arXiv subjects

Lei Xin

Publications and source records attributed to Lei Xin.

25 records · Page 2Linked to original sources

arXiv2022

Finite Sample Guarantees for Distributed Online Parameter Estimation with Communication Costs

We study the problem of estimating an unknown parameter in a distributed and online manner. Existing work on distributed online learning typically either focuses on asymptotic analysis, or provides bounds on regret. However, these results may not directly translate into bounds on the error of the learned model after a finite number of time-steps. In this paper, we propose a distributed online estimation algorithm which enables each agent in a network to improve its estimation accuracy by communicating with neighbors. We provide non-asymptotic bounds on the estimation error, leveraging the statistical properties of the underlying model. Our analysis demonstrates a trade-off between estimation error and communication costs. Further, our analysis allows us to determine a time at which the communication can be stopped (due to the costs associated with communications), while meeting a desired estimation accuracy. We also provide a numerical example to validate our results.

eess.SY↗

arXiv2022

Identifying the Dynamics of a System by Leveraging Data from Similar Systems

We study the problem of identifying the dynamics of a linear system when one has access to samples generated by a similar (but not identical) system, in addition to data from the true system. We use a weighted least squares approach and provide finite sample performance guarantees on the quality of the identified dynamics. Our results show that one can effectively use the auxiliary data generated by the similar system to reduce the estimation error due to the process noise, at the cost of adding a portion of error that is due to intrinsic differences in the models of the true and auxiliary systems. We also provide numerical experiments to validate our theoretical results. Our analysis can be applied to a variety of important settings. For example, if the system dynamics change at some point in time (e.g., due to a fault), how should one leverage data from the prior system in order to learn the dynamics of the new system? As another example, if there is abundant data available from a simulated (but imperfect) model of the true system, how should one weight that data compared to the real data from the system? Our analysis provides insights into the answers to these questions.

eess.SY↗

arXiv2022

Learning the Dynamics of Autonomous Linear Systems From Multiple Trajectories

We consider the problem of learning the dynamics of autonomous linear systems (i.e., systems that are not affected by external control inputs) from observations of multiple trajectories of those systems, with finite sample guarantees. Existing results on learning rate and consistency of autonomous linear system identification rely on observations of steady state behaviors from a single long trajectory, and are not applicable to unstable systems. In contrast, we consider the scenario of learning system dynamics based on multiple short trajectories, where there are no easily observed steady state behaviors. We provide a finite sample analysis, which shows that the dynamics can be learned at a rate $\mathcal{O}(\frac{1}{\sqrt{N}})$ for both stable and unstable systems, where $N$ is the number of trajectories, when the initial state of the system has zero mean (which is a common assumption in the existing literature). We further generalize our result to the case where the initial state has non-zero mean. We show that one can adjust the length of the trajectories to achieve a learning rate of $\mathcal{O}(\sqrt{\frac{\log{N}}{N})}$ for strictly stable systems and a learning rate of $\mathcal{O}(\frac{(\log{N})^d}{\sqrt{N}})$ for marginally stable systems, where $d$ is some constant.

eess.SY↗

arXiv2020

PointIso: Point Cloud Based Deep Learning Model for Detecting Arbitrary-Precision Peptide Features in LC-MS Map through Attention Based Segmentation

A promising technique of discovering disease biomarkers is to measure the relative protein abundance in multiple biofluid samples through liquid chromatography with tandem mass spectrometry (LC-MS/MS) based quantitative proteomics. The key step involves peptide feature detection in LC-MS map, along with its charge and intensity. Existing heuristic algorithms suffer from inaccurate parameters since different settings of the parameters result in significantly different outcomes. Therefore, we propose PointIso, to serve the necessity of an automated system for peptide feature detection that is able to find out the proper parameters itself, and is easily adaptable to different types of datasets. It consists of an attention based scanning step for segmenting the multi-isotopic pattern of peptide features along with charge and a sequence classification step for grouping those isotopes into potential peptide features. PointIso is the first point cloud based, arbitrary-precision deep learning network to address the problem and achieves 98% detection of high quality MS/MS identifications in a benchmark dataset, which is higher than several other widely used algorithms. Besides contributing to the proteomics study, we believe our novel segmentation technique should serve the general image processing domain as well.

cs.CV↗

arXiv2019

DeepNovoV2: Better de novo peptide sequencing with deep learning

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 mass spectrometry data. In this paper we introduce DeepNovoV2, the state-of-the-art model for peptide sequencing. In DeepNovoV2, a spectrum is directly represented as a set of (m/z, intensity) pairs, therefore it does not suffer from the accuracy-speed/memory trade-off problem. The model combines an order invariant network structure (T-Net) and recurrent neural networks and provides a complete end-to-end training and prediction framework to sequence patterns of peptides. Our experiments on a wide variety of data from different species show that DeepNovoV2 outperforms previous state-of-the-art methods, achieving 13.01-23.95\% higher accuracy at the peptide level.

cs.LG↗

arXiv2017

DeepIso: A Deep Learning Model for Peptide Feature Detection

Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based proteomics is a well-established research field with major applications such as identification of disease biomarkers, drug discovery, drug design and development. In proteomics, protein identification and quantification is a fundamental task, which is done by first enzymatically digesting it into peptides, and then analyzing peptides by LC-MS/MS instruments. The peptide feature detection and quantification from an LC-MS map is the first step in typical analysis workflows. In this paper we propose a novel deep learning based model, DeepIso, that uses Convolutional Neural Networks (CNNs) to scan an LC-MS map to detect peptide features and estimate their abundance. Existing tools are often designed with limited engineered features based on domain knowledge, and depend on pretrained parameters which are hardly updated despite huge amount of new coming proteomic data. Our proposed model, on the other hand, is capable of learning multiple levels of representation of high dimensional data through its many layers of neurons and continuously evolving with newly acquired data. To evaluate our proposed model, we use an antibody dataset including a heavy and a light chain, each digested by Asp-N, Chymotrypsin, Trypsin, thus giving six LC-MS maps for the experiment. Our model achieves 93.21% sensitivity with specificity of 99.44% on this dataset. Our results demonstrate that novel deep learning tools are desirable to advance the state-of-the-art in protein identification and quantification.

q-bio.QM↗

arXiv2017

Protein identification with deep learning: from abc to xyz

Proteins are the main workhorses of biological functions in a cell, a tissue, or an organism. Identification and quantification of proteins in a given sample, e.g. a cell type under normal/disease conditions, are fundamental tasks for the understanding of human health and disease. In this paper, we present DeepNovo, a deep learning-based tool to address the problem of protein identification from tandem mass spectrometry data. The idea was first proposed in the context of de novo peptide sequencing [1] in which convolutional neural networks and recurrent neural networks were applied to predict the amino acid sequence of a peptide from its spectrum, a similar task to generating a caption from an image. We further develop DeepNovo to perform sequence database search, the main technique for peptide identification that greatly benefits from numerous existing protein databases. We combine two modules de novo sequencing and database search into a single deep learning framework for peptide identification, and integrate de Bruijn graph assembly technique to offer a complete solution to reconstruct protein sequences from tandem mass spectrometry data. This paper describes a comprehensive protocol of DeepNovo for protein identification, including training neural network models, dynamic programming search, database querying, estimation of false discovery rate, and de Bruijn graph assembly. Training and testing data, model implementations, and comprehensive tutorials in form of IPython notebooks are available in our GitHub repository (https://github.com/nh2tran/DeepNovo).

cs.CE↗