Nuclear magnetic resonance (NMR) spectroscopy is one of the leading techniques for protein studies. The method features a number of properties, allowing to explain macromolecular interactions mechanistically and resolve structures with atomic resolution. However, due to laborious data analysis, a full potential of NMR …
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48 results for “NMR spectroscopy”
Nuclear magnetic resonance (NMR) spectroscopy exploits the magnetic properties of atomic nuclei to discover the structure, reaction state and chemical environment of molecules. We propose a probabilistic generative model and inference procedures for NMR spectroscopy. Specifically, we use a weighted sum of trigonometric…
High-dimensional data common in genomics, proteomics, and chemometrics often contains complicated correlation structures. Recently, partial least squares (PLS) and Sparse PLS methods have gained attention in these areas as dimension reduction techniques in the context of supervised data analysis. We introduce a framewo…
Unified method for simultaneous denoising and clustering.
problem Clustering noisy signals.
method Sparse convex wavelet clustering with fusion and group-sparse penalties.
result Unified approach that denoises and clusters simultaneously.
Novel process model for metabolomics data analysis.
problem Analyzing complex metabolomics data.
method Data-driven and hypothesis-driven data mining approaches using various techniques.
result Demonstrated applicability and strengths of MeKDDaM model.
Graph Informer improves molecular prediction tasks with expressive route-based attention.
problem Challenges in applying machine learning to molecular graphs due to information bottlenecks.
method Introduces a multi-attention mechanism that attends to nodes several steps away in molecular graphs.
result Improves 13C NMR spectra prediction with MAE of 1.35 ppm and drug bioactivity/toxicity prediction.
Graph-neural-network predictions of solid-state NMR parameters from spherical tensor decompositioncond-mat.mtrl-sci
Graph neural networks predict solid-state NMR parameters from atomic structures.
problem Efficiently predicting NMR parameters from atomic structures for complex materials.
method Graph neural networks applied to tensor quantities for anisotropic magnetic shielding and electric field gradient.
result Improved accuracy in predicting NMR properties from diverse and complex materials.
This paper explores robust recovery of a superposition of distinct complex exponential functions from a few random Gaussian projections. We assume that the signal of interest is of dimensional and . This framework covers a large class of signals arising from real applications in biology, automation,…
Machine Learning approach to muon spectroscopy analysiscond-mat.mtrl-sci
ML PCA detects phase transitions in muon spectroscopy data.
problem Detecting phase transitions in materials using muon spectroscopy data.
method Unsupervised Machine Learning (PCA) applied to asymmetry functions.
result PCA method effectively detects phase transitions in muon spectroscopy experiments.
AI enhances cancer diagnostics using spectroscopy.
problem Early and accurate cancer diagnosis.
method Combining AI with spectroscopy-based techniques.
result AI improves cancer diagnostics speed and safety.
Robust Classification of High-Dimensional Spectroscopy Data Using Deep Learning and Data Synthesiscs.LG
Improved spectroscopy classification with deep learning and synthetic data.
problem Identifying chlorinated solvents in Raman spectra.
method Locally-connected neural network (NN) for binary classification, autoencoder-based outlier detection, and synthetic training data.
result The proposed method outperforms existing algorithms in accuracy and robustness.
This work uses neural density estimation to analyze laser-induced breakdown spectroscopy data, enabling accurate predictions and uncertainty quantification.
problem Inference of probability densities in high-dimensional spectral data is often intractable.
method Normalizing flows on structured spectral latent spaces for density estimation and uncertainty quantification.
result The approach enables generation of realistic spectral samples and accurate prediction of state vectors with well-calibrated uncertainties.
Develops a Bayesian non-parametric approach for signal separation with varying components.
problem Signal separation with varying components across different input locations.
method Augments Gaussian Process Latent Variable Models with weighted sums of pure component signals and incorporates priors for linear weights.
result Framework allows for non-linear variations in signals and incorporates useful priors for linear weights.
High-dimensional spectroscopy data makes ML models achieve near-perfect accuracy, even when chemical distinctions are absent.
problem Why machine learning models achieve near-perfect accuracy in spectroscopic classification tasks without chemically meaningful features.
method Theoretical analysis grounded in the Feldman-Hajek theorem and concentration of measure, combined with specific experiments on synthetic and real fluorescence spectra.
result Infinitesimal distributional differences in high-dimensional spaces can lead to perfect separability, making models achieve near-perfect accuracy in spectroscopy.
Dynamic Time Warping improves regression accuracy on spectroscopy data.
problem Improving regression accuracy on spectroscopy data with DTW when data is across multiple wavelengths.
method Illustrated DTW's effectiveness on spectroscopy time-series data, showing its benefits in improving regression accuracy when only a single wavelength is considered. DTW combined with k-Nearest Neighbour reveals similarities and differences at the time-series level.
result DTW improves regression accuracy on spectroscopy data, especially when considering a single wavelength.
Active learning improves neutron spectroscopy experiments by automating measurement selection.
problem Efficiently searching for signals in neutron scattering experiments with limited beam time.
method Probabilistic active learning using log-Gaussian processes.
result Automated selection of informative measurements improves experimental efficiency.
This work uses Sylvester normalizing flows for more accurate metabolite quantification in MRS.
problem Challenges in accurate metabolite quantification in MRS due to spectral overlap, low SNR, and artifacts.
method Bayesian inference framework with physics-informed Sylvester normalizing flows.
result Accurate metabolite quantification, well-calibrated uncertainties, and insights into parameter correlations and multi-modal distributions.
PCA improves detection of phase transitions in muon spectroscopy data from various materials.
problem Subtle changes in asymmetry function indicate phase transitions, but existing methods require material-specific knowledge.
method Applied unsupervised PCA to muon spectroscopy asymmetry data from multiple materials.
result PCA can recover phase transition indicators and improve detection of material-specific variations.
The spectroscopy measurement is one of main pathways for exploring and understanding the nature. Today, it seems that racing artificial intelligence will remould its styles. The algorithms contained in huge neural networks are capable of substituting many of expensive and complex components of spectrum instruments. In …
Optimizes tensor completion using geodesics on Segre manifolds.
problem Incomplete tensor data in recommender systems and spectroscopy.
method Riemannian conjugate gradient optimization with explicit geodesic expressions.
result Recovery of tensor decomposition from as little as 10% of data.
RAMANMETRIX: a delightful way to analyze Raman spectraphysics.data-an
RAMANMETRIX simplifies Raman spectroscopy data analysis.
problem Complexity of Raman spectroscopy data processing.
method User-friendly software with chemometric analysis workflow.
result Facilitates integration of Raman spectroscopy into clinical routines.
Currently there is no validated objective measure of pain. Recent neuroimaging studies have explored the feasibility of using functional near-infrared spectroscopy (fNIRS) to measure alterations in brain function in evoked and ongoing pain. In this study, we applied multi-task machine learning methods to derive a pract…
Recognizing an object's material can inform a robot on the object's fragility or appropriate use. To estimate an object's material during manipulation, many prior works have explored the use of haptic sensing. In this paper, we explore a technique for robots to estimate the materials of objects using spectroscopy. We d…
Log-Gaussian Gamma Processes for Training Bayesian Neural Networks in Raman and CARS Spectroscopiesstat.AP
Proposes a method for training Bayesian neural networks using synthetic data from Raman and CARS spectra.
problem Limited real observations in Raman and CARS spectroscopy.
method Log-Gaussian Gamma Processes and Bayesian Neural Networks.
result Trained Bayesian neural networks provide accurate estimates of Raman and CARS spectra with uncertainty quantification.
According to a recent investigation, an estimated 33-50% of the world's coral reefs have undergone degradation, believed to be as a result of climate change. A strong driver of climate change and the subsequent environmental impact are greenhouse gases such as methane. However, the exact relation climate change has to …
New method speeds up NIR spectroscopy calibration by 400x.
problem Efficient preprocessing selection in NIR spectroscopy.
method Operator-adaptive PLS and Ridge regression.
result Significant reduction in fitting time with comparable prediction quality.
MSFA clusters high-dimensional spatial data using spline-based covariance structures.
problem Clustering high-dimensional spatial data with flexible covariance structures.
method Mixture of spatial factor analyzers with spline-based covariance and matrix variate factor analyzers for dimensionality reduction.
result Proposed models accurately infer and differentiate distinct spatial patterns in tensor-variate data.
Raman spectroscopy's capability to provide meaningful composition predictions is heavily reliant on a pre-processing step to remove insignificant spectral variation. This is crucial in biofluid analysis. Widespread adoption of diagnostics using Raman requires a robust model which can withstand routine spectra discrepan…
Logistic regression with wavelets achieves bacterial infection detection accuracy.
problem Interpreting complex biomedical signal models for high-stakes decisions.
method Wavelet features and knockoff variables for feature selection.
result Logistic regression outperforms neural networks in bacterial infection detection.
CNN identifies AGN host galaxies from Sloan Digital Sky Survey data.
problem Identifying AGN host galaxies using traditional methods is time-consuming.
method Trained a convolutional neural network on 210,000 galaxies.
result CNN can distinguish AGN host galaxies from non-active galaxies.
This paper gives a generalization of the AJL algorithm and unitary braid group representation for quantum computation of the Jones polynomial to continuous ranges of values on the unit circle of the Jones parameter. We show that our 3-strand algorithm for the Jones polynomial is a special case of this generalization of…
This paper presents a study in task-oriented approach to stroke rehabilitation by controlling a haptic device via near-infrared spectroscopy-based brain-computer interface (BCI). The task is to command the haptic device to move in opposing directions of leftward and rightward movement. Our study consists of data acquis…
This study assesses the reproducibility of 1H-MRS scans across different vendors and sessions.
problem Lack of harmonization in magnetic resonance spectroscopy protocols among vendors.
method Analysis of CV and ICC for within- and between-sessions, and correlation coefficients for across machines.
result Metabolite concentrations are highly reproducible across different vendors and sessions.
Hankel Matrix Nuclear Norm Regularized Tensor Completion for -dimensional Exponential Signalsstat.ML
Signals are generally modeled as a superposition of exponential functions in spectroscopy of chemistry, biology and medical imaging. For fast data acquisition or other inevitable reasons, however, only a small amount of samples may be acquired and thus how to recover the full signal becomes an active research topic. Bu…
We propose a novel exponentially-modified Gaussian (EMG) mixture residual model. The EMG mixture is well suited to model residuals that are contaminated by a distribution with positive support. This is in contrast to commonly used robust residual models, like the Huber loss or , which assume a symmetric contami…
Analytical results for uncertainty propagation through trained machine learning regression modelscs.LG
The paper derives uncertainty quantification for ML models used in metrology.
problem Uncertainty quantification for ML models in metrology applications.
method Analytical expressions for mean and variance of model output are derived for various ML models.
result The derived expressions cover multiple ML models and are validated against Monte Carlo methods.
Multi-label Classification with Optimal Thresholding for Multi-composition Spectroscopic Analysiscs.LG
In this paper, we implement multi-label neural networks with optimal thresholding to identify gas species among a multi gas mixture in a cluttered environment. Using infrared absorption spectroscopy and tested on synthesized spectral datasets, our approach outperforms conventional binary relevance - partial least squar…
Human-Expert-Level Brain Tumor Detection Using Deep Learning with Data Distillation and Augmentationcs.CV
Deep learning improves brain tumor detection with few data.
problem Scarce training data and data corruption in medical diagnosis.
method Data distillation and augmentation to improve deep neural network training.
result Reaches human expert-level accuracy with just a few thousand training examples.
LatentNN corrects neural network attenuation bias in astronomical data.
problem Neural networks underestimate extreme values due to measurement errors.
method Jointly optimizes network parameters and latent input values.
result LatentNN reduces attenuation bias across various signal-to-noise ratios.
A convex model for non-negative matrix factorization and dimensionality reduction on physical spacestat.ML
A collaborative convex framework for factoring a data matrix into a non-negative product , with a sparse coefficient matrix , is proposed. We restrict the columns of the dictionary matrix to coincide with certain columns of the data matrix , thereby guaranteeing a physically meaningful dictionary and …
Bayesian model clusters brain activity time series.
problem Heterogeneous multivariate time series in brain imaging.
method Group-based Bayesian mixture of smoothing splines with covariate effects.
result Distinct brain activity patterns identified.
New approach combines PCA and t-sne for better data analysis.
problem Multiscale complexity in high-dimensional data.
method Multiscale joint characterization using PCA and t-sne.
result Joint characterization detects signals not seen by PCA or t-sne alone.
Rapid identification of bacteria is essential to prevent the spread of infectious disease, help combat antimicrobial resistance, and improve patient outcomes. Raman optical spectroscopy promises to combine bacterial detection, identification, and antibiotic susceptibility testing in a single step. However, achieving cl…
Convolutional neural networks (CNN) have been shown to provide a good solution for classification problems that utilize data obtained from vibrational spectroscopy. Moreover, CNNs are capable of identification from noisy spectra without the need for additional preprocessing. However, their application in practical spec…
Current popular methods for Magnetic Resonance Fingerprint (MRF) recovery are bottlenecked by the heavy storage and computation requirements of a dictionary-matching (DM) step due to the growing size and complexity of the fingerprint dictionaries in multi-parametric quantitative MRI applications. In this paper we study…
Study compares data-driven vs model-based MRS quantification strategies, focusing on resilience to out-of-distribution effects.
problem Resilience to out-of-distribution effects in data-driven MRS quantification.
method Compared three data-driven strategies (supervised regression, self-supervised learning, test-time adaptation) against model-based fitting tools.
result Test-time adaptation proved most resilient to out-of-distribution effects, while self-supervised learning achieved intermediate performance.
A new method interprets astrophysical spectra using geometric paths to distinguish line profiles.
problem Tackling the indistinguishability of spectral line profiles under scalar summaries.
method Introduces a geometric representation of line profiles using rough path theory, mapping profiles to a common velocity grid and defining descriptors from path properties.
result Compact descriptors separate morphologies with similar scalar summaries, revealing ordered line structures.
Motivation: Proteins are known to undergo conformational changes in the course of their functions. The changes in conformation are often attributable to a small fraction of residues within the protein. Therefore identification of these variable regions is important for an understanding of protein function. Results: We …