DynaMaR: Dynamic Prompt with Mask Token Representation

Recent research has shown that large language models pretrained using unsupervised approaches can achieve significant performance improvement on many downstream tasks. Typically when adapting these language models to downstream tasks, like a classification or regression task, we employ a fine-tuning paradigm in which the sentence representation from the language model is input to a task-specific head; the model is then fine-tuned end-to-end. However, with the emergence of models like GPT-3, prompt-based fine-tuning has been proven to be a successful approach for few-shot tasks. Inspired by this work, we study discrete prompt technologies in practice. There are two issues that arise with the standard prompt approach. First, it can overfit on the prompt template. Second, it requires manual effort to formulate the downstream task as a language model problem. In this paper, we propose an improvement to prompt-based fine-tuning that addresses these two issues. We refer to our approach as DynaMaR -- Dynamic Prompt with Mask Token Representation. Results show that DynaMaR can achieve an average improvement of 10% in few-shot settings and improvement of 3.7% in data-rich settings over the standard fine-tuning approach on four e-commerce applications.

Accurate Protein Structure Prediction by Embeddings and Deep Learning Representations

Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design. This motivates predicting the structure of a protein from its sequence of amino acids, a fundamental problem in computational biology. In this work, we demonstrate state-of-the-art protein structure prediction (PSP) results using embeddings and deep learning models for prediction of backbone atom distance matrices and torsion angles. We recover 3D coordinates of backbone atoms and reconstruct full atom protein by optimization. We create a new gold standard dataset of proteins which is comprehensive and easy to use. Our dataset consists of amino acid sequences, Q8 secondary structures, position specific scoring matrices, multiple sequence alignment co-evolutionary features, backbone atom distance matrices, torsion angles, and 3D coordinates. We evaluate the quality of our structure prediction by RMSD on the latest Critical Assessment of Techniques for Protein Structure Prediction (CASP) test data and demonstrate competitive results with the winning teams and AlphaFold in CASP13 and supersede the results of the winning teams in CASP12. We make our data, models, and code publicly available.