Haplotype-based autoencoders can reduce the dataset dimension and estimate haplotype block effects in different crop species. - Philipp Georg Heilmann; Emanuel Grosch; Matthias Frisch; Matthias Herrmann; Steffen Beuch; Vivek Kurra; Martin Mascher; Raz Avni; Klaus Oldach; Ina Röhrs; Anja Hanemann; Raja Ram Mehta; et al. (BMC Bioinform., 2025)