Changepoint detection, a technique for identifying significant shifts within data sequences, is crucial in various fields such as finance, genomics, medicine, etc. Dynamic programming changepoint detection algorithms are employed to identify the locations of changepoints within a sequence, which rely on a penalty parameter to regulate the number of changepoints. To estimate this penalty parameter, previous work uses simple models such as linear or tree-based models. This study introduces a novel deep learning method for predicting penalty parameters, leading to demonstrably improved changepoint detection accuracy on large benchmark supervised labeled datasets compared to previous methods.
Automatic estimation of cardiac ultrasound image quality can be beneficial for guiding operators and ensuring the accuracy of clinical measurements. Previous work often fails to distinguish the view correctness of the echocardiogram from the image quality. Additionally, previous studies only provide a global image quality value, which limits their practical utility. In this work, we developed and compared three methods to estimate image quality: 1) classic pixel-based metrics like the generalized contrast-to-noise ratio (gCNR) on myocardial segments as region of interest and left ventricle lumen as background, obtained using a U-Net segmentation 2) local image coherence derived from a U-Net model that predicts coherence from B-Mode images 3) a deep convolutional network that predicts the quality of each region directly in an end-to-end fashion. We evaluate each method against manual regional image quality annotations by three experienced cardiologists. The results indicate poor performance of the gCNR metric, with Spearman correlation to the annotations of rho = 0.24. The end-to-end learning model obtains the best result, rho = 0.69, comparable to the inter-observer correlation, rho = 0.63. Finally, the coherence-based method, with rho = 0.58, outperformed the classical metrics and is more generic than the end-to-end approach. The image quality prediction tool is available as an open source Python library at https://github.com/GillesVanDeVyver/arqee.
Modern medical image registration approaches predict deformations using deep networks. These approaches achieve state-of-the-art (SOTA) registration accuracy and are generally fast. However, deep learning (DL) approaches are, in contrast to conventional non-deep-learning-based approaches, anatomy-specific. Recently, a universal deep registration approach, uniGradICON, has been proposed. However, uniGradICON focuses on monomodal image registration. In this work, we therefore develop multiGradICON as a first step towards universal *multimodal* medical image registration. Specifically, we show that 1) we can train a DL registration model that is suitable for monomodal *and* multimodal registration; 2) loss function randomization can increase multimodal registration accuracy; and 3) training a model with multimodal data helps multimodal generalization. Our code and the multiGradICON model are available at https://github.com/uncbiag/uniGradICON.
We present RelBench, a public benchmark for solving predictive tasks over relational databases with graph neural networks. RelBench provides databases and tasks spanning diverse domains and scales, and is intended to be a foundational infrastructure for future research. We use RelBench to conduct the first comprehensive study of Relational Deep Learning (RDL) (Fey et al., 2024), which combines graph neural network predictive models with (deep) tabular models that extract initial entity-level representations from raw tables. End-to-end learned RDL models fully exploit the predictive signal encoded in primary-foreign key links, marking a significant shift away from the dominant paradigm of manual feature engineering combined with tabular models. To thoroughly evaluate RDL against this prior gold-standard, we conduct an in-depth user study where an experienced data scientist manually engineers features for each task. In this study, RDL learns better models whilst reducing human work needed by more than an order of magnitude. This demonstrates the power of deep learning for solving predictive tasks over relational databases, opening up many new research opportunities enabled by RelBench.
Medical image analysis using deep learning frameworks has advanced healthcare by automating complex tasks, but many existing frameworks lack flexibility, modularity, and user-friendliness. To address these challenges, we introduce Yucca, an open-source AI framework available at https://github.com/Sllambias/yucca, designed specifically for medical imaging applications and built on PyTorch and PyTorch Lightning. Yucca features a three-tiered architecture: Functional, Modules, and Pipeline, providing a comprehensive and customizable solution. Evaluated across diverse tasks such as cerebral microbleeds detection, white matter hyperintensity segmentation, and hippocampus segmentation, Yucca achieves state-of-the-art results, demonstrating its robustness and versatility. Yucca offers a powerful, flexible, and user-friendly platform for medical image analysis, inviting community contributions to advance its capabilities and impact.
Tipping points occur in many real-world systems, at which the system shifts suddenly from one state to another. The ability to predict the occurrence of tipping points from time series data remains an outstanding challenge and a major interest in a broad range of research fields. Particularly, the widely used methods based on bifurcation theory are neither reliable in prediction accuracy nor applicable for irregularly-sampled time series which are commonly observed from real-world systems. Here we address this challenge by developing a deep learning algorithm for predicting the occurrence of tipping points in untrained systems, by exploiting information about normal forms. Our algorithm not only outperforms traditional methods for regularly-sampled model time series but also achieves accurate predictions for irregularly-sampled model time series and empirical time series. Our ability to predict tipping points for complex systems paves the way for mitigation risks, prevention of catastrophic failures, and restoration of degraded systems, with broad applications in social science, engineering, and biology.
Ellipsometry is used to indirectly measure the optical properties and thickness of thin films. However, solving the inverse problem of ellipsometry is time-consuming since it involves human expertise to apply the data fitting techniques. Many studies use traditional machine learning-based methods to model the complex mathematical fitting process. In our work, we approach this problem from a deep learning perspective. First, we introduce a large-scale benchmark dataset to facilitate deep learning methods. The proposed dataset encompasses 98 types of thin film materials and 4 types of substrate materials, including metals, alloys, compounds, and polymers, among others. Additionally, we propose a deep learning framework that leverages residual connections and self-attention mechanisms to learn the massive data points. We also introduce a reconstruction loss to address the common challenge of multiple solutions in thin film thickness prediction. Compared to traditional machine learning methods, our framework achieves state-of-the-art (SOTA) performance on our proposed dataset. The dataset and code will be available upon acceptance.
Epitope identification is vital for antibody design yet challenging due to the inherent variability in antibodies. While many deep learning methods have been developed for general protein binding site prediction tasks, whether they work for epitope prediction remains an understudied research question. The challenge is also heightened by the lack of a consistent evaluation pipeline with sufficient dataset size and epitope diversity. We introduce a filtered antibody-antigen complex structure dataset, AsEP (Antibody-specific Epitope Prediction). AsEP is the largest of its kind and provides clustered epitope groups, allowing the community to develop and test novel epitope prediction methods and evaluate their generalisability. AsEP comes with an easy-to-use interface in Python and pre-built graph representations of each antibody-antigen complex while also supporting customizable embedding methods. Using this new dataset, we benchmark several representative general protein-binding site prediction methods and find that their performances fall short of expectations for epitope prediction. To address this, we propose a novel method, WALLE, which leverages both unstructured modeling from protein language models and structural modeling from graph neural networks. WALLE demonstrate up to 3-10X performance improvement over the baseline methods. Our empirical findings suggest that epitope prediction benefits from combining sequential features provided by language models with geometrical information from graph representations. This provides a guideline for future epitope prediction method design. In addition, we reformulate the task as bipartite link prediction, allowing convenient model performance attribution and interpretability. We open source our data and code at https://github.com/biochunan/AsEP-dataset.
Recent advancements in computer vision have significantly improved image analysis tasks. Yet, deep learning models often struggle when applied to domains outside their training distribution, such as in geosciences, where domain-specific data can be scarce. This study investigates the classification, segmentation, and interpretability of CT-scan images of rock samples, focusing on the application of modern computer vision techniques to geoscientific tasks. We compare a range of segmentation methods to assess their efficacy, efficiency, and adaptability in geological image analysis. The methods evaluated include Otsu thresholding, clustering techniques (K-means, fuzzy C-means), a supervised machine learning approach (Random Forest), and deep learning models (UNet, ResNet152, and DINOv2), using ten binary sandstone datasets and three multi-class calcite datasets. DINOv2 was selected for its promising results in feature extraction and its potential applicability in geoscientific tasks, prompting further assessment of its interpretability and effectiveness in processing CT-scanned rock data. For classification, a non-fine-tuned DINOv2 demonstrates strong performance in classifying rock images, even when the CT-scans are outside its original training set. In segmentation tasks, thresholding and clustering techniques, though computationally efficient, produce subpar results despite preprocessing efforts. In contrast, supervised methods achieve better performance. While deep learning methods demand greater computational resources, they require minimal intervention and offer superior generalization. A LoRA fine-tuned DINOv2, in particular, excels in out-of-distribution segmentation and outperforms other methods in multi-class tasks, even with limited data. Notably, the segmentation masks generated by DINOv2 often appear more accurate than the original targets, based on visual inspection.
Deep learning kernels exhibit predictable memory accesses and compute patterns, making GPUs' parallel architecture well-suited for their execution. Software and runtime systems for GPUs are optimized to better utilize the stream multiprocessors, on-chip cache, and off-chip high-bandwidth memory. As deep learning models and GPUs evolve, access to newer GPUs is often limited, raising questions about the performance of new model architectures on existing GPUs, existing models on new GPUs, and new model architectures on new GPUs. To address these questions, we introduce NeuSight, a framework to predict the performance of various deep learning models, for both training and inference, on unseen GPUs without requiring actual execution. The framework leverages both GPU hardware behavior and software library optimizations to estimate end-to-end performance. Previous work uses regression models that capture linear trends or multilayer perceptrons to predict the overall latency of deep learning kernels on GPUs. These approaches suffer from higher error percentages when forecasting performance on unseen models and new GPUs. Instead, NeuSight decomposes the prediction problem into smaller problems, bounding the prediction through fundamental performance laws. NeuSight decomposes a single deep learning kernel prediction into smaller working sets called tiles, which are executed independently on the GPU. Tile-granularity predictions are determined using a machine learning approach and aggregated to estimate end-to-end latency. NeuSight outperforms prior work across various deep learning workloads and the latest GPUs. It reduces the percentage error from 121.4% and 30.8% to 2.3% in predicting the latency of GPT3 model for training and inference on H100, compared to state-of-the-art prior work, where both GPT3 and H100 were not used to train the framework.
Despite the prevalence and significance of tabular data across numerous industries and fields, it has been relatively underexplored in the realm of deep learning. Even today, neural networks are often overshadowed by techniques such as gradient boosted decision trees (GBDT). However, recent models are beginning to close this gap, outperforming GBDT in various setups and garnering increased attention in the field. Inspired by this development, we introduce a novel stochastic deep learning model specifically designed for tabular data. The foundation of this model is a Transformer-based architecture, carefully adapted to cater to the unique properties of tabular data through strategic architectural modifications and leveraging two forms of stochastic competition. First, we employ stochastic "Local Winner Takes All" units to promote generalization capacity through stochasticity and sparsity. Second, we introduce a novel embedding layer that selects among alternative linear embedding layers through a mechanism of stochastic competition. The effectiveness of the model is validated on a variety of widely-used, publicly available datasets. We demonstrate that, through the incorporation of these elements, our model yields high performance and marks a significant advancement in the application of deep learning to tabular data.
The Moving Sofa Problem, formally proposed by Leo Moser in 1966, seeks to determine the largest area of a two-dimensional shape that can navigate through an $L$-shaped corridor with unit width. The current best lower bound is about 2.2195, achieved by Joseph Gerver in 1992, though its global optimality remains unproven. In this paper, we investigate this problem by leveraging the universal approximation strength and computational efficiency of neural networks. We report two approaches, both supporting Gerver's conjecture that his shape is the unique global maximum. Our first approach is continuous function learning. We drop Gerver's assumptions that i) the rotation of the corridor is monotonic and symmetric and, ii) the trajectory of its corner as a function of rotation is continuously differentiable. We parameterize rotation and trajectory by independent piecewise linear neural networks (with input being some pseudo time), allowing for rich movements such as backward rotation and pure translation. We then compute the sofa area as a differentiable function of rotation and trajectory using our "waterfall" algorithm. Our final loss function includes differential terms and initial conditions, leveraging the principles of physics-informed machine learning. Under such settings, extensive training starting from diverse function initialization and hyperparameters is conducted, unexceptionally showing rapid convergence to Gerver's solution. Our second approach is via discrete optimization of the Kallus-Romik upper bound, which converges to the maximum sofa area from above as the number of rotation angles increases. We uplift this number to 10000 to reveal its asymptotic behavior. It turns out that the upper bound yielded by our models does converge to Gerver's area (within an error of 0.01% when the number of angles reaches 2100). We also improve their five-angle upper bound from 2.37 to 2.3337.
Generating synthetic samples from the convex space of the minority class is a popular oversampling approach for imbalanced classification problems. Recently, deep-learning approaches have been successfully applied to modeling the convex space of minority samples. Beyond oversampling, learning the convex space of neighborhoods in training data has not been used to generate entire tabular datasets. In this paper, we introduce a deep learning architecture (NextConvGeN) with a generator and discriminator component that can generate synthetic samples by learning to model the convex space of tabular data. The generator takes data neighborhoods as input and creates synthetic samples within the convex space of that neighborhood. Thereafter, the discriminator tries to classify these synthetic samples against a randomly sampled batch of data from the rest of the data space. We compared our proposed model with five state-of-the-art tabular generative models across ten publicly available datasets from the biomedical domain. Our analysis reveals that synthetic samples generated by NextConvGeN can better preserve classification and clustering performance across real and synthetic data than other synthetic data generation models. Synthetic data generation by deep learning of the convex space produces high scores for popular utility measures. We further compared how diverse synthetic data generation strategies perform in the privacy-utility spectrum and produced critical arguments on the necessity of high utility models. Our research on deep learning of the convex space of tabular data opens up opportunities in clinical research, machine learning model development, decision support systems, and clinical data sharing.
This paper introduces a novel approach that combines unsupervised active contour models with deep learning for robust and adaptive image segmentation. Indeed, traditional active contours, provide a flexible framework for contour evolution and learning offers the capacity to learn intricate features and patterns directly from raw data. Our proposed methodology leverages the strengths of both paradigms, presenting a framework for both unsupervised and one-shot approaches for image segmentation. It is capable of capturing complex object boundaries without the need for extensive labeled training data. This is particularly required in histology, a field facing a significant shortage of annotations due to the challenging and time-consuming nature of the annotation process. We illustrate and compare our results to state of the art methods on a histology dataset and show significant improvements.
Breast cancer remains a leading cause of cancer-related deaths among women worldwide, with mammography screening as the most effective method for the early detection. Ensuring proper positioning in mammography is critical, as poor positioning can lead to diagnostic errors, increased patient stress, and higher costs due to recalls. Despite advancements in deep learning (DL) for breast cancer diagnostics, limited focus has been given to evaluating mammography positioning. This paper introduces a novel DL methodology to quantitatively assess mammogram positioning quality, specifically in mediolateral oblique (MLO) views using attention and coordinate convolution modules. Our method identifies key anatomical landmarks, such as the nipple and pectoralis muscle, and automatically draws a posterior nipple line (PNL), offering robust and inherently explainable alternative to well-known classification and regression-based approaches. We compare the performance of proposed methodology with various regression and classification-based models. The CoordAtt UNet model achieved the highest accuracy of 88.63% $\pm$ 2.84 and specificity of 90.25% $\pm$ 4.04, along with a noteworthy sensitivity of 86.04% $\pm$ 3.41. In landmark detection, the same model also recorded the lowest mean errors in key anatomical points and the smallest angular error of 2.42 degrees. Our results indicate that models incorporating attention mechanisms and CoordConv module increase the accuracy in classifying breast positioning quality and detecting anatomical landmarks. Furthermore, we make the labels and source codes available to the community to initiate an open research area for mammography, accessible at https://github.com/tanyelai/deep-breast-positioning.
Graph clustering, which aims to divide a graph into several homogeneous groups, is a critical area of study with applications that span various fields such as social network analysis, bioinformatics, and image segmentation. This paper explores both traditional and more recent approaches to graph clustering. Firstly, key concepts and definitions in graph theory are introduced. The background section covers essential topics, including graph Laplacians and the integration of Deep Learning in graph analysis. The paper then delves into traditional clustering methods, including Spectral Clustering and the Leiden algorithm. Following this, state-of-the-art clustering techniques that leverage deep learning are examined. A comprehensive comparison of these methods is made through experiments. The paper concludes with a discussion of the practical applications of graph clustering and potential future research directions.
The heterogeneity of neurological conditions, ranging from structural anomalies to functional impairments, presents a significant challenge in medical imaging analysis tasks. Moreover, the limited availability of well-annotated datasets constrains the development of robust analysis models. Against this backdrop, this study introduces a novel approach leveraging the inherent anatomical symmetrical features of the human brain to enhance the subsequent detection and segmentation analysis for brain diseases. A novel Symmetry-Aware Cross-Attention (SACA) module is proposed to encode symmetrical features of left and right hemispheres, and a proxy task to detect symmetrical features as the Symmetry-Aware Head (SAH) is proposed, which guides the pretraining of the whole network on a vast 3D brain imaging dataset comprising both healthy and diseased brain images across various MRI and CT. Through meticulous experimentation on downstream tasks, including both classification and segmentation for brain diseases, our model demonstrates superior performance over state-of-the-art methodologies, particularly highlighting the significance of symmetry-aware learning. Our findings advocate for the effectiveness of incorporating symmetry awareness into pretraining and set a new benchmark for medical imaging analysis, promising significant strides toward accurate and efficient diagnostic processes. Code is available at https://github.com/bitMyron/sa-swin.
Shadow removal aims at restoring the image content within shadow regions, pursuing a uniform distribution of illumination that is consistent between shadow and non-shadow regions. {Comparing to other image restoration tasks, there are two unique challenges in shadow removal:} 1) The patterns of shadows are arbitrary, varied, and often have highly complex trace structures, making ``trace-less'' image recovery difficult. 2) The degradation caused by shadows is spatially non-uniform, resulting in inconsistencies in illumination and color between shadow and non-shadow areas. Recent developments in this field are primarily driven by deep learning-based solutions, employing a variety of learning strategies, network architectures, loss functions, and training data. Nevertheless, a thorough and insightful review of deep learning-based shadow removal techniques is still lacking. In this paper, we are the first to provide a comprehensive survey to cover various aspects ranging from technical details to applications. We highlight the major advancements in deep learning-based single-image shadow removal methods, thoroughly review previous research across various categories, and provide insights into the historical progression of these developments. Additionally, we summarize performance comparisons both quantitatively and qualitatively. Beyond the technical aspects of shadow removal methods, we also explore potential future directions for this field.
The spatial location of cells within tissues and organs is crucial for the manifestation of their specific functions.Spatial transcriptomics technology enables comprehensive measurement of the gene expression patterns in tissues while retaining spatial information. However, current popular spatial transcriptomics techniques either have shallow sequencing depth or low resolution. We present stEnTrans, a deep learning method based on Transformer architecture that provides comprehensive predictions for gene expression in unmeasured areas or unexpectedly lost areas and enhances gene expression in original and inputed spots. Utilizing a self-supervised learning approach, stEnTrans establishes proxy tasks on gene expression profile without requiring additional data, mining intrinsic features of the tissues as supervisory information. We evaluate stEnTrans on six datasets and the results indicate superior performance in enhancing spots resolution and predicting gene expression in unmeasured areas compared to other deep learning and traditional interpolation methods. Additionally, Our method also can help the discovery of spatial patterns in Spatial Transcriptomics and enrich to more biologically significant pathways. Our source code is available at https://github.com/shuailinxue/stEnTrans.
Graph combinatorial optimization problems are widely applicable and notoriously difficult to compute; for example, consider the traveling salesman or facility location problems. In this paper, we explore the feasibility of using convolutional neural networks (CNNs) on graph images to predict the cardinality of combinatorial properties of random graphs and networks. Specifically, we use image representations of modified adjacency matrices of random graphs as training samples for a CNN model to predict the stability number of random graphs; where the stability number is the cardinality of a maximum set of vertices in a graph that contains no pairwise adjacency between vertices. The model and results presented in this study suggest potential for applying deep learning in combinatorial optimization problems previously not considered by simple deep learning techniques.