Dr.-Ing. Christian Rohlfing
![[team/Rohlfing_web.jpg]](https://www.ient.rwth-aachen.de/cms/uploads/images/team/Rohlfing_web.jpg "[team/Rohlfing_web.jpg]")
Oberingenieur
Arbeitsgruppe Bio Signal Processing
Kontakt
E-Mail: rohlfing@ient.rwth-aachen.de
(PGP Public Key: 65EB9123)
Tel.: +49 241 80-27672
Fax: +49 241 80-22196
Sprechzeiten
Freitag, 10:00 bis 12:00 und 14:00 bis 16:00 Uhr nach Vereinbarung
Zoom / Raum 23
Anschrift
Dr.-Ing. Christian Rohlfing
Institut für Nachrichtentechnik
RWTH Aachen
D-52056 Aachen
Forschungsthema
Kompression von Genomdaten
Seit dem Aufkommen der DNA-Sequenzierungsmethoden der nächsten Generation (engl. next generation sequencing, NGS)
haben sich die Sequenzierungskosten des menschlichen Genoms in den letzten zehn Jahren um den Faktor 1000 verringert.
Demzufolge wächst das Volumen der weltweit anfallenden Daten (ungefähr 2 TB Rohdaten pro menschlichem Genom)
derzeit rapide an und verdoppelt sich ca. alle sieben Monate.
Effiziente Kompression der Genomdaten kann an mehreren Stellen betrieben werden:
![[ResearchTopics/block_diag.png]](https://www.ient.rwth-aachen.de/cms/uploads/images/ResearchTopics/block_diag.png "[ResearchTopics/block_diag.png]")
Nach der NGS-Sequenzierung liegen zunächst Fragmente, sogenannte Reads, vor. Darin ist die Abfolge der vier Nukleinbasen (Adenin, Guanin, Cytosin, und Thymin als elementare Bestandteile der DNA) mit ihrem jeweiligen Anfangsbuchstaben codiert. Bei NGS-Verfahren haben Reads üblicherweise eine Länge von 300 Basen. Durch einen Alignment-Schritt werden die Position sowie lokale Änderungen (z.B. Einfügungen und Löschungen) der Reads im Genom anhand eines Referenzgenoms bestimmt. Mithilfe dieser Informationen kann anschließend auf die einzigartigen Charakteristiken des zu untersuchenden Organismus, sogenannte genomische Varianten, geschlossen werden. Da sich sowohl Referenzgenome als auch Algorithmen zum Alignment häufiger ändern können, werden oft alle Daten in diesem Prozess archiviert und müssen daher effizient komprimiert werden.
Durch die hohe Redundanz der Basen in Reads bieten sich zur Kompression Verfahren der Entropiecodierung an, die auch im aktuellen MPEG-G Standard "Coding of Genomic Information" (ISO/IEC 23092-2) eingesetzt werden. Am Institut wurde Prädiktion von Basenfolgen mit anschließender (arithmetischer) Codierung von Residuen untersucht. Im Fall von Genomvarianten können Millionen von Varianten von bis zu Tausenden von Individuen vorliegen. Auch hier können lokale Statistiken, z.B. pro Individuum oder pro Variation, geschickt zur Kompression ausgenutzt werden. Am Institut konnte gezeigt werden, dass durch Kontext-basierte Codierung ähnliche Kompressionsraten erzielt werden wie durch deutlich komplexere Referenzverfahren. Das Institut nimmt in diesem Kontext an aktuellen Standardisierungsaktivitäten von MPEG-G "Coding of Genomic Annotations" (ISO/IEC 23092-6) teil.
Publikationen
T. Meyer, D. Mehlem, and C. Rohlfing, “Adaptive entropy coding of graph transform coefficients for point cloud attribute compression,” in Visual Communications and Image Processing VCIP '23, (Jeju, South Korea), IEEE, Piscataway, Dec. 2023. [ bib | DOI | .pdf ]
C. Rohlfing, T. Meyer, J. Schneider, and J. Voges, “Python wrapper for context-based adaptive binary arithmetic coding,” in Visual Communications and Image Processing VCIP '23, (Jeju, South Korea), IEEE, Piscataway, Dec. 2023. [ bib | DOI | .pdf ]
Y. Gunawan Adhisantoso, J. Voges, C. Rohlfing, V. Tunev, J.-R. Ohm, and J. Ostermann, “GVC: Efficient random access compression for gene sequence variations,” in BMC Bioinformatics, vol. 24, Mar. 2023. [ bib | DOI | .pdf ]
T. Meyer, M. Meyer, D. Mehlem, and C. Rohlfing, “Attribute-aware partitioning for graph-based point cloud attribute coding,” in Proc. of International Picture Coding Symposium PCS '22, (San Jose, USA), pp. 121–125, IEEE, Piscataway, Dec. 2022. [ bib | DOI | .pdf ]
A. Jose, D. Filbert, C. Rohlfing, and J.-R. Ohm, “Deep hashing with hash center update for efficient image retrieval,” in Proc. of IEEE International Conference on Acoustics, Speech and Signal Processing ICASSP '22, pp. 4773 – 4777, IEEE, Piscataway, May 2022. [ bib | DOI ]
A. Jose, E. S. Ottlik, C. Rohlfing, and J.-R. Ohm, “Optimized feature space learning for generating efficient binary codes for image retrieval,” Signal Processing: Image Communication, vol. 100, p. 116529, Jan. 2022. [ bib | DOI ]
J. Schneider and C. Rohlfing, “Dictionary learning-based reference picture resampling in VVC,” in Visual Communications and Image Processing VCIP '21, (Munich), IEEE, Piscataway, Dec. 2021. [ bib | .pdf ]
H. B. Golestani, J. Sauer, C. Rohlfing, and J.-R. Ohm, “3D Geometry-based Global Motion Compensation for VVC,” in IEEE International Conference on Image Processing (ICIP), (Anchorage-Alaska, US), IEEE, Piscataway, Sept. 2021. [ bib ]
J. Schneider, D. Mehlem, M. Meyer, and C. Rohlfing, “Sparse Coding-based Intra Prediction in VVC,” in Picture Coding Symposium (PCS'21), (Bristol, UK), IEEE, Piscataway, June 2021. [ bib | .pdf ]
M. Meyer, J. Wiesner, and C. Rohlfing, “Optimized convolutional neural networks for video intra prediction,” in Proc. of IEEE International Conference on Image Processing ICIP '20, IEEE, Piscataway, Oct. 2020. [ bib | more… | .pdf ]
J. Schneider, J. Sauer, and C. Rohlfing, “Adaptive Resolution Change using Uncoded Areas and Dictionary Learning-based Super-Resolution in Versatile Video Coding,” in Proc. of IEEE International Conference on Acoustics, Speech and Signal Processing ICASSP '20, (Barcelona, Spain), pp. 2203–2207, IEEE, Piscataway, May 2020. [ bib | DOI | .pdf ]
H. B. Golestani, C. Rohlfing, and J.-R. Ohm, “Reference Picture Synthesis for Video Sequences Captured with a Monocular Moving Camera,” in IEEE International Conference on Visual Communications and Image Processing (VCIP), (Sydney, AUSTRALIA), IEEE, Piscataway, Dec. 2019. [ bib | more… | https ]
M. Bläser, H. Gao, S. Esenlik, E. Alshina, Z. Zhao, C. Rohlfing, and E. Steinbach, “Low-Complexity Geometric Inter-Prediction for Versatile Video Coding,” in Proc. of International Picture Coding Symposium PCS '19, IEEE, Piscataway, Nov. 2019. [ bib ]
M. Meyer, J. Wiesner, J. Schneider, and C. Rohlfing, “Convolutional neural networks for video intra prediction using cross-component adaptation,” in Proc. of IEEE International Conference on Acoustics, Speech and Signal Processing ICASSP '19, pp. 1607–1611, IEEE, Piscataway, May 2019. [ bib | more… | .pdf ]
C. Rohlfing, Low-bit-rate informed source separation using decoder NTF and efficient parameter coding, vol. 18 of Aachen Series on Multimedia and Communications Engineering. Aachen: Shaker Verlag, July 2018. [ bib | DOI | .pdf ]
A. Liutkus, C. Rohlfing, and A. Deleforge, “Audio source separation with magnitude priors: the BEADS model,” in Proc. of IEEE International Conference on Acoustics, Speech and Signal Processing ICASSP '18, pp. 56–60, IEEE, Piscataway, Apr. 2018. [ bib | DOI | more… | .pdf ]
M. Bläser, C. Rohlfing, Y. Gao, and M. Wien, “Adaptive coding of non-negative factorization parameters with application to informed source separation,” in Proc. of IEEE International Conference on Acoustics, Speech and Signal Processing ICASSP '18, pp. 751–755, IEEE, Piscataway, Apr. 2018. [ bib | DOI | more… | .pdf ]
C. Rohlfing, J. E.Cohen, and A. Liutkus, “Very low bitrate spatial audio coding with dimensionality reduction,” in Proc. of IEEE International Conference on Acoustics, Speech and Signal Processing ICASSP '17, pp. 741–745, IEEE, Piscataway, Mar. 2017. [ bib | DOI | more… | .pdf ]
C. Rohlfing, A. Liutkus, and J. Becker, “Quantization-aware parameter estimation for audio upmixing,” in Proc. of IEEE International Conference on Acoustics, Speech and Signal Processing ICASSP '17, pp. 746–750, IEEE, Piscataway, Mar. 2017. [ bib | DOI | more… | .pdf ]
C. Rohlfing and J. Becker, “Generalized constraints for NMF with application to informed source separation,” in Proc. of European Signal Processing Conference EUSIPCO '16, pp. 597–601, IEEE, Piscataway, Aug. 2016. [ bib | DOI | more… | .pdf ]
C. Rohlfing, J. Becker, and M. Wien, “NMF-based informed source separation,” in Proc. of IEEE International Conference on Acoustics, Speech and Signal Processing ICASSP '16, pp. 474–478, IEEE, Piscataway, Mar. 2016. [ bib | DOI | more… | .pdf ]
C. Rohlfing and J. Becker, “Extended semantic initialization for NMF-based audio source separation,” in Proc. of IEEE International Workshop on Intelligent Signal Processing and Communication Systems ISPACS '15, (Nusa Dua, Bali, Indonesia), pp. 95–100, IEEE, Piscataway, Nov. 2015. [ bib | DOI | .pdf ]
J. Becker, M. Rohbeck, and C. Rohlfing, “Adaptive weights for NMF with additional priors,” in Proc. of IEEE International Workshop on Intelligent Signal Processing and Communication Systems ISPACS '15, (Nusa Dua, Bali, Indonesia), IEEE, Piscataway, Nov. 2015. [ bib | DOI | .pdf ]
J. Becker and C. Rohlfing, “Component-adaptive priors for NMF,” in Latent Variable Analysis and Signal Separation, Springer, Heidelberg/Berlin, Aug. 2015. [ bib | .pdf ]
J. Becker, M. Menzel, and C. Rohlfing, “Complex SVD initialization for NMF source separation on audio spectrograms,” in Fortschritte der Akustik DAGA '15, (Nürnberg, Germany), Mar. 2015. [ bib | .pdf ]
J. Becker, C. Sohn, and C. Rohlfing, “NMF with spectral and temporal continuity criteria for monaural sound source separation,” in Proc. of European Signal Processing Conference EUSIPCO '14, (Lisbon, Portugal), IEEE, Piscataway, Sept. 2014. [ bib | .pdf ]
J. Becker and C. Rohlfing, “Custom sized non-negative matrix factor deconvolution for sound source separation,” in Proc. of IEEE International Conference on Acoustics, Speech and Signal Processing ICASSP '14, (Florence, Italy), IEEE, Piscataway, May 2014. [ bib | DOI | .pdf ]
C. Rohlfing and J. Becker, “Generalized cepstral features for clustering in blind audio source separation,” in Fortschritte der Akustik DAGA '14, (Düsseldorf, Germany), Mar. 2014. [ bib | .pdf ]
J. Becker and C. Rohlfing, “A segmental spectral flatness measure for harmonic-percussive discrimination,” in Proc. of International Student Conference on Electrical Engineering POSTER '13, (Prague, Czech Republic), May 2013. [ bib | .pdf ]
C. Rohlfing, H. Krüger, and P. Vary, “Logarithmic cubic vector quantization: Concept and analysis,” in Proc. of International Symposium on Information Theory and its Applications (ISITA), (Honolulu, USA), pp. 294–298, IEEE, Piscataway, Oct. 2012. [ bib | .pdf ]
C. Rohlfing, H. Krüger, and P. Vary, “Logarithmic cubic vector quantization,” in Proc. of ITG-Fachtagung Sprachkommunikation, (Braunschweig, Germany), pp. 203–206, IEEE, Piscataway, Sept. 2012. [ bib | .pdf ]
C. Rohlfing, M. Spiertz, and V. Gnann, “Score-informed sparseness for source separation,” in Fortschritte der Akustik DAGA '11, (Düsseldorf, Germany), Mar. 2011. [ bib | .pdf ]
Standardisierungsdokumente
H. B. Golestani, C. Rohlfing, and M. Wien, “AHG12: 3D Geometry for Global Motion Compensation,” Doc. JVET-V0129, Joint Video Experts Team of ITU-T VCEG and ISO/IEC MPEG, Teleconference, online, Apr. 2021. [ bib ]
M. Meyer and C. Rohlfing, “Ahg11-related: Investigation on cnn-based intra prediction,” Doc. JVET-U0106, Joint Video Exploration Team (on Future Video coding) of ITU-T VCEG and ISO/IEC MPEG, online, Jan. 2021. [ bib | https ]
J. Voges, F. Müntefering, Y. Gunawan, J. Ahmad, S. Chandak, L. Mainzer, M. Hernaez, I. Ochoa, C. Rohlfing, and J. Ostermann, “Draft text reference encoder software,” Doc. m54889, ISO/IEC JTC1/SC29/WG11, Teleconference, online, Oct. 2020. [ bib | http ]
Y. Gunawan, J. Voges, C. Rohlfing, and J. Ostermann, “Extension to method for coding of genomic variants,” Doc. m55355, ISO/IEC JTC1/SC29/WG11, Teleconference, online, Oct. 2020. [ bib | http ]
Y. Gunawan, J. Voges, C. Rohlfing, and J. Ostermann, “Method for the coding of genotype likelihood of variants,” Doc. m55356, ISO/IEC JTC1/SC29/WG11, Teleconference, online, Oct. 2020. [ bib | http ]
Y. Gunawan, J. Voges, C. Rohlfing, and J. Ostermann, “CE3 Results LUH and RWTH Aachen on GL Field of VCF,” Doc. m55357, ISO/IEC JTC1/SC29/WG11, Teleconference, online, Oct. 2020. [ bib | http ]
Y. Gunawan, V. Tunev, J. Voges, and C. Rohlfing, “MPEG-G Part 6 CE3 Results Leibniz University Hannover, RWTH Aachen University,” Doc. m53496, ISO/IEC JTC1/SC29/WG11, Teleconference, online, Apr. 2020. [ bib | http ]
D. Mehlem and C. Rohlfing, “Versatile Video Coding for VPCC,” Doc. JVET-R0376, Joint Video Exploration Team (on Future Video coding) of ITU-T VCEG and ISO/IEC MPEG, Teleconference, online, Apr. 2020. [ bib | http ]
D. Mehlem and C. Rohlfing, “[V-PCC] Versatile Video Coding for VPCC,” Doc. m53510, ISO/IEC JTC1/SC29/WG11, Teleconference, online, Apr. 2020. [ bib | http ]
J. Voges, C. Rohlfing, V. Tunev, Y. Gunawan, and J. Ostermann, “Method for the coding of genomic variants,” Doc. m52489, ISO/IEC JTC1/SC29/WG11, Brussels, Belgium, Jan. 2020. [ bib | http ]
C. Rohlfing, V. Tunev, and J. Voges, “Proposed updates to the MPEG-G genomic information database,” Doc. m51192, ISO/IEC JTC1/SC29/WG11, Geneva, Switzerland, Oct. 2019. [ bib | http ]
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