<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><blockquote type="cite"><div>I was going through the changelog of GenABEL and saw that Gulya's<br>poly_eigen is the default method for polygenic() since version 1.6-8. I<br>did a quick comparison on the computation speed of the three methods<br>(polygenic_hglm, polygenic with polylik and with poly_eigen) on our<br>population and even though I knew what to expect from Yurii's results, I<br>am still impressed at the speedup! <br></div></blockquote><div><br></div>This was indeed a major step -- with multiple improvements after that -- and now 'polygenic' can estimate the model for say 3k people in few minutes (in contrast with few hours / days? in old implementation). This development is thanks to Gulya's brilliant decomposition idea, comments of other people about it, and -- in some part -- my coding. </div><div><br><blockquote type="cite"><div>I was wondering, is there a publication on this method/implementation?<br></div></blockquote><div><br></div><div>Not yet, and it is not very clear (at least to me) how to sell this. There are many issues with moving this idea to the point of a pub -- basically, this type of ideas was around for years (e.g. William Astle's TurboGC is quite similar; Paolo Bientinesi & Diego Fabregat suggested something related in some parts; looking into literature, I see similar ideas in gene expression analysis, e.g. from Tibshirani; ), and it is difficult to figure out how to serve such pub out. While Gulya developed these ideas independently of others, while for GenABEL and practical GWAS this is a big thing; theoretically, it seems to be not that new... Well, more discussion will follow. </div><br><blockquote type="cite"><div>Has there been any comparison of poly_eigen vs. the old method (in terms<br>of variance, lambda etc.? </div></blockquote><div><br></div><div>It is 100% identical (there is an GenA's RUnit test running 'old' vs 'new', and it passes checkEquals with tolerance of 1e-6 :) ). No approximation, just speed-up and still full ML. Cool, he?</div><div><br></div>best wishes,</div><div>Yurii</div><div><br></div><div><div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>-------------------------------------------------------</div><div>Yurii Aulchenko, PhD, Dr. Habil.</div><div>Independent researcher and consultant</div><div>yurii [dot] aulchenko [at] gmail [dot] com</div></div><div><br></div></div></span></div></span></span></div></div></body></html>