arXiv subjects

I-Ping Tu

Publications and source records attributed to I-Ping Tu.

8 recordsLinked to original sources

arXiv2021

Two-stage dimension reduction for noisy high-dimensional images and application to Cryogenic Electron Microscopy

Principal component analysis (PCA) is arguably the most widely used dimension-reduction method for vector-type data. When applied to a sample of images, PCA requires vectorization of the image data, which in turn entails solving an eigenvalue problem for the sample covariance matrix. We propose herein a two-stage dimension reduction (2SDR) method for image reconstruction from high-dimensional noisy image data. The first stage treats the image as a matrix, which is a tensor of order 2, and uses multilinear principal component analysis (MPCA) for matrix rank reduction and image denoising. The second stage vectorizes the reduced-rank matrix and achieves further dimension and noise reduction. Simulation studies demonstrate excellent performance of 2SDR, for which we also develop an asymptotic theory that establishes consistency of its rank selection. Applications to cryo-EM (cryogenic electronic microscopy), which has revolutionized structural biology, organic and medical chemistry, cellular and molecular physiology in the past decade, are also provided and illustrated with benchmark cryo-EM datasets. Connections to other contemporaneous developments in image reconstruction and high-dimensional statistical inference are also discussed.

eess.IV↗

arXiv2020

Cryo-RALib -- a modular library for accelerating alignment in cryo-EM

Thanks to automated cryo-EM and GPU-accelerated processing, single-particle cryo-EM has become a rapid structure determination method that permits capture of dynamical structures of molecules in solution, which has been recently demonstrated by the determination of COVID-19 spike protein in March, shortly after its breakout in late January 2020. This rapidity is critical for vaccine development in response to emerging pandemic. This explains why a 2D classification approach based on multi-reference alignment (MRA) is not as popular as the Bayesian-based approach despite that the former has advantage in differentiating structural variations under low signal-to-noise ratio. This is perhaps because that MRA is a time-consuming process and a modular GPU-acceleration library for MRA is lacking. Here, we introduce a library called Cryo-RALib that expands the functionality of CUDA library used by GPU ISAC. It contains a GPU-accelerated MRA routine for accelerating MRA-based classification algorithms. In addition, we connect the cryo-EM image analysis with the python data science stack so as to make it easier for users to perform data analysis and visualization. Benchmarking on the TaiWan Computing Cloud (TWCC) container shows that our implementation can accelerate the computation by one order of magnitude. The library is available at https://github.com/phonchi/Cryo-RAlib.

q-bio.QM↗

arXiv2019

An Evaluation of Bitcoin Address Classification based on Transaction History Summarization

Bitcoin is a cryptocurrency that features a distributed, decentralized and trustworthy mechanism, which has made Bitcoin a popular global transaction platform. The transaction efficiency among nations and the privacy benefiting from address anonymity of the Bitcoin network have attracted many activities such as payments, investments, gambling, and even money laundering in the past decade. Unfortunately, some criminal behaviors which took advantage of this platform were not identified. This has discouraged many governments to support cryptocurrency. Thus, the capability to identify criminal addresses becomes an important issue in the cryptocurrency network. In this paper, we propose new features in addition to those commonly used in the literature to build a classification model for detecting abnormality of Bitcoin network addresses. These features include various high orders of moments of transaction time (represented by block height) which summarizes the transaction history in an efficient way. The extracted features are trained by supervised machine learning methods on a labeling category data set. The experimental evaluation shows that these features have improved the performance of Bitcoin address classification significantly. We evaluate the results under eight classifiers and achieve the highest Micro-F1/Macro-F1 of 87%/86% with LightGBM.

cs.CR↗

arXiv2018

Personalized Difficulty Adjustment for Countering the Double-Spending Attack in Proof-of-Work Consensus Protocols

Bitcoin is the first secure decentralized electronic currency system. However, it is known to be inefficient due to its proof-of-work (PoW) consensus algorithm and has the potential hazard of double spending. In this paper, we aim to reduce the probability of double spending by decreasing the probability of consecutive winning. We first formalize a PoW-based decentralized secure network model in order to present a quantitative analysis. Next, to resolve the risk of double spending, we propose the personalized difficulty adjustment (PDA) mechanism which modifies the difficulty of each participant such that those who win more blocks in the past few rounds have a smaller probability to win in the next round. To analyze the performance of the PDA mechanism, we observe that the system can be modeled by a high-order Markov chain. Finally, we show that PDA effectively decreases the probability of consecutive winning and results in a more trustworthy PoW-based system.

cs.CR↗

arXiv2015

Functional Inverse Regression in an Enlarged Dimension Reduction Space

We consider an enlarged dimension reduction space in functional inverse regression. Our operator and functional analysis based approach facilitates a compact and rigorous formulation of the functional inverse regression problem. It also enables us to expand the possible space where the dimension reduction functions belong. Our formulation provides a unified framework so that the classical notions, such as covariance standardization, Mahalanobis distance, SIR and linear discriminant analysis, can be naturally and smoothly carried out in our enlarged space. This enlarged dimension reduction space also links to the linear discriminant space of Gaussian measures on a separable Hilbert space.

math.ST↗

arXiv2014

$γ$-SUP: A clustering algorithm for cryo-electron microscopy images of asymmetric particles

Cryo-electron microscopy (cryo-EM) has recently emerged as a powerful tool for obtaining three-dimensional (3D) structures of biological macromolecules in native states. A minimum cryo-EM image data set for deriving a meaningful reconstruction is comprised of thousands of randomly orientated projections of identical particles photographed with a small number of electrons. The computation of 3D structure from 2D projections requires clustering, which aims to enhance the signal to noise ratio in each view by grouping similarly oriented images. Nevertheless, the prevailing clustering techniques are often compromised by three characteristics of cryo-EM data: high noise content, high dimensionality and large number of clusters. Moreover, since clustering requires registering images of similar orientation into the same pixel coordinates by 2D alignment, it is desired that the clustering algorithm can label misaligned images as outliers. Herein, we introduce a clustering algorithm $γ$-SUP to model the data with a $q$-Gaussian mixture and adopt the minimum $γ$-divergence for estimation, and then use a self-updating procedure to obtain the numerical solution. We apply $γ$-SUP to the cryo-EM images of two benchmark macromolecules, RNA polymerase II and ribosome. In the former case, simulated images were chosen to decouple clustering from alignment to demonstrate $γ$-SUP is more robust to misalignment outliers than the existing clustering methods used in the cryo-EM community. In the latter case, the clustering of real cryo-EM data by our $γ$-SUP method eliminates noise in many views to reveal true structure features of ribosome at the projection level.

stat.AP↗

arXiv2011

On Multilinear Principal Component Analysis of Order-Two Tensors

Principal Component Analysis (PCA) is a commonly used tool for dimension reduction in analyzing high dimensional data; Multilinear Principal Component Analysis (MPCA) has the potential to serve the similar function for analyzing tensor structure data. MPCA and other tensor decomposition methods have been proved effective to reduce the dimensions for both real data analyses and simulation studies (Ye, 2005; Lu, Plataniotis and Venetsanopoulos, 2008; Kolda and Bader, 2009; Li, Kim and Altman, 2010). In this paper, we investigate MPCA's statistical properties and provide explanations for its advantages. Conventional PCA, vectorizing the tensor data, may lead to inefficient and unstable prediction due to its extremely large dimensionality. On the other hand, MPCA, trying to preserve the data structure, searches for low-dimensional multilinear projections and decreases the dimensionality efficiently. The asymptotic theories for order-two MPCA, including asymptotic distributions for principal components, associated projections and the explained variance, are developed. Finally, MPCA is shown to improve conventional PCA on analyzing the {\sf Olivetti Faces} data set, by constructing more module oriented basis in reconstructing the test faces.

math.ST↗

arXiv2011

Estimate the Occurrence Rate of the DNA Palindromes

A DNA palindrome is a segment of double-stranded DNA sequence with inver- sion symmetry which may form secondary structures conferring significant biolog- ical functions ranging from RNA transcription to DNA replication. To test if the clusters of DNA palindromes distribute randomly is an interesting bioinformatic problem, where the occurrence rate of the DNA palindromes is a key estimator for setting up a test. The most commonly used statistics for estimating the occur- rence rate for scan statistics is the average rate. However, in our simulation, the average rate may double the null occurrence rate of DNA palindromes due to hot spot regions of 3000 bp's in a herpes virus genome. Here, we propose a formula to estimate the occurrence rate through an analytic derivation under a Markov assumption on DNA sequence. Our simulation study shows that the performance of this method has improved the accuracy and robustness against hot spots, as compared to the commonly used average rate. In addition, we derived analytical formula for the moment-generating functions of various statistics under a Markov model, enabling further calculations of p-values.

stat.AP↗