F. Alexander Wolf

Postdoc in
Machine Learning Group

Institute of Computational Biology /
Helmholtz Munich

alex.*surname*@helmholtz-muenchen.de / +49 89 3187 2388 / building 58a / room 113

// Since 2015 // Postdoc in Machine Learning applied to Single-Cell Biology // 2013 - 2015 // PhD in Computational Physics at LMU Munich, spring 2015 at Columbia U // 2012 - 2013 // PhD in Electrical Engineering at Bosch Research, Stuttgart // 2011 - 2012 // Research Associate at U Augsburg // 2006 - 2011 // Studies of Physics at U Augsburg (MSc 2011, BSc 2009), ENS Paris and Georgetown U

More information here (CV), on google scholar, GitHub and on LinkedIn. News on twitter.

In the past years, machine learning has started to improve our understanding of molecular biology of single cells. In this context, we've written the single-cell analysis toolkit Scanpy [P22], which is currently the only package that can fully tackle the recently exploding dataset sizes. Most of the time, we develop new methods that target specific biological questions, hence originate from many different areas of machine learning. For example, *manifold learning* [P19], *causal inference* [T20] or deep learning [P20, see below]. With F. J. Theis.

The goal of the Data Science Bowl 2017 was to predict lung cancer based on 3d CT scans. We participated and won the 7th prize among almost 2000 teams; the best result among all participating German teams [code].

We showed how to reconstruct continuous biological processes using deep learning for the examples of cell cycle and disease progression in diabetic retinopathy [P20]. This is more powerful than approaches based on pseudotime-based trajectory inference.

Tensor Trains (MPS, DMRG) rank, with quantum Monte Carlo and the Numerical Renormalization Group, among the most popular numerical approaches for tackling the exponential computational complexity of models of strongly correlated materials. Being a topic in applied Mathematics since a few years, they have recently appeared within Machine Learning. I developed a way to use Tensor Trains within Dynamical Mean-Field Theory to improve our ability of simulating strongly correlated materials [O6,P12-P18, with U. Schollwöck]. Before that, I modeled diffusion-reaction processes to enhance material properties of solar cells [O5,P8-P11, with P. Pichler] and investigated the quantum Rabi model, which is, for example, important for understanding technical foundations of quantum computing [P6,P7, with D. Braak].

During studies, I focused on emergent properties of quantum-many body systems and their applications, for example, in showing how grain boundaries limit high-temperature superconductivity [P5, with T. Kopp]. Also, I did research on the non-equilibrium behavior of these systems [P1-P4], in particular, the fundamental problem of how such systems transition from an excited state to equilibrium. This happens through chaotic dynamics in the classical case, but is an active area of research in the quantum case. We showed that the transition proceeds through an intermediate, prethermalized, plateau for which a statistical theory applies - M. Kollar posed this as a problem for a summer project, during which I contributed the central analytical calculation [T1] to the highly cited paper [P3]. With M. Rigol, I investigated *collapse and revival oscillations* and *coherent expansions*, as suggested for realizing matter-wave lasers [P2,P4].

During high school, I tried to gain a better understanding of how philosophical and political ideas stimulate change in society and culture. My thesis investigated why J.-P. Sartre publicly supported the German terrorist group RAF upon his visit in Stammheim in 1974 [O1].

More information on google scholar, ORCID, ResearchGate, ResearcherID and arXiv.

P22 Scanpy for analysis of large-scale single-cell gene expression data

**FA Wolf**, P Angerer, FJ Theis

bioRxiv (2017) pdf code

P20 Reconstructing cell cycle and disease progression using deep learning

P Eulenberg, N Köhler, T Blasi, A Filby, AE Carpenter, P Rees, FJ Theis, **FA Wolf**

bioRxiv, accepted in Nat. Comms. (2016) pdf

P21 Model-based branching point detection in single-cell data by K-Branches clustering

NK Chlis, **FA Wolf**, FJ Theis

Bioinformatics (2017) bioRxiv pdf code

P19 Diffusion pseudotime robustly reconstructs branching cellular lineages

L Haghverdi, M Büttner, **FA Wolf**, F Buettner, FJ Theis

Nature Methods (2016) bioRxiv pdf code

P18 Imaginary-time matrix product state impurity solver for dynamical mean-field theory

**FA Wolf**, A Go, IP McCulloch, AJ Millis, U Schollwöck

Physical Review X (2015) arXiv pdf

P17 How to discretize a quantum bath for real-time evolution

Id Vega, U Schollwöck, **FA Wolf**

Physical Review B (2015) arXiv pdf

P16 Non-thermal melting of Neel order in the Hubbard model

K Balzer, **FA Wolf**, IP McCulloch, P Werner, M Eckstein

Physical Review X (2015) arXiv pdf

P15 Strictly Single-Site DMRG Algorithm with Subspace Expansion

C Hubig, IP McCulloch, U Schollwöck, **FA Wolf**

Physical Review B (2015) arXiv pdf

P14 Spectral functions and time evolution from the Chebyshev recursion

**FA Wolf**, JA Justiniano, IP McCulloch, U Schollwöck

Physical Review B (2015) arXiv pdf

P13 Solving nonequilibrium dynamical mean-field theory using matrix product states

**FA Wolf**, IP McCulloch, U Schollwöck

Physical Review B (2014) arXiv pdf

P12 Chebyshev matrix product state impurity solver for dynamical mean-field theory

**FA Wolf**, IP McCulloch, O Parcollet, U Schollwöck

Physical Review B (2014) arXiv pdf

P11 Electrical and Structural Analysis of Crystal Defects After High-Temperature Rapid Thermal Annealing of Highly Boron Ion-Implanted Emitters

J Krügener, R Peibst, **FA Wolf**, E Bugiel, T Ohrdes, F Kiefer, C Schollhorn, A Grohe, R Brendel, HJ Osten

IEEE Journal of Photovoltaics (2014) ResearchGate pdf

P10 Diffusion and Segregation Model for the Annealing of Silicon Solar Cells Implanted With Phosphorus

**FA Wolf**, A Martinez-Limia, D Grote, D Stichtenoth, P Pichler

IEEE Journal of Photovoltaics (2014) ResearchGate pdf

P9 Modeling the Annealing of Dislocation Loops in Implanted c-Si Solar Cells

**FA Wolf**, A Martinez-Limia, D Stichtenoth, P Pichler

IEEE Journal of Photovoltaics (2014) ResearchGate pdf

P8 A comprehensive model for the diffusion of boron in silicon in presence of fluorine

**FA Wolf**, A Martinez-Limia, P Pichler

Solid-State Electronics (2013) ResearchGate pdf

P7 Dynamical correlation functions and the quantum Rabi model

**FA Wolf**, F Vallone, G Romero, M Kollar, E Solano, D Braak

Physical Review A (2013) arXiv pdf

P6 Exact real-time dynamics of the quantum Rabi model

**FA Wolf**, M Kollar, D Braak

Physical Review A (2012) arXiv pdf

P5 Supercurrent through grain boundaries in the presence of strong correlations

**FA Wolf**, S Graser, F Loder, T Kopp

Physical Review Letters (2012) arXiv pdf

P4 Expansion of Bose-Hubbard Mott insulators in optical lattices

M Jreissaty, J Carrasquilla, **FA Wolf**, M Rigol

Physical Review A (2011) arXiv pdf

P3 Generalized Gibbs ensemble prediction of prethermalization plateaus and their relation to nonthermal steady states in integrable systems

M Kollar, **FA Wolf**, M Eckstein

Physical Review B (2011) arXiv pdf

P2 Collapse and revival oscillations as a probe for the tunneling amplitude in an ultra-cold Bose gas

**FA Wolf**, I Hen, M Rigol

Physical Review A (2010) arXiv pdf

P1 New theoretical approaches for correlated systems in nonequilibrium

M Eckstein, A Hackl, S Kehrein, M Kollar, M Moeckel, P Werner, **FA Wolf**

The European Physical Journal Special Topics (2009) arXiv pdf

O6 Solving dynamical mean-field theory using matrix product states

PhD Thesis (2015) pdf

O5 Modeling of annealing processes for ion-implanted single-crystalline silicon solar cells

PhD Thesis (2014) pdf

O4 Supercurrent through grain boundaries in the presence of strong correlations

Master’s Thesis (2011) pdf

O3 Collapse and revival oscillations as a probe for the tunneling amplitude in an ultra-cold Bose gas

Report (2010) pdf

O2 Orbital order in a spin-polarized two-band Hubbard model

Bachelor’s Thesis (2009) pdf

O1 Sartre à Stammheim: son éxistentialisme et l'idéologie de la fraction armée rouge

High School Thesis (2005) pdf

Slides available as *html* have been generated with
reveal.js.

T22 Scanpy for large-scale single-cell analysis

Retreat Seminar, *Single-Cell Mingling* of groups from Berlin and Munich

Charité Berlin (May 2017) pdf

T21 From Matrix Product States and Dynamical Mean-Field Theory to Machine Learning

Theory Colloquium, Department of Physics

LMU Munich (Nov 2016) pdf

T20 Causal Inference in Machine Learning

Retreat Seminar, Institute of Computational Biology, Helmholtz Munich

Kloster Irsee, Germany (Oct 2016) pdf

T19 Causality in branching time series

Retreat Seminar, Theoretical Systems Biology, German Cancer Research Center, Heidelberg

Kloster Ellwangen, Germany (Jun 2016) html

T18 Machine Learning Basics

Seminar, Research and Development Department

Nanotemper Technologies, Munich (Jun 2016) html

T17 Convolutional Neural Networks

Seminar, Institute of Computational Biology

Helmholtz Munich (May 2016) html

T16 Inference of gene regulation using pseudotemporal ordering of single cell snapshots

Seminar, Institute of Computational Biology

Helmholtz Munich (Feb 2016) html

T15 Matrix product state based quantum impurity solvers: DMFT + DMRG

Seminar, Theoretical Quantum Chemistry (G Chan)

Princeton U (May 2015) pdf

T14 Matrix product states: defeating the curse of dimensionality

Seminar, Condensed Matter Theory (AJ Millis)

Columbia U (Apr 2015) pdf

T13 Matrix product state based quantum impurity solvers: DMFT + DMRG

Contributed Talk, International conference on advanced numerical algorithms for strongly correlated quantum systems

U Würzburg (Feb 2015) pdf

T12 Tensor Trains: defeating the curse of dimensionality

Job Talk, Institute of Computational Biology (FJ Theis)

Helmholtz Munich (Feb 2015) pdf

T11 Spectral functions and time evolution from the Chebyshev recursion

Seminar, Theoretical Nanophysics (U Schollwöck, L Pollet)

LMU Munich (Dec 2014) pdf

T10 Matrix product state based quantum impurity solvers: DMFT + DMRG

Seminar, Many-body Theory (M Eckstein, M Potthoff)

U Hamburg / MPI Structure and Dynamics of Matter (Oct 2014) pdf

T9 Matrix product state based quantum impurity solvers: DMFT + DMRG

Retreat Seminar, DFG Forschergruppe 1807

U Würzburg (Jan 2014) pdf

T8 Matrix product state based quantum impurity solvers: DMFT + DMRG

Seminar, Theoretical Nanophysics (U Schollwöck, L Pollet)

LMU Munich (Nov 2013) pdf

T7 Modeling annealing processes for implanted c-Si solar cells

Institute Colloquium

Fraunhofer IISB, Erlangen (Jul 2013)

T6 A subjectivist view on probabilities in statistical mechanics

Seminar within Studienstiftung Summer School (C Beisbach, S Hartmann)

Schloss Neubeuern, Germany (Aug 2011) pdf

T5 Collapse and revival oscillations as a probe for the tunneling amplitude in an ultra-cold Bose gas

Job Talk, Theoretical Solid State Physics (J von Delft, S Kehrein)

LMU Munich (Jul 2011) pdf

T4 Supercurrent through grain boundaries in the presence of strong correlations

Seminar, Experimental Physics VI (J Mannhart)

U Augsburg (Jul 2011) pdf

T3 Bethe Ansatz: Heisenberg model and generalizations

Seminar, Theoretical Physics II (U Eckern)

U Augsburg (Jun 2011) pdf

T2 Collapse and revival oscillations as a probe for the tunneling amplitude in an ultra-cold Bose gas

Seminar, Theoretical Physics III (D Vollhardt)

U Augsburg (Jun 2010) pdf

T1 Statistical description of prethermalization plateaus

Seminar, Theoretical Physics III (D Vollhardt)

U Augsburg (Oct 2009) pdf