Accurate prediction of enzyme kinetic parameters is crucial for drug discovery, metabolic engineering, and synthetic biology applications. Current computational approaches face limitations in capturing complex enzyme-substrate interactions and often focus on single parameters while neglecting the joint prediction of catalytic turnover numbers (Kcat) and Michaelis-Menten constants (Km). We present EnzyCLIP, a novel dual-encoder framework that leverages contrastive learning and cross-attention mechanisms to predict enzyme kinetic parameters from protein sequences and substrate molecular structures. Our approach integrates ESM-2 protein language model embeddings with ChemBERTa chemical representations through a CLIP-inspired architecture enhanced with bidirectional cross-attention for dynamic enzyme-substrate interaction modeling. EnzyCLIP combines InfoNCE contrastive loss with Huber regression loss to learn aligned multimodal representations while predicting log10-transformed kinetic parameters. The model is trained on the CatPred-DB database containing 23,151 Kcat and 41,174 Km experimentally validated measurements, and achieved competitive performance with R2 scores of 0.593 for Kcat and 0.607 for Km prediction. XGBoost ensemble methods applied to the learned embeddings further improved Km prediction (R2 = 0.61) while maintaining robust Kcat performance.

The conditional generation of proteins with desired functions and/or properties is a key goal for generative models. Existing methods based on prompting of language models can generate proteins conditioned on a target functionality, such as a desired enzyme family. However, these methods are limited to simple, tokenized conditioning and have not been shown to generalize to unseen functions. In this study, we propose ProCALM (Protein Conditionally Adapted Language Model), an approach for the conditional generation of proteins using adapters to protein language models. Our specific implementation of ProCALM involves finetuning ProGen2 to incorporate conditioning representations of enzyme function and taxonomy. ProCALM matches existing methods at conditionally generating sequences from target enzyme families. Impressively, it can also generate within the joint distribution of enzymatic function and taxonomy, and it can generalize to rare and unseen enzyme families and taxonomies. Overall, ProCALM is a flexible and computationally efficient approach, and we expect that it can be extended to a wide range of generative language models. Proteins, sequences of amino acids, are important molecules in all living organisms and have many industrial applications. Protein sequences can be modified or designed to have desired function(s) or optimized properties so that they are more useful for applications ranging from greener chemical synthesis to gene-editing for disease treatment (Buller et al., 2023).

Predicting gene function from its DNA sequence is a fundamental challenge in biology. Many deep learning models have been proposed to embed DNA sequences and predict their enzymatic function, leveraging information in public databases linking DNA sequences to an enzymatic function label. However, much of the scientific community's knowledge of biological function is not represented in these categorical labels, and is instead captured in unstructured text descriptions of mechanisms, reactions, and enzyme behavior. These descriptions are often captured alongside DNA sequences in biological databases, albeit in an unstructured manner. Deep learning of models predicting enzymatic function are likely to benefit from incorporating this multi-modal data encoding scientific knowledge of biological function. There is, however, no dataset designed for machine learning algorithms to leverage this multi-modal information. Here we propose a novel dataset and benchmark suite that enables the exploration and development of large multi-modal neural network models on gene DNA sequences and natural language descriptions of gene function. We present baseline performance on benchmarks for both unsupervised and supervised tasks that demonstrate the difficulty of this modeling objective, while demonstrating the potential benefit of incorporating multi-modal data types in function prediction compared to DNA sequences alone. Our dataset is at: https://hoarfrost-lab.github.io/BioTalk/.

We take the first step in studying general sequential decision-making under two adaptivity constraints: rare policy switch and batch learning. First, we provide a general class called the Eluder Condition class, which includes a wide range of reinforcement learning classes. Then, for the rare policy switch constraint, we provide a generic algorithm to achieve a $\widetilde{\mathcal{O}}(\log K) $ switching cost with a $\widetilde{\mathcal{O}}(\sqrt{K})$ regret on the EC class. For the batch learning constraint, we provide an algorithm that provides a $\widetilde{\mathcal{O}}(\sqrt{K}+K/B)$ regret with the number of batches $B.$ This paper is the first work considering rare policy switch and batch learning under general function classes, which covers nearly all the models studied in the previous works such as tabular MDP (Bai et al. 2019; Zhang et al. 2020), linear MDP (Wang et al. 2021; Gao et al. 2021), low eluder dimension MDP (Kong et al. 2021; Gao et al. 2021), generalized linear function approximation (Qiao et al. 2023), and also some new classes such as the low $D_\Delta$-type Bellman eluder dimension problem, linear mixture MDP, kernelized nonlinear regulator and undercomplete partially observed Markov decision process (POMDP).