Christian Rohlfing, Dr.-Ing.
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Chief Engineer
Bio Signal Processing Group
Contact Information
email: rohlfing@ient.rwth-aachen.de
(PGP Public Key: 65EB9123)
phone: +49 241 80-27672
fax: +49 241 80-22196
Visiting Times
Friday, 10:00 to 12:00 and 14:00 to 16:00, by appointment
Zoom / Room 23
Mailing Address
Dr.-Ing. Christian Rohlfing
Institut für Nachrichtentechnik
RWTH Aachen
D-52056 Aachen
Research Topic
Compression of Genomdata
With the advent of next generation sequencing (NGS) methods, the cost of sequencing the human genome has decreased by a factor of 1000 over the past decade. As a result, the volume of data generated worldwide (approximately 2 TB of raw data per human genome) is currently growing rapidly and doubling approximately every seven months.
Efficient compression of genomic data can be conducted in several places:
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The output NGS sequencing are so-called reads, small fragments of genomic data. The sequence of the four nucleobases (adenine, guanine, cytosine and thymine as basic components of DNA) is coded with their respective first letter. The length of NGS reads is usually around 300 bases. The position as well as local changes (e.g. insertions and deletions) of the reads in the genome are determined by means of an alignment step using a reference genome. With the help of this information, conclusions can be drawn about the unique characteristics of the organism to be examined, so-called genomic variants. Since both reference genomes and algorithms for alignment are updated or modified quite often, all data is archived in this process and must therefore be efficiently compressed.
Due to the high redundancy of the bases in reads, entropy coding methods are available for compression, which are also used in the current MPEG-G standard “Coding of Genomic Information” (ISO / IEC 23092-2). At the institute, prediction of base sequences with subsequent (arithmetic) coding of residuals is investigated. In the case of genome variants, there are usually millions of variants of up to thousands of individuals at hand. Local statistics, e.g. per individual or per variation, can be exploited for compression. At the institute it was possible to show that context-based coding achieves compression rates similar to those achieved with significantly more complex reference methods. In this context, the institute participates in standardization activities of MPEG-G "Coding of Genomic Annotations" (ISO / IEC 23092-6).
Publications
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 ]
Standard Documents
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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