multiple sequence alignment

RMSAGen: Integrating Multiple Sequence Alignment for Function RNA Design AAAI 2026 Beyond cognacy ACL 2025 Fast Uncovering of Protein Sequence Diversity from Structure ICLR 2025 G2PDiffusion: Cross-Species Genotype-to-Phenotype Prediction via Evolutionary Diffusion ICCV 2025 Protriever: End-to-End Differentiable Protein Homology Search for Fitness Prediction ICML 2025 Universal Biological Sequence Reranking for Improved De Novo Peptide Sequencing ICML 2025 Evolution-Inspired Loss Functions for Protein Representation Learning ICML 2024 MSA Generation with Seqs2Seqs Pretraining: Advancing Protein Structure Predictions NeurIPS 2024 MSAGPT: Neural Prompting Protein Structure Prediction via MSA Generative Pre-Training NeurIPS 2024 Retrieved Sequence Augmentation for Protein Representation Learning EMNLP 2024 Ultrafast classical phylogenetic method beats large protein language models on variant effect prediction NeurIPS 2024 Multiple sequence alignment as a sequence-to-sequence learning problem ICLR 2023 OpenProteinSet: Training data for structural biology at scale NeurIPS 2023 PoET: A generative model of protein families as sequences-of-sequences NeurIPS 2023 Contact-Distil: Boosting Low Homologous Protein Contact Map Prediction by Self-Supervised Distillation AAAI 2022 Exploring evolution-aware & -free protein language models as protein function predictors NeurIPS 2022 A Structured Observation Distribution for Generative Biological Sequence Prediction and Forecasting ICML 2021 Co-evolution Transformer for Protein Contact Prediction NeurIPS 2021 MSA Transformer ICML 2021 PSSM-Distil: Protein Secondary Structure Prediction (PSSP) on Low-Quality PSSM by Knowledge Distillation with Contrastive Learning AAAI 2021 Scalable Convex Multiple Sequence Alignment via Entropy-Regularized Dual Decomposition AISTATS 2017 A Convex Atomic-Norm Approach to Multiple Sequence Alignment and Motif Discovery ICML 2016 Variational Inference over Combinatorial Spaces NeurIPS 2010 Efficient Inference in Phylogenetic InDel Trees NeurIPS 2008