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Abstract Engineering stabilized proteins is a fundamental challenge in the development of industrial and pharmaceutical biotechnologies. We present Stability Oracle: a structure-based graph-transformer framework that achieves SOTA performance on accurately identifying thermodynamically stabilizing mutations. Our framework introduces several innovations to overcome well-known challenges in data scarcity and bias, generalization, and computation time, such as: Thermodynamic Permutations for data augmentation, structural amino acid embeddings to model a mutation with a single structure, a protein structure-specific attention-bias mechanism that makes transformers a viable alternative to graph neural networks. We provide training/test splits that mitigate data leakage and ensure proper model evaluation. Furthermore, to examine our data engineering contributions, we fine-tune ESM2 representations (Prostata-IFML) and achieve SOTA for sequence-based models. Notably, Stability Oracle outperforms Prostata-IFML even though it was pretrained on 2000X less proteins and has 548X less parameters. Our framework establishes a path for fine-tuning structure-based transformers to virtually any phenotype, a necessary task for accelerating the development of protein-based biotechnologies.
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Robust (Controlled) Table-to-Text Generation with Structure-Aware Equivariance Learning
Controlled table-to-text generation seeks to generate natural language descriptions for highlighted subparts of a table. Previous SOTA systems still employ a sequence-to-sequence generation method, which merely captures the table as a linear structure and is brittle when table layouts change. We seek to go beyond this paradigm by (1) effectively expressing the relations of content pieces in the table, and (2) making our model robust to content-invariant structural transformations. Accordingly, we propose an equivariance learning framework, which encodes tables with a structure-aware self-attention mechanism. This prunes the full self-attention structure into an order-invariant graph attention that captures the connected graph structure of cells belonging to the same row or column, and it differentiates between relevant cells and irrelevant cells from the structural perspective. Our framework also modifies the positional encoding mechanism to preserve the relative position of tokens in the same cell but enforce position invariance among different cells. Our technology is free to be plugged into existing table-to-text generation models, and has improved T5-based models to offer better performance on ToTTo and HiTab. Moreover, on a harder version of ToTTo, we preserve promising performance, while previous SOTA systems, even with transformation-based data augmentation, have seen significant performance drops.
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- Award ID(s):
- 2105329
- PAR ID:
- 10343362
- Date Published:
- Journal Name:
- Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies
- Page Range / eLocation ID:
- 5037 to 5048
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.18653/v1/2022.naacl-main.371
