Steering Generative Models with Experimental Data for Protein Fitness Optimization

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent developments in steering protein generative models (e.g diffusion models, language models) offer a promising approach. However, by and large, past studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured by low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages compared to alternatives such as reinforcement learning with protein language models.

Automatic Screening for Children with Speech Disorder using Automatic Speech Recognition: Opportunities and Challenges

Speech is a fundamental aspect of human life, crucial not only for communication but also for cognitive, social, and academic development. Children with speech disorders (SD) face significant challenges that, if unaddressed, can result in lasting negative impacts. Traditionally, speech and language assessments (SLA) have been conducted by skilled speech-language pathologists (SLPs), but there is a growing need for efficient and scalable SLA methods powered by artificial intelligence. This position paper presents a survey of existing techniques suitable for automating SLA pipelines, with an emphasis on adapting automatic speech recognition (ASR) models for children's speech, an overview of current SLAs and their automated counterparts to demonstrate the feasibility of AI-enhanced SLA pipelines, and a discussion of practical considerations, including accessibility and privacy concerns, associated with the deployment of AI-powered SLAs.

Conditional Enzyme Generation Using Protein Language Models with Adapters

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.