arXiv subjects

Joakim Andén

Publications and source records attributed to Joakim Andén.

24 records · Page 2Linked to original sources

arXiv2018

APPLE Picker: Automatic Particle Picking, a Low-Effort Cryo-EM Framework

Particle picking is a crucial first step in the computational pipeline of single-particle cryo-electron microscopy (cryo-EM). Selecting particles from the micrographs is difficult especially for small particles with low contrast. As high-resolution reconstruction typically requires hundreds of thousands of particles, manually picking that many particles is often too time-consuming. While semi-automated particle picking is currently a popular approach, it may suffer from introducing manual bias into the selection process. In addition, semi-automated particle picking is still somewhat time-consuming. This paper presents the APPLE (Automatic Particle Picking with Low user Effort) picker, a simple and novel approach for fast, accurate, and fully automatic particle picking. While our approach was inspired by template matching, it is completely template-free. This approach is evaluated on publicly available datasets containing micrographs of $β$-galactosidase and keyhole limpet hemocyanin projections.

cs.CV↗

arXiv2018

Structural Variability from Noisy Tomographic Projections

In cryo-electron microscopy, the 3D electric potentials of an ensemble of molecules are projected along arbitrary viewing directions to yield noisy 2D images. The volume maps representing these potentials typically exhibit a great deal of structural variability, which is described by their 3D covariance matrix. Typically, this covariance matrix is approximately low-rank and can be used to cluster the volumes or estimate the intrinsic geometry of the conformation space. We formulate the estimation of this covariance matrix as a linear inverse problem, yielding a consistent least-squares estimator. For $n$ images of size $N$-by-$N$ pixels, we propose an algorithm for calculating this covariance estimator with computational complexity $\mathcal{O}(nN^4+\sqrtκN^6 \log N)$, where the condition number $κ$ is empirically in the range $10$--$200$. Its efficiency relies on the observation that the normal equations are equivalent to a deconvolution problem in 6D. This is then solved by the conjugate gradient method with an appropriate circulant preconditioner. The result is the first computationally efficient algorithm for consistent estimation of 3D covariance from noisy projections. It also compares favorably in runtime with respect to previously proposed non-consistent estimators. Motivated by the recent success of eigenvalue shrinkage procedures for high-dimensional covariance matrices, we introduce a shrinkage procedure that improves accuracy at lower signal-to-noise ratios. We evaluate our methods on simulated datasets and achieve classification results comparable to state-of-the-art methods in shorter running time. We also present results on clustering volumes in an experimental dataset, illustrating the power of the proposed algorithm for practical determination of structural variability.

stat.AP↗

arXiv2017

Factor Analysis for Spectral Estimation

Power spectrum estimation is an important tool in many applications, such as the whitening of noise. The popular multitaper method enjoys significant success, but fails for short signals with few samples. We propose a statistical model where a signal is given by a random linear combination of fixed, yet unknown, stochastic sources. Given multiple such signals, we estimate the subspace spanned by the power spectra of these fixed sources. Projecting individual power spectrum estimates onto this subspace increases estimation accuracy. We provide accuracy guarantees for this method and demonstrate it on simulated and experimental data from cryo-electron microscopy.

math.ST↗

arXiv2015

Joint Time-Frequency Scattering for Audio Classification

We introduce the joint time-frequency scattering transform, a time shift invariant descriptor of time-frequency structure for audio classification. It is obtained by applying a two-dimensional wavelet transform in time and log-frequency to a time-frequency wavelet scalogram. We show that this descriptor successfully characterizes complex time-frequency phenomena such as time-varying filters and frequency modulated excitations. State-of-the-art results are achieved for signal reconstruction and phone segment classification on the TIMIT dataset.

cs.SD↗

arXiv2015

Covariance estimation using conjugate gradient for 3D classification in Cryo-EM

Classifying structural variability in noisy projections of biological macromolecules is a central problem in Cryo-EM. In this work, we build on a previous method for estimating the covariance matrix of the three-dimensional structure present in the molecules being imaged. Our proposed method allows for incorporation of contrast transfer function and non-uniform distribution of viewing angles, making it more suitable for real-world data. We evaluate its performance on a synthetic dataset and an experimental dataset obtained by imaging a 70S ribosome complex.

cs.CV↗

arXiv2014

Deep Scattering Spectrum

A scattering transform defines a locally translation invariant representation which is stable to time-warping deformations. It extends MFCC representations by computing modulation spectrum coefficients of multiple orders, through cascades of wavelet convolutions and modulus operators. Second-order scattering coefficients characterize transient phenomena such as attacks and amplitude modulation. A frequency transposition invariant representation is obtained by applying a scattering transform along log-frequency. State-the-of-art classification results are obtained for musical genre and phone classification on GTZAN and TIMIT databases, respectively.

cs.SD↗