The paper presents the application of Variational Autoencoders (VAE) for data dimensionality reduction and explorative analysis of mass spectrometry imaging data (MSI). The results confirm that VAEs are capable of detecting the patterns associated with the different tissue sub-types with performance than standard appro…
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48 results for “Mass Spectrometry”
Deep Relevance Regularization improves neural network performance in tumor typing.
problem Confounding factors hinder neural network performance in multi-laboratory imaging mass spectrometry data.
method Introduces Deep Relevance Regularization to restrict neural network focus.
result Deep Relevance Regularization robustifies neural networks and improves interpretability.
Neural network predicts electron-ionization mass spectra quickly.
problem Identifying unknown molecules not in existing libraries.
method Lightweight neural network model for predicting mass spectra.
result High accuracy predictions of small molecule mass spectra.
We study a simple modification to the conventional time of flight mass spectrometry (TOFMS) where a \emph{variable} and (pseudo)-\emph{random} pulsing rate is used which allows for traces from different pulses to overlap. This modification requires little alteration to the currently employed hardware. However, it requi…
Background: High-throughput proteomics techniques, such as mass spectrometry (MS)-based approaches, produce very high-dimensional data-sets. In a clinical setting one is often interested in how mass spectra differ between patients of different classes, for example spectra from healthy patients vs. spectra from patients…
DeepNovoV2 improves de novo peptide sequencing from mass spectrometry data.
problem De novo peptide sequencing from mass spectrometry data for personalized cancer vaccines.
method DeepNovoV2 combines T-Net and recurrent neural networks for end-to-end training and prediction.
result DeepNovoV2 achieves 13.01-23.95\% higher accuracy than previous methods.
Improved peptide identification from mass spectrometry data.
problem Lack of large ground truth datasets for protein identification.
method Deep neural networks trained on imperfect hand-coded models.
result 43% improvement over standard matching methods.
Neural networks predict substructures from mass spectra to identify chemical threats.
problem Identifying unknown chemical threats from mass spectra and formulas.
method Data-driven approach using neural networks to rank and match substructures.
result Substructure classifiers achieve over 90% micro F1-score and correctly identify structures in 88-71% of cases.
Motivation: Tumor classification using Imaging Mass Spectrometry (IMS) data has a high potential for future applications in pathology. Due to the complexity and size of the data, automated feature extraction and classification steps are required to fully process the data. Deep learning offers an approach to learn featu…
Improved protein identification in mass spectrometry data.
problem Expanding peptide scoring capabilities in tandem mass spectrometry.
method Deriving concave emission distributions for dynamic Bayesian networks.
result Efficiently learned scoring function outperforms state-of-the-art.
New method recovers relative rates in spatial compositional data from IMS.
problem Challenges in analyzing spatial data from IMS due to competitive sampling.
method Hierarchical Variational Graph Fused Lasso using heavy-tailed graphical lasso prior and automatic differentiation variational inference.
result Our method outperforms state-of-the-practice point estimate methodologies in IMS and has superior posterior coverage.
New framework distinguishes lung cancer subtypes using MALDI mass spectrometry.
problem Distinguishing between adenocarcinoma and squamous cell carcinoma subtypes in lung cancer.
method Supervised topological data analysis on MALDI mass spectrometry imaging data.
result The proposed framework successfully classifies lung cancer subtypes with competitive results.
Mass spectrometry (MS) is an important technique for chemical profiling which calculates for a sample a high dimensional histogram-like spectrum. A crucial step of MS data processing is the peak picking which selects peaks containing information about molecules with high concentrations which are of interest in an MS in…
Paper presents a method for identifying isotope envelopes in MALDI-ToF data.
problem Deisotoping of isotopic peaks in MALDI-ToF molecular imaging data.
method Uses Mamdani-Assilan fuzzy system and spatial maps of molecular distribution to identify isotope envelopes.
result Proposed method detects overlapping envelopes and analyzes large data sets.
Deep learning aligns GC-MS peaks for biomarker discovery.
problem Aligning retention times of GC-MS peaks across different samples.
method ChromAlignNet, a deep learning model for peak alignment.
result ChromAlignNet outperforms existing methods on complex data sets.
Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical classification where the proximity between species is generally measured in terms o…
Many proteoforms - arising from alternative splicing, post-translational modifications (PTMs), or paralogous genes - have distinct biological functions, such as histone PTM proteoforms. However, their quantification by existing bottom-up mass-spectrometry (MS) methods is undermined by peptide-specific biases. To avoid …
ForestDSH hashes improve nearest neighbor search in high-dimensional data.
problem High-dimensional classification and nearest neighbor search.
method Distribution-sensitive hashing using a forest of decision trees.
result ForestDSH hashes outperform LSH and state-of-the-art methods in speed and accuracy.
Generative model gradients enhance MS/MS peptide identification.
problem Improving peptide identification from MS/MS spectra.
method Leverage log-likelihood gradients of generative models in a kernel-based classifier.
result Fisher kernel outperforms other methods on MS/MS datasets.
Selective prediction framework reduces errors in molecular structure identification from MS/MS.
problem High-stakes applications require reliable molecular structure identification from MS/MS data.
method Selective prediction framework using risk-coverage tradeoff and uncertainty quantification.
result First-order confidence measures and retrieval-level aleatoric uncertainty achieve strong risk-coverage tradeoffs.
Clustering in high-dimensional spaces is nowadays a recurrent problem in many scientific domains but remains a difficult task from both the clustering accuracy and the result understanding points of view. This paper presents a discriminative latent mixture (DLM) model which fits the data in a latent orthonormal discrim…
Random small feature subsets outperform FS in diverse datasets.
problem The significance of selected features in high-dimensional datasets is questionable.
method Analysis of 28 diverse datasets (microarray, RNA-Seq, etc.).
result Any arbitrary set of features performs as well as or better than selected features across datasets.
New scalable algorithm for non-negative linear regression with entropy-regularized OT loss.
problem Generalizing task-specific linear models to broader applications.
method Sinkhorn-like scaling iterations for convex penalty and datafit terms.
result Simple multiplicative updates for various penalty and datafit terms.
SMM improves signal recovery from noisy data.
problem Estimating signals from noisy and scaled observations.
method Spiked mixture model (SMM) with EM algorithm.
result SMM outperforms GMM in signal recovery.
Probabilistic PARAFAC2stat.ML
Probabilistic PARAFAC2 improves robustness to noise.
problem Improving robustness of PARAFAC2 to noise and determining the number of factors.
method Developed two probabilistic formulations of PARAFAC2 with variational procedures for inference.
result Probabilistic PARAFAC2 is more robust to noise and model order misspecification.
Liquid chromatography coupled with tandem mass spectrometry, also known as shotgun proteomics, is a widely-used high-throughput technology for identifying proteins in complex biological samples. Analysis of the tens of thousands of fragmentation spectra produced by a typical shotgun proteomics experiment begins by assi…
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.
A Mathematical Framework for Feature Selection from Real-World Data with Non-Linear Observationsstat.ML
In this paper, we study the challenge of feature selection based on a relatively small collection of sample pairs . The observations are thereby supposed to follow a noisy single-index model, depending on a certain set of signal variables. A major difficulty is tha…
OLCS-Ranker improves peptide identification accuracy and speed on hard datasets.
problem Efficiently identifying peptides from MS/MS data, especially on hard datasets with many false positives.
method Cost-sensitive online learning model and iterative online learning algorithm.
result OLCS-Ranker outperforms existing methods in accuracy and speed on large datasets.
Two masses on surfaces with boundary converge to ADM mass.
problem Evaluating quasi-local masses on surfaces with boundaries.
method Hawking mass and Huisken's isoperimetric mass on surfaces with boundary, convergence to ADM mass.
result Convergence of Hawking and Huisken's masses to ADM mass.
The X-ADM mass is shown to be equivalent to the ADM mass, proving the X-positive mass theorem in all dimensions.
problem Proving the X-positive mass theorem for all dimensions.
method Conformal reduction argument.
result The X-ADM mass is equivalent to the ADM mass, proving the X-positive mass theorem in all dimensions.
The paper studies nonlinear mass concepts in 3-manifolds with nonnegative scalar curvature.
problem Nonlinear isocapacitary mass in 3-manifolds with nonnegative scalar curvature.
method Derives positive mass theorems and shows mass coincides with ADM mass under mild conditions.
result Nonlinear masses coincide with ADM mass and prove the Penrose inequality.
Untargeted Region of Interest Selection for GC-MS Data using a Pseudo F-Ratio Moving Window (FRMV)stat.ML
A new method selects regions of interest in GC-MS data without prior target selection.
problem Challenges in GC-MS data analysis due to fragmentation and shared fragment ions.
method Uses a pseudo F-ratio moving window (FRMV) to automatically select regions of interest.
result Algorithm can accurately identify signal regions in GC-MS data.
Equivalence proven for isocapacitary mass notions.
problem Proving equivalence of isocapacitary mass notions.
method Proof of equivalence for G. Huisken's and J. L. Jauregui's isocapacitary mass.
result Equivalence of isocapacitary mass notions proven.
The paper defines a new mass quantity for 3-manifolds and proves a positive mass theorem.
problem Proving the positive mass theorem for a new geometric quantity.
method Defining -ADM mass and using a monotonicity formula.
result Established a relative positive mass theorem for asymptotically flat 3-manifolds.
Introduce new boundary mass for asymptotically flat half-manifolds
problem Define boundary mass for asymptotically flat half-manifolds
method Introduce new boundary mass
result Define boundary mass for asymptotically flat half-manifolds
The paper establishes geometric inequalities for quasi-local masses.
problem Lower bounds for quasi-local masses in terms of charge, angular momentum, and horizon area.
method Hamiltonian approach to three quasi-local masses: Brown-York, Liu-Yau, and Wang-Yau.
result Geometric inequalities motivated by ADM mass, interpreted as localized versions.
Study on Hawking and Bartnik masses for specific surfaces.
problem Analyzing the positivity and bounds of Hawking and Bartnik masses for constant mean curvature surfaces.
method Intrinsic conditions and estimates for the masses of constant mean curvature surfaces.
result Positivity and estimates of Hawking and Bartnik masses for surfaces with nonnegative scalar curvature.
Researchers calculate quasi-local mass on unit spheres at infinity.
problem Computing quasi-local mass on unit spheres at spatial infinity.
method Developed new techniques to evaluate quasi-local mass.
result Leading order term of quasi-local mass recovers stress-energy tensor for vacuum spacetime.
We prove directly without using a density theorem that (i) the ADM mass defined in the usual way on an asymptotically flat manifold is equal to the mass defined intrinsically using Ricci tensor; (ii) the Hamiltonian formulation of center of mass and the center of mass defined intrinsically using Ricci tensor are the sa…
Continuous metrics on R^3 with specific properties have non-negative harmonic mass.
problem Proving non-negativity of mass for continuous metrics.
method Defining harmonic mass and using properties of approximating smooth metrics.
result The harmonic mass of continuous metrics is non-negative.
The paper examines mass aspects at future null infinity and limits of quasilocal mass.
problem Understanding mass aspects and limits of quasilocal mass at future null infinity.
method Review and extension of Bondi mass and mass loss formula in Bondi-Sachs coordinate system.
result New results about the limit of quasilocal mass of unit spheres at null infinity.
A definition of the mass aspect function for weakly regular asymptotically hyperbolic manifoldsmath.DG
Unified definition of mass aspect function for weakly regular hyperbolic manifolds.
problem Ambiguity in mass definition for asymptotically hyperbolic manifolds.
method Introduced an ADM-style mass aspect function for broad asymptotics and low regularity.
result Unified mass aspect function exhibits favorable covariance properties.
Study the mass of flat 3-manifolds with boundary using specific methods.
problem Calculate the mass of asymptotically flat 3-manifolds with boundary.
method Use the method of Bray-Kazaras-Khuri-Stern to derive a mass formula.
result Derive sufficient conditions for the positivity of the mass.
Local mass perspective on Bayesian inference
problem Measuring distributional discrepancy in Bayesian inference
method Introducing Mass Index and Regularised Extended KL
result Proving inequalities for comparing local small-ball masses
Computes quasi-local mass at null infinity using Bondi-Sachs coordinates.
problem Global properties of quasi-local mass at null infinity.
method Evaluation of Wang-Yau quasi-local mass on unit spheres in Bondi-Sachs coordinates.
result Quasi-local mass is related to the news function in Bondi-Sachs coordinates.
Simple proof for sphere mass calculation.
problem Computing the ADM mass of static sphere extensions.
method Uses mass formula for static asymptotically flat manifolds.
result Validated mass formula for small spheres.
On asymptotically flat and asymptotically hyperbolic manifolds, by evaluating the total mass via the Ricci tensor, we show that the limits of certain Brown-York type and Hawking type quasi-local mass integrals equal the total mass of the manifold in all dimensions.