[{"external_id":{"isi":["001396233806078"]},"oa_version":"Submitted Version","OA_place":"repository","day":"19","month":"04","year":"2024","oa":1,"date_published":"2024-04-19T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_status":"published","abstract":[{"text":"Efficient utilization of large-scale biobank data is crucial for inferring the genetic basis of disease and predicting health outcomes from the DNA. Yet we lack efficient, accurate methods that scale to data where electronic health records are linked to whole genome sequence information. To address this issue, our paper develops a new algorithmic paradigm based on Approximate Message Passing (AMP), which is specifically tailored for genomic prediction and association testing. Our method yields comparable out-of-sample prediction accuracy to the state of the art on UK Biobank traits, whilst dramatically improving computational complexity, with a 8x-speed up in the run time. In addition, AMP theory provides a joint association testing framework, which outperforms the currently used REGENIE method, in roughly a third of the compute time. This first, truly large-scale application of the AMP framework lays the foundations for a far wider range of statistical analyses for hundreds of millions of variables measured on millions of people.","lang":"eng"}],"_id":"17147","publisher":"IEEE","main_file_link":[{"url":"https://openreview.net/forum?id=aQYCDxfZV0","open_access":"1"}],"date_created":"2024-06-16T22:01:07Z","author":[{"last_name":"Depope","first_name":"Al","full_name":"Depope, Al","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli"},{"orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","last_name":"Robinson","first_name":"Matthew Richard"}],"doi":"10.1109/ICASSP48485.2024.10447198","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181"}],"type":"conference","corr_author":"1","department":[{"_id":"MaMo"},{"_id":"MaRo"}],"status":"public","publication":"2024 IEEE International Conference on Acoustics, Speech, and Signal Processing","citation":{"ama":"Depope A, Mondelli M, Robinson MR. Inference of genetic effects via approximate message passing. In: <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>. IEEE; 2024:13151-13155. doi:<a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">10.1109/ICASSP48485.2024.10447198</a>","apa":"Depope, A., Mondelli, M., &#38; Robinson, M. R. (2024). Inference of genetic effects via approximate message passing. In <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i> (pp. 13151–13155). Seoul, Korea: IEEE. <a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">https://doi.org/10.1109/ICASSP48485.2024.10447198</a>","ieee":"A. Depope, M. Mondelli, and M. R. Robinson, “Inference of genetic effects via approximate message passing,” in <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, Seoul, Korea, 2024, pp. 13151–13155.","chicago":"Depope, Al, Marco Mondelli, and Matthew Richard Robinson. “Inference of Genetic Effects via Approximate Message Passing.” In <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, 13151–55. IEEE, 2024. <a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">https://doi.org/10.1109/ICASSP48485.2024.10447198</a>.","ista":"Depope A, Mondelli M, Robinson MR. 2024. Inference of genetic effects via approximate message passing. 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing. ICASSP: International Conference on Acoustics, Speech and Signal Processing, 13151–13155.","mla":"Depope, Al, et al. “Inference of Genetic Effects via Approximate Message Passing.” <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, IEEE, 2024, pp. 13151–55, doi:<a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">10.1109/ICASSP48485.2024.10447198</a>.","short":"A. Depope, M. Mondelli, M.R. Robinson, in:, 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing, IEEE, 2024, pp. 13151–13155."},"page":"13151-13155","scopus_import":"1","isi":1,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"start_date":"2024-04-14","name":"ICASSP: International Conference on Acoustics, Speech and Signal Processing","end_date":"2024-04-19","location":"Seoul, Korea"},"quality_controlled":"1","OA_type":"green","title":"Inference of genetic effects via approximate message passing","publication_identifier":{"issn":["1520-6149"],"isbn":["9798350344851"]},"acknowledgement":"This work was supported by a Lopez-Loreta Prize to MM, an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and core funding from ISTA. The authors thank Philip Schniter, Matthew Stephens and Pragya Sur for valuable suggestions on an early version of the work. The authors acknowledge the participants and investigators of the UK Biobank study. High-performance\r\ncomputing was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","date_updated":"2026-07-13T14:57:55Z","article_processing_charge":"No"},{"abstract":[{"text":"This paper proposes a novel cooperative approach for two-hop amplify-and-forward (A&F) relaying that exploits both the signal forwarded by the relay and the one directly transmitted by the source in impulse-radio ultra-wideband (IR-UWB) systems. Specifically, we focus on a non-coherent setup employing a double-differential encoding scheme at the source node and a single differential demodulation at the relay and destination. The log-likelihood ratio based decision rule is derived at the destination node. A semi-analytical power allocation strategy is presented by evaluating a closed-form expression for the effective signal to noise ratio (SNR) at the destination, which is maximized by exhaustive search. Numerical simulations show that the proposed system outperforms both the direct transmission with single differential encoding and the non-cooperative multi-hop approach in different scenarios.","lang":"eng"}],"publication_status":"published","citation":{"ieee":"M. Mondelli, Q. Zhou, X. Ma, and V. Lottici, “A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems,” in <i>2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)</i>, Kyoto, Japan, 2012, pp. 2905–2908.","apa":"Mondelli, M., Zhou, Q., Ma, X., &#38; Lottici, V. (2012). A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. In <i>2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)</i> (pp. 2905–2908). Kyoto, Japan: IEEE. <a href=\"https://doi.org/10.1109/icassp.2012.6288524\">https://doi.org/10.1109/icassp.2012.6288524</a>","ama":"Mondelli M, Zhou Q, Ma X, Lottici V. A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. In: <i>2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)</i>. IEEE; 2012:2905-2908. doi:<a href=\"https://doi.org/10.1109/icassp.2012.6288524\">10.1109/icassp.2012.6288524</a>","short":"M. Mondelli, Q. Zhou, X. Ma, V. Lottici, in:, 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), IEEE, 2012, pp. 2905–2908.","ista":"Mondelli M, Zhou Q, Ma X, Lottici V. 2012. A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems. 2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP). ICASSP: International Conference on Acoustics, Speech and Signal Processing, 2905–2908.","mla":"Mondelli, Marco, et al. “A Cooperative Approach for Amplify-and-Forward Differential Transmitted Reference IR-UWB Relay Systems.” <i>2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)</i>, IEEE, 2012, pp. 2905–08, doi:<a href=\"https://doi.org/10.1109/icassp.2012.6288524\">10.1109/icassp.2012.6288524</a>.","chicago":"Mondelli, Marco, Qi Zhou, Xiaoli Ma, and Vincenzo Lottici. “A Cooperative Approach for Amplify-and-Forward Differential Transmitted Reference IR-UWB Relay Systems.” In <i>2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)</i>, 2905–8. IEEE, 2012. <a href=\"https://doi.org/10.1109/icassp.2012.6288524\">https://doi.org/10.1109/icassp.2012.6288524</a>."},"page":"2905-2908","publication":"2012 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)","status":"public","date_published":"2012-07-31T00:00:00Z","year":"2012","extern":"1","month":"07","day":"31","oa_version":"None","type":"conference","date_updated":"2021-01-12T08:08:49Z","doi":"10.1109/icassp.2012.6288524","publication_identifier":{"issn":["1520-6149"]},"title":"A cooperative approach for amplify-and-forward differential transmitted reference IR-UWB relay systems","date_created":"2019-07-31T09:14:48Z","author":[{"last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"full_name":"Zhou, Qi","first_name":"Qi","last_name":"Zhou"},{"full_name":"Ma, Xiaoli","first_name":"Xiaoli","last_name":"Ma"},{"last_name":"Lottici","first_name":"Vincenzo","full_name":"Lottici, Vincenzo"}],"publisher":"IEEE","_id":"6746","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"ICASSP: International Conference on Acoustics, Speech and Signal Processing","location":"Kyoto, Japan","end_date":"2012-03-30","start_date":"2012-03-25"}}]