Joakim Andén

Deep Scattering Spectrum

A scattering transform defines a locally translation invariant representation which is stable to time-warping deformation. 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.

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.

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.

Synthesizing developmental trajectories

Dynamical processes in biology are studied using an ever-increasing number of techniques, each of which brings out unique features of the system. One of the current challenges is to develop systematic approaches for fusing heterogeneous datasets into an integrated view of multivariable dynamics. We demonstrate that heterogeneous data fusion can be successfully implemented within a semi-supervised learning framework that exploits the intrinsic geometry of high-dimensional datasets. We illustrate our approach using a dataset from studies of pattern formation in Drosophila. The result is a continuous trajectory that reveals the joint dynamics of gene expression, subcellular protein localization, protein phosphorylation, and tissue morphogenesis. Our approach can be readily adapted to other imaging modalities and forms a starting point for further steps of data analytics and modeling of biological dynamics.

Low dimensional manifold embedding for scattering coefficients of intrapartum fetale heart rate variability.

Intrapartum fetal surveillance for early detection of fetal acidosis in clinical practice focuses on reducing neonatal morbidity via early detection. It is the subject of on going research studies attempting notably to improve detection performance by reducing false positive rate. In that context, the present contribution tailors to fetal heart rate variability analysis a graph-based dimensionality reduction procedure performed on scattering coefficients. Applied to a high quality and well-documented database constituted by obstetricians from a French academic hospital, the low dimensional embedding enables to distinguish between the temporal dynamics of healthy and acidotic fetuses, as well as to achieve satisfactory detection performance detection compared to those obtained by the clinical-benchmark FIGO criteria.

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.

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 template-based particle picking is currently a popular approach, it may suffer from introducing manual bias into the selection process. In addition, this approach 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 template-free particle picking. This approach is evaluated on publicly available datasets containing micrographs of β-galactosidase, T20S proteasome, 70S ribosome and keyhole limpet hemocyanin projections.