Related papers: Open Mass Spectrometry Search Algorithm
We have developed an algorithm for non-parametric fitting and extraction of statistically significant peaks in the presence of statistical and systematic uncertainties. Applications of this algorithm for analysis of high-energy collision…
In physics, it is sometimes desirable to compute the so-called \emph{Density Of States} (DOS), also known as the \emph{spectral density}, of a real symmetric matrix $A$. The spectral density can be viewed as a probability density…
Imaging mass spectrometry (IMS) has transformed proteomics by providing an avenue for collecting spatially distributed molecular data. Mass spectrometry data acquired with matrix assisted laser desorption ionization (MALDI) IMS consist of…
Recently, many software tools have been developed to perform quantification in LC-MS analyses. However, most of them are specific to either a quantification strategy (e.g. label-free or isotopic labelling) or a mass-spectrometry system…
Score matching is an estimation procedure that has been developed for statistical models whose probability density function is known up to proportionality but whose normalizing constant is intractable, so that maximum likelihood is…
We consider the sensitivity of algorithms for the maximum matching problem against edge and vertex modifications. Algorithms with low sensitivity are desirable because they are robust to edge failure or attack. In this work, we show a…
OPUS is a branch and bound search algorithm that enables efficient admissible search through spaces for which the order of search operator application is not significant. The algorithm's search efficiency is demonstrated with respect to…
Particle Size Analysis (PSA) is an important process carried out in a number of industries, which can significantly influence the properties of the final product. A ubiquitous instrument for this purpose is the Optical Microscope (OM).…
An algorithm for extracting identity submatrices of small rank and pivotal units from large and sparse matrices is proposed. The procedure has already been satisfactorily applied for solving the label switching problem in Bayesian mixture…
We present Bayesian Binary Search (BBS), a novel probabilistic variant of the classical binary search/bisection algorithm. BBS leverages machine learning/statistical techniques to estimate the probability density of the search space and…
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncovering novel phenomena that occur at very large scales. We…
Accurate and efficient detection of ovarian cancer at early stages is critical to ensure proper treatments for patients. Among the first-line modalities investigated in studies of early diagnosis are features distilled from protein mass…
Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…
Score matching is a recently developed parameter learning method that is particularly effective to complicated high dimensional density models with intractable partition functions. In this paper, we study two issues that have not been…
We formulate low-level malware detection using algorithms based on feature matching as Order-based Malware Detection with Critical Instructions (General-OMDCI): given a pattern in the form of a sequence \(M\) of colored blocks, where each…
In object detection, post-processing methods like Non-maximum Suppression (NMS) are widely used. NMS can substantially reduce the number of false positive detections but may still keep some detections with low objectness scores. In order to…
Multivariate Singular Spectrum Analysis (MSSA) is a powerful and widely used nonparametric method for multivariate time series, which allows the analysis of complex temporal data from diverse fields such as finance, healthcare, ecology, and…
Propensity scores are commonly used to reduce the confounding bias in non-randomized observational studies for estimating the average treatment effect. An important assumption underlying this approach is that all confounders that are…
Propensity score matching is a common tool for adjusting for observed confounding in observational studies, but is known to have limitations in the presence of unmeasured confounding. In many settings, researchers are confronted with…
Open Set Recognition (OSR) has been an emerging topic. Besides recognizing predefined classes, the system needs to reject the unknowns. Prototype learning is a potential manner to handle the problem, as its ability to improve intra-class…