Method predicts rarity of image features to support research integrity investigations.
problem Difficulty in determining if image reuse is by chance or intentional.
method Statistical estimation of ORB features' chance occurrence across PubMed Open Access Subset dataset.
result The method produces decreasingly smaller p-values for more complex imagery, supporting null hypothesis.
New method quantifies uncertainty in imaging problems.
problem Uncertainty quantification in imaging inverse problems.
method Equivariant bootstrapping based on parametric bootstrap algorithm.
result Delivers accurate high-dimensional confidence regions.
Planetary exploration missions with Mars rovers are complicated, which generally require elaborated task planning by human experts, from the path to take to the images to capture. NASA has been using this process to acquire over 22 million images from the planet Mars. In order to improve the degree of automation and th…
New method extracts biological concepts from cell microscopy images.
problem Extracting meaningful concepts from vision foundation models trained on cell microscopy images.
method Sparse dictionary learning (DL) combined with PCA whitening pre-processing.
result Successfully retrieved biologically meaningful concepts like cell types and genetic perturbations.
Instrumented data enables causal scientific machine learning
problem Insufficient data for causal scientific machine learning
method Instrumented data with explicit model, uncertainty, and counterfactuals
result Supports causal interventions through Pearl's do-operator
Figures are an important channel for scientific communication, used to express complex ideas, models and data in ways that words cannot. However, this visual information is mostly ignored in analyses of the scientific literature. In this paper, we demonstrate the utility of using scientific figures as markers of knowle…
AutoSciDACT detects scientific anomalies in noisy data.
problem Detecting anomalies in large, noisy scientific datasets.
method Contrastive pre-training for low-dimensional data representations, two-sample test using NPLM.
result Strong sensitivity to small anomalies across various scientific domains.
PIMA autoencoders discover shared features in multimodal scientific data.
problem Discovering shared information in high-throughput scientific datasets.
method Physics-informed multimodal autoencoders (PIMA) with Gaussian mixture prior and product of experts formulation.
result Accurate cross-modal inference between images and mechanical stress-strain response in lattice metamaterials.
New approach uses interpolation models and error bounds for verifiable scientific machine learning.
problem Challenges in verifying and validating modern scientific machine learning workflows.
method Combines multiple standard interpolation techniques with error bounds for efficient computation and comparative performance analysis.
result Error bounds for interpolation techniques can be computed or estimated efficiently, aiding in validation goals.
Automated detection of new, interesting, unusual, or anomalous images within large data sets has great value for applications from surveillance (e.g., airport security) to science (observations that don't fit a given theory can lead to new discoveries). Many image data analysis systems are turning to convolutional neur…
We present a new, fully generative model of optical telescope image sets, along with a variational procedure for inference. Each pixel intensity is treated as a Poisson random variable, with a rate parameter dependent on latent properties of stars and galaxies. Key latent properties are themselves random, with scientif…
There has been a lot of recent interest in adopting machine learning methods for scientific and engineering applications. This has in large part been inspired by recent successes and advances in the domains of Natural Language Processing (NLP) and Image Classification (IC). However, scientific and engineering problems …
We study the problem of object detection over scanned images of scientific documents. We consider images that contain objects of varying aspect ratios and sizes and range from coarse elements such as tables and figures to fine elements such as equations and section headers. We find that current object detectors fail to…
FreB protocol uses AI to infer hidden parameters with valid confidence regions.
problem Generating biased or overconfident conclusions from AI-generated posterior distributions.
method Frequentist-Bayes (FreB) protocol reshapes AI-generated posterior distributions into valid confidence regions.
result FreB provides valid confidence regions that consistently include true parameters with expected probability.
New method generates clean data from corrupted observations.
problem Generating clean data from corrupted observations.
method Iterative update of a transport map using black-box corruption channel access.
result Converges to a self-consistent transport map that effectively inverts the corruption channel.
The paper clarifies conditions for using benchmark scores in machine learning.
problem Using benchmark scores to draw scientific inferences about learning problems.
method Developing conditions of construct validity inspired by psychological measurement theory.
result Clarifies conditions under which benchmark scores support diverse scientific claims.
DET unifies geometric and functional alignment for high-dimensional scientific data.
problem Challenges in nonrigid registration for high-dimensional, irregular data.
method Domain Elastic Transform (DET) treats data as functions on irregular domains, using a Bayesian framework for elastic motion registration.
result DET achieves 92% topological preservation on MERFISH data and successfully registers whole-embryo Stereo-seq atlases.
New method learns signals from binary measurements, surpassing existing techniques.
problem Learning signals from noisy, incomplete, and quantized binary measurements.
method Self-supervised learning approach (SSBM) for binary data.
result SSBM outperforms supervised learning and sparse reconstruction methods.
We introduce novel communication strategies in synchronous distributed Deep Learning consisting of decentralized gradient reduction orchestration and computational graph-aware grouping of gradient tensors. These new techniques produce an optimal overlap between computation and communication and result in near-linear sc…
Machine learning techniques have been successfully applied to super-resolution tasks on natural images where visually pleasing results are sufficient. However in many scientific domains this is not adequate and estimations of errors and uncertainties are crucial. To address this issue we propose a Bayesian framework th…
Paper proposes a new framework for hypothesis testing in imaging.
problem Challenges in hypothesis testing for imaging data.
method Combines self-supervised imaging, vision-language models, and non-parametric hypothesis testing.
result Demonstrates improved power and robust error control in image-based phenotyping.
Successful multimodal search and retrieval requires the automatic understanding of semantic cross-modal relations, which, however, is still an open research problem. Previous work has suggested the metrics cross-modal mutual information and semantic correlation to model and predict cross-modal semantic relations of ima…
Deep Learning has managed to push boundaries in a wide variety of tasks. One area of interest is to tackle problems in reasoning and understanding, with an aim to emulate human intelligence. In this work, we describe a deep learning model that addresses the reasoning task of question-answering on categorical plots. We …
This chapter introduces reproducibility in machine learning for medical imaging.
problem Lack of reproducibility in machine learning for medical imaging.
method Distinguishes and defines types of reproducibility, outlines requirements, and discusses utility.
result Discussion on benefits and a plea for a non-dogmatic approach to reproducibility.
Gaudy images help train deep neural networks with less data.
problem Training deep neural networks with limited real data from visual cortex neurons.
method Used high-contrast binarized natural images (gaudy images) to train DNNs.
result Reduced training data needed for accurate DNN predictions of visual cortex neuron responses.
Celeste is a procedure for inferring astronomical catalogs that attains state-of-the-art scientific results. To date, Celeste has been scaled to at most hundreds of megabytes of astronomical images: Bayesian posterior inference is notoriously demanding computationally. In this paper, we report on a scalable, parallel v…
Generative model connects physical properties to latent vectors for solar magnetic patches.
problem Disconnection between generative latent vectors and scientifically relevant quantities.
method Integrating GAN, SVM, and SSL to generate and retrieve physically interpretable solar magnetic patches.
result GAN-SVM combination enables smooth changes in physical parameters with generated patches.
New neural network captures spatial correlations in wind speed predictions.
problem Uncertainty quantification in neural network predictions for high-dimensional, correlated data.
method Training neural networks with multidimensional Gaussian loss, preserving spatial correlation and computational tractability.
result Demonstrated super-resolution of surface wind speed with explicit correlation modeling.
New function-space autoencoders improve data handling across resolutions.
problem Handling data as functions rather than discrete points.
method Introducing function-space autoencoders (FAE and FVAE) and neural operator architectures.
result Function-space autoencoders are more broadly applicable than variational autoencoders.
We consider the problem of precision matrix estimation where, due to extraneous confounding of the underlying precision matrix, the data are independent but not identically distributed. While such confounding occurs in many scientific problems, our approach is inspired by recent neuroscientific research suggesting that…
Framework for confidence estimation in deep CT reconstructions.
problem Uncertainty in deep learning-based CT reconstructions.
method Sequential likelihood mixing framework with log-linear forward model.
result Deep models yield tighter confidence regions than classical methods.
ECS evaluates synthetic CXR images' distributional fidelity.
problem Evaluating synthetic CXR images' distributional fidelity under privacy constraints.
method Characteristic function transforms of feature embeddings.
result ECS uncovers clinically relevant distributional discrepancies.
Paper extends causal inference to non-Euclidean data like images and distributions.
problem Causal inference for non-Euclidean data like images and distributions.
method Hilbert space embeddings, Fréchet mean estimation, nonparametric doubly-debiased causal inference.
result Validated approach for causal inference with continuous treatments on non-Euclidean data.
BLISS detects and separates astronomical sources quickly and accurately.
problem Detecting and separating overlapping astronomical sources in large images.
method Bayesian Light Source Separator (BLISS) using deep generative models and variational inference.
result BLISS can process megapixel images in seconds and produce highly accurate catalogs.
xVal tokenizes numbers continuously for better scientific model training.
problem Lack of continuous numerical tokenization for scientific datasets in LLMs.
method xVal: Continuous numerical tokenization strategy.
result xVal outperforms other numerical tokenization methods on scientific datasets.
Bayesian imaging methods deliver trustworthy probabilities in some cases but struggle with uncertainty quantification.
problem Uncertainty quantification in Bayesian imaging methods.
method Monte Carlo method to explore reliability of probabilities.
result Modern Bayesian imaging techniques deliver reliable probabilities in some cases but not for uncertainty quantification.
Galactica learns from scientific literature to help researchers.
problem Information overload in scientific literature makes it hard to find useful insights.
method Trained on a large corpus of scientific papers, reference material, and knowledge bases.
result Outperforms existing models on various scientific tasks, including LaTeX equations and mathematical reasoning.
New method for fMRI missing value imputation improves robustness.
problem High frequency of missing values in fMRI data.
method Spatial and time-dependent regularization with a novel recurrent layer.
result Improved robustness against state-of-the-art alternatives.
Data science models, although successful in a number of commercial domains, have had limited applicability in scientific problems involving complex physical phenomena. Theory-guided data science (TGDS) is an emerging paradigm that aims to leverage the wealth of scientific knowledge for improving the effectiveness of da…
Social media enhances or diminishes scientific status, depending on usage.
problem Impact of social media on scientific stratification and mobility.
method Logistic Attribution Analysis combining statistical and machine learning methods.
result Social media promotes stratification and mobility, but beyond a threshold, it negatively impacts status.
Deep neural networks provide meaningful uncertainty estimates for large-scale simulations.
problem Uncertainty estimates for deep neural network predictions from large-scale simulations.
method General variational inference approach to calibrate Bayesian uncertainties.
result Calibrated Bayesian uncertainties preserved physics-correlations in predicted quantities.
New methods estimate brain connectivity from calcium imaging data with missing data.
problem Estimating functional neuronal connectivity from calcium imaging data with missing data.
method Two approaches for nonparanormal Graph Quilting based on the Gaussian copula graphical model.
result Our methods yield more meaningful functional connectivity estimates than existing Gaussian graph quilting methods.
daep learns from irregular, multimodal astronomical data.
problem Learning from irregular, multimodal astronomical sequences.
method Diffusion Autoencoder with Perceivers (daep) tokenizes, compresses, and reconstructs data.
result daep outperforms VAE and maep baselines in reconstruction and fine-scale structure preservation.
Evidence shows that in a significant number of cases the current methods of research do not allow for reproducible and falsifiable procedures of scientific investigation. As a consequence, the majority of critical decisions at all levels, from personal investment choices to overreaching global policies, rely on some va…
Historically, games of all kinds have often been the subject of study in scientific works of Computer Science, including the field of machine learning. By using machine learning techniques and applying them to a game with defined rules or a structured dataset, it's possible to learn and improve on the already existing …
There is significant interest in using modern neural networks for scientific applications due to their effectiveness in modeling highly complex, non-linear problems in a data-driven fashion. However, a common challenge is to verify the scientific plausibility or validity of outputs predicted by a neural network. This w…
Paper proposes a method to estimate scientific parameters in hybrid models without relying on model architecture.
problem Estimating unknown parameters in hybrid models combining machine learning and scientific models.
method Sharpness-aware minimization adapted for hybrid modeling, focusing on model simplicity.
result Demonstrates effectiveness of SAM-based hybrid model learning for scientific parameter estimation.
Scientific imaging techniques such as optical and electron microscopy and computed tomography (CT) scanning are used to study the 3D structure of an object through 2D observations. These observations are related to the original 3D object through orthogonal integral projections. For common 3D reconstruction algorithms, …