been the standard for image classification tasks for a long time, but more recently attention-based mechanisms have gained traction. This project aims to compare traditional CNNs with attention-augmented CNNs across an image classification task. By evaluating and comparing their performance, accuracy and computational efficiency, the project will highlight benefits and trade-off of the localized feature extraction of traditional CNNs and the global context capture in attention-augmented CNNs. By doing this, we can reveal further insights into their respective strengths and weaknesses, guide the selection of models based on specific application needs and ultimately, enhance understanding of these architectures in the deep learning community. This was our final project for CS7643 Deep Learning course at Georgia Tech.
Traditional methods employed in matrix volatility forecasting often overlook the inherent Riemannian manifold structure of symmetric positive definite matrices, treating them as elements of Euclidean space, which can lead to suboptimal predictive performance. Moreover, they often struggle to handle high-dimensional matrices. In this paper, we propose a novel approach for forecasting realized covariance matrices of asset returns using a Riemannian-geometry-aware deep learning framework. In this way, we account for the geometric properties of the covariance matrices, including possible non-linear dynamics and efficient handling of high-dimensionality. Moreover, building upon a Fr\'echet sample mean of realized covariance matrices, we are able to extend the HAR model to the matrix-variate. We demonstrate the efficacy of our approach using daily realized covariance matrices for the 50 most capitalized companies in the S&P 500 index, showing that our method outperforms traditional approaches in terms of predictive accuracy.
Ptychographic imaging confronts inherent challenges in applying deep learning for phase retrieval from diffraction patterns. Conventional neural architectures, both convolutional neural networks and Transformer-based methods, are optimized for natural images with Euclidean spatial neighborhood-based inductive biases that exhibit geometric mismatch with the concentric coherent patterns characteristic of diffraction data in reciprocal space. In this paper, we present PPN, a physics-inspired deep learning network with Polar Coordinate Attention (PoCA) for ptychographic imaging, that aligns neural inductive biases with diffraction physics through a dual-branch architecture separating local feature extraction from non-local coherence modeling. It consists of a PoCA mechanism that replaces Euclidean spatial priors with physically consistent radial-angular correlations. PPN outperforms existing end-to-end models, with spectral and spatial analysis confirming its greater preservation of high-frequency details. Notably, PPN maintains robust performance compared to iterative methods even at low overlap ratios, making it well suited for high-throughput imaging in real-world acquisition scenarios for samples with consistent structural characteristics.
GraphNeuralNetworks.jl is an open-source framework for deep learning on graphs, written in the Julia programming language. It supports multiple GPU backends, generic sparse or dense graph representations, and offers convenient interfaces for manipulating standard, heterogeneous, and temporal graphs with attributes at the node, edge, and graph levels. The framework allows users to define custom graph convolutional layers using gather/scatter message-passing primitives or optimized fused operations. It also includes several popular layers, enabling efficient experimentation with complex deep architectures. The package is available on GitHub: \url{https://github.com/JuliaGraphs/GraphNeuralNetworks.jl}.
Recent advancements in deep learning for tabular data have shown promise, but challenges remain in achieving interpretable and lightweight models. This paper introduces Table2Image, a novel framework that transforms tabular data into realistic and diverse image representations, enabling deep learning methods to achieve competitive classification performance. To address multicollinearity in tabular data, we propose a variance inflation factor (VIF) initialization, which enhances model stability and robustness by incorporating statistical feature relationships. Additionally, we present an interpretability framework that integrates insights from both the original tabular data and its transformed image representations, by leveraging Shapley additive explanations (SHAP) and methods to minimize distributional discrepancies. Experiments on benchmark datasets demonstrate the efficacy of our approach, achieving superior accuracy, area under the curve, and interpretability compared to recent leading deep learning models. Our lightweight method provides a scalable and reliable solution for tabular data classification.
Bankart lesions, or anterior-inferior glenoid labral tears, are diagnostically challenging on standard MRIs due to their subtle imaging features-often necessitating invasive MRI arthrograms (MRAs). This study develops deep learning (DL) models to detect Bankart lesions on both standard MRIs and MRAs, aiming to improve diagnostic accuracy and reduce reliance on MRAs. We curated a dataset of 586 shoulder MRIs (335 standard, 251 MRAs) from 558 patients who underwent arthroscopy. Ground truth labels were derived from intraoperative findings, the gold standard for Bankart lesion diagnosis. Separate DL models for MRAs and standard MRIs were trained using the Swin Transformer architecture, pre-trained on a public knee MRI dataset. Predictions from sagittal, axial, and coronal views were ensembled to optimize performance. The models were evaluated on a 20% hold-out test set (117 MRIs: 46 MRAs, 71 standard MRIs). Bankart lesions were identified in 31.9% of MRAs and 8.6% of standard MRIs. The models achieved AUCs of 0.87 (86% accuracy, 83% sensitivity, 86% specificity) and 0.90 (85% accuracy, 82% sensitivity, 86% specificity) on standard MRIs and MRAs, respectively. These results match or surpass radiologist performance on our dataset and reported literature metrics. Notably, our model's performance on non-invasive standard MRIs matched or surpassed the radiologists interpreting MRAs. This study demonstrates the feasibility of using DL to address the diagnostic challenges posed by subtle pathologies like Bankart lesions. Our models demonstrate potential to improve diagnostic confidence, reduce reliance on invasive imaging, and enhance accessibility to care.
Recently, there has been an increasing interest in performing post-hoc uncertainty estimation about the predictions of pre-trained deep neural networks (DNNs). Given a pre-trained DNN via back-propagation, these methods enhance the original network by adding output confidence measures, such as error bars, without compromising its initial accuracy. In this context, we introduce a novel family of sparse variational Gaussian processes (GPs), where the posterior mean is fixed to any continuous function when using a universal kernel. Specifically, we fix the mean of this GP to the output of the pre-trained DNN, allowing our approach to effectively fit the GP's predictive variances to estimate the DNN prediction uncertainty. Our approach leverages variational inference (VI) for efficient stochastic optimization, with training costs that remain independent of the number of training points, scaling efficiently to large datasets such as ImageNet. The proposed method, called fixed mean GP (FMGP), is architecture-agnostic, relying solely on the pre-trained model's outputs to adjust the predictive variances. Experimental results demonstrate that FMGP improves both uncertainty estimation and computational efficiency when compared to state-of-the-art methods.