Machine learning techniques have been previously used to assist clinicians to select embryos for human-assisted reproduction. This work aims to show how an appropriate modeling of the problem can contribute to improve machine learning techniques for embryo selection. In this study, a dataset of 330 consecutive cycles (and associated embryos) carried out by the Unit of Assisted Reproduction of the Hospital Donostia (Spain) throughout 18 months has been analyzed. The problem of the embryo selection has been modeled by a novel weakly supervised paradigm, learning from label proportions, which considers all the available data, including embryos whose fate cannot be certainly established. Furthermore, all the collected features, describing cycles and embryos, have been considered in a multi-variate data analysis. Our integral solution has been successfully tested. Experimental results show that the proposed technique consistently outperforms an equivalent approach based on standard supervised classification. Embryos in this study were selected for transference according to the criteria of the Spanish Association for Reproduction Biology Studies. Obtained classification models outperform these criteria, specifically reordering medium-quality embryos.