arXiv research

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…

Deep Relevance Regularization improves neural network performance in tumor typing.

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…

New method recovers relative rates in spatial compositional data from IMS.

New framework distinguishes lung cancer subtypes using MALDI mass spectrometry.

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…

When confronted with a substance of unknown identity, researchers often perform mass spectrometry on the sample and compare the observed spectrum to a library of previously-collected spectra to identify the molecule. While popular, this approach will fail to identify molecules that are not in the existing library. In r…

Paper presents a method for identifying isotope envelopes in MALDI-ToF data.

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…

We present ChromAlignNet, a deep learning model for alignment of peaks in Gas Chromatography-Mass Spectrometry (GC-MS) data. In GC-MS data, a compound's retention time (RT) may not stay fixed across multiple chromatograms. To use GC-MS data for biomarker discovery requires alignment of identical analyte's RT from diffe…

Chemical structure elucidation is a serious bottleneck in analytical chemistry today. We address the problem of identifying an unknown chemical threat given its mass spectrum and its chemical formula, a task which might take well trained chemists several days to complete. Given a chemical formula, there could be over a…

Random small feature subsets outperform FS in diverse datasets.

SMM improves signal recovery from noisy data.

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 …

In this paper, we consider the problem of classification of $M$ high dimensional queries $y^1,\cdots,y^M\in B^S$ to $N$ high dimensional classes $x^1,\cdots,x^N\in A^S$ where $A$ and $B$ are discrete alphabets and the probabilistic model that relates data to the classes $P(x,y)$ is known. This problem has applications …

Tandem mass spectrometry (MS/MS) is a high-throughput technology used toidentify the proteins in a complex biological sample, such as a drop of blood. A collection of spectra is generated at the output of the process, each spectrum of which is representative of a peptide (protein subsequence) present in the original co…

As in many other scientific domains, we face a fundamental problem when using machine learning to identify proteins from mass spectrometry data: large ground truth datasets mapping inputs to correct outputs are extremely difficult to obtain. Instead, we have access to imperfect hand-coded models crafted by domain exper…

Selective prediction framework reduces errors in molecular structure identification from MS/MS.

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…

Personalized cancer vaccines are envisioned as the next generation rational cancer immunotherapy. The key step in developing personalized therapeutic cancer vaccines is to identify tumor-specific neoantigens that are on the surface of tumor cells. A promising method for this is through de novo peptide sequencing from m…

The most widely used technology to identify the proteins present in a complex biological sample is tandem mass spectrometry, which quickly produces a large collection of spectra representative of the peptides (i.e., protein subsequences) present in the original sample. In this work, we greatly expand the parameter lear…

Machine learning detects subhalos in lensed images with high accuracy and low false positives.

New scalable algorithm for non-negative linear regression with entropy-regularized OT loss.

SML improves pancreatic mass diagnosis accuracy using CT images.

This work originates from a heart's images tracking which is to generate an apparent continuous motion, observable through intensity variation from one starting image to an ending one both supposed segmented. Given two images p0 and p1, we calculate an evolution process p(t, \cdot) which transports p0 to p1 by using th…

The PARAFAC2 is a multimodal factor analysis model suitable for analyzing multi-way data when one of the modes has incomparable observation units, for example because of differences in signal sampling or batch sizes. A fully probabilistic treatment of the PARAFAC2 is desirable in order to improve robustness to noise an…

Supervised learning is the workhorse for regression and classification tasks, but the standard approach presumes ground truth for every measurement. In real world applications, limitations due to expense or general in-feasibility due to the specific application are common. In the context of agriculture applications, yi…

Early detection of breast cancer has a major contribution to curability, and using mammographic images, this can be achieved non-invasively. Supervised deep learning, the dominant CADe tool currently, has played a great role in object detection in computer vision, but it suffers from a limiting property: the need of a …

This work demonstrates the execution of a novel process model for knowledge discovery and data mining for metabolomics (MeKDDaM). It aims to illustrate MeKDDaM process model applicability using four different real-world applications and to highlight its strengths and unique features. The demonstrated applications provi…

Obesity is an important concern in public health, and Body Mass Index is one of the useful (and proliferant) measures. We use Convolutional Neural Networks to determine Body Mass Index from photographs in a study with 161 participants. Low data, a common problem in medicine, is addressed by reducing the information in …

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…

In this paper, we study the challenge of feature selection based on a relatively small collection of sample pairs $\{(x_i, y_i)\}_{1 \leq i \leq m}$. The observations $y_i \in \mathbb{R}$ are thereby supposed to follow a noisy single-index model, depending on a certain set of signal variables. A major difficulty is tha…

Let B be a fiber bundle with compact fiber F over a compact Riemannian n-manifold M. There is a natural Riemannian metric on the total space B consistent with the metric on M. With respect to that metric, the volume of a rectifiable section s:M--> B is the mass of the image s(M) as a rectifiable n-current in B. Theorem…

The article calculates the near horizon limit of Wang--Yau quasi-local mass.

New method calibrates classifier probabilities with guaranteed coverage.

Recently it's been shown that neural networks can use images of human faces to accurately predict Body Mass Index (BMI), a widely used health indicator. In this paper we demonstrate that a neural network performing BMI inference is indeed vulnerable to test-time adversarial attacks. This extends test-time adversarial a…

We propose a deep-learning approach based on generative adversarial networks (GANs) to reduce noise in weak lensing mass maps under realistic conditions. We apply image-to-image translation using conditional GANs to the mass map obtained from the first-year data of Subaru Hyper Suprime-Cam (HSC) survey. We train the co…

Method generates joint posterior samples of source and foreground mass distributions for gravitational lensing.

In this paper, we study the boundary behaviors of compact manifolds with nonnegative scalar curvature and with nonempty boundary. Using a general version of Positive Mass Theorem of Schoen-Yau and Witten, we prove the following theorem: For any compact manifold with boundary and nonnegative scalar curvature, if it is s…

Motivation: Post-database searching is a key procedure in peptide dentification with tandem mass spectrometry (MS/MS) strategies for refining peptide-spectrum matches (PSMs) generated by database search engines. Although many statistical and machine learning-based methods have been developed to improve the accuracy of …

We use an idea of Wang and Yau to give a new definition of quasi-local mass for a topological sphere in an initial date set. The new definition modifies Brown-York's definition by using certain spinor norm as lapse function. And it requires mean curvature of the topological sphere satisfies apparent horizon conditions,…

New method converts and optimizes sampling schedules for generative models.

A rapidly growing area of work has studied the existence of adversarial examples, datapoints which have been perturbed to fool a classifier, but the vast majority of these works have focused primarily on threat models defined by $\ell_p$ norm-bounded perturbations. In this paper, we propose a new threat model for adver…

Unsupervised domain transfer is the task of transferring or translating samples from a source distribution to a different target distribution. Current solutions unsupervised domain transfer often operate on data on which the modes of the distribution are well-matched, for instance have the same frequencies of classes b…

We improve image perturbation defenses using a better-defined Wasserstein threat model.

QHMC improves HMC for sampling from complex distributions.