@inproceedings{pic:hal-04056181,

title = {A constrained Shannon-Fano entropy coder for image storage in synthetic DNA},

author = {Xavier Pic and Marc Antonini},

doi = {10.23919/EUSIPCO55093.2022.9909833},

year  = {2022},

date = {2022-01-01},

booktitle = {European Signal Processing Conference (EUSIPCO 2022)},

publisher = {IEEE},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}

@inproceedings{9835534,

title = {Optimizing the Accuracy of Randomized Embedding for Sequence Alignment},

author = {Yiqing Yan and Nimisha Chaturvedi and Raja Appuswamy},

doi = {10.1109/IPDPSW55747.2022.00036},

year  = {2022},

date = {2022-01-01},

booktitle = {International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}

@inproceedings{10.1145/3465998.3466012,

title = {XJoin: Portable, Parallel Hash Join across Diverse XPU Architectures with OneAPI},

author = {Eugenio Marinelli and Raja Appuswamy},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

booktitle = {International Workshop on Data Management on New Hardware (DaMoN 2021)},

abstract = {Modern server hardware is increasingly heterogeneous with a diverse mix of XPU architectures deployed across CPU, GPU, and FPGAs. However, till date, database developers have had to rely on either proprietary, architecture-specific solutions (like CUDA), or low-level, cross-architecture solutions that complicate development (like OpenCL). The lack of portable parallelism caused by the absence of a common high-level programming framework is one of the main reasons preventing a wider adoption of XPUs by database systems.In this paper, we take the first steps towards solving this problem using oneAPI-a cross-industry effort for developing an open, standards-based unified programming model that extends standard C++ to provide portable parallelism across diverse processor architectures. In particular, we port a recently-proposed, highly-optimized, GPU-based hash join algorithm from CUDA to Data Parallel C++ (DPC++). We then execute the hash join on multicore CPUs, integrated GPUs (Intel GEN9), and discrete GPUs (Intel DG1 and NVIDIA GeForce) without changing a single line of kernel code to demonstrate that DPC++ enables portable parallelism. We compare the performance of DPC++ kernels with hand-optimized CUDA kernels and model-based theoretical performance bounds to demonstrate the performance-portability trade off in using DPC++.},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}

@inproceedings{9506592,

title = {Decoding Of Nanopore-Sequenced Synthetic DNA Storing Digital Images},

author = {Eva Gil San Antonio and Melpomeni Dimopoulou and Marc Antonini and Pascal Barbry and Raja Appuswamy},

doi = {10.1109/ICIP42928.2021.9506592},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

booktitle = {2021 IEEE International Conference on Image Processing (ICIP)},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}

@inproceedings{9675366,

title = {Generative DNA: Representation Learning for DNA-based Approximate Image Storage},

author = {Giulio Franzese and Yiqing Yan and Giuseppe Serra and Ivan DÓnofrio and Raja Appuswamy and Pietro Michiardi},

doi = {10.1109/VCIP53242.2021.9675366},

year  = {2021},

date = {2021-01-01},

booktitle = {International Conference on Visual Communications and Image Processing (VCIP)},

pages = {01-05},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}

@inproceedings{dimopoulou:hal-02549746,

title = {Storing Digital Data into DNA: A Comparative Study of Quaternary Code Construction},

author = {Melpomeni Dimopoulou and Marc Antonini and Pascal Barbry and Raja Appuswamy},

url = {https://hal.archives-ouvertes.fr/hal-02549746},

year  = {2020},

date = {2020-01-01},

booktitle = {ICASSP},

address = {Barcelona, Spain},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}

@inproceedings{DBLP:conf/cidr/AppuswamyBBAMFM19,

title = {OligoArchive: Using DNA in the DBMS Storage Hierarchy},

author = {Raja Appuswamy and Kevin Le Brigand and Pascal Barbry and Marc Antonini and Olivier Madderson and Paul Freemont and James McDonald and Thomas Heinis},

url = {http://cidrdb.org/cidr2019/papers/p98-appuswamy-cidr19.pdf},

year  = {2019},

date = {2019-01-01},

booktitle = {CIDR 2019, 9th Biennial Conference on Innovative Data Systems Research, 

Asilomar, CA, USA, 2019},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}

@inproceedings{78110.1007/978-3-030-26807-7_3,

title = {Efficient Approximation of Sequence Hybridization},

author = {David Buterez and Thomas Heinis},

isbn = {978-3-030-26807-7},

year  = {2019},

date = {2019-01-01},

booktitle = {DNA Computing and Molecular Programming},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}

@inproceedings{10.1007/978-3-030-26807-7_31,

title = {Encoding Information in Primers},

author = {Jeremy Ling and Thomas Heinis},

isbn = {978-3-030-26807-7},

year  = {2019},

date = {2019-01-01},

booktitle = {DNA Computing and Molecular Programming},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}

@inproceedings{EURECOM+5841,

title = {A Biologically Constrained Encoding Solution for Long-term Storage of Images onto Synthetic DNA},

author = {Dimopoulou Melpomeni and Marc Antonini and Pascal Barbry and Raja Appuswamy},

url = {http://www.eurecom.fr/publication/5841},

year  = {2019},

date = {2019-01-01},

booktitle = {EUSIPCO 2019, 27th European Signal Processing Conference, Coruna, Spain},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}

@inproceedings{EURECOM+5858,

title = {Cold Storage Data Archives: More Than Just A Bunch of Tapes},

author = {Bunjamin Memishi and Raja Appuswamy and Marcus Paradies},

url = {http://www.eurecom.fr/publication/5858},

year  = {2019},

date = {2019-01-01},

booktitle = {DAMON 2019, 15th International Workshop on Data Management on New Hardware, Held with ACM SIGMOD/PODS, Amsterdam, Netherlands},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}

@inproceedings{EURECOM+5788,

title = {DNA Coding for Image Storage Using Image Compression Techniques},

author = {Melpomeni Dimopoulou and Marc Antonini and Pascal Barbry and Raja Appuswamy},

url = {http://www.eurecom.fr/publication/5788},

year  = {2018},

date = {2018-01-01},

booktitle = {CORESA 2018, 20emes journées d'étude et d'échange sur la COmpression et la REprésentation des Signaux Audiovisuels, Poitiers, France},

keywords = {},

pubstate = {published},

tppubtype = {inproceedings}

}