Protein language models (pLMs) are powerful predictors of protein structure and function, learning through unsupervised training on millions of protein sequences. pLMs are thought to capture common motifs in protein sequences, but the specifics of pLM features are not well understood. Identifying these features would not only shed light on how pLMs work, but potentially uncover novel protein biologystudying the model to study the biology. Motivated by this, we train sparse autoencoders (SAEs) on the residual stream of a pLM, ESM-2. By characterizing SAE features, we determine that pLMs use a combination of generic features and family-specific features to represent a protein. In addition, we demonstrate how known sequence determinants of properties such as thermostability and subcellular localization can be identified by linear probing of SAE features. For predictive features without known functional associations, we hypothesize their role in unknown mechanisms and provide visualization tools to aid their interpretation. Our study gives a better understanding of the limitations of pLMs, and demonstrates how SAE features can be used to help generate hypotheses for biological mechanisms. We release our code, model weights, and feature visualizer.

A wide range of visualization authoring interfaces enable the creation of highly customized visualizations. However, prioritizing expressiveness often impedes the learnability of the authoring interface. The diversity of users, such as varying computational skills and prior experiences in user interfaces, makes it even more challenging for a single authoring interface to satisfy the needs of a broad audience. In this paper, we introduce a framework to balance learnability and expressivity in a visualization authoring system. Adopting insights from learnability studies, such as multimodal interaction and visualization literacy, we explore the design space of blending multiple visualization authoring interfaces for supporting authoring tasks in a complementary and flexible manner. To evaluate the effectiveness of blending interfaces, we implemented a proof-of-concept system, Blace, that combines four common visualization authoring interfaces-template-based, shelf configuration, natural language, and code editor-that are tightly linked to one another to help users easily relate unfamiliar interfaces to more familiar ones. Using the system, we conducted a user study with 12 domain experts who regularly visualize genomics data as part of their analysis workflow. Participants with varied visualization and programming backgrounds were able to successfully reproduce unfamiliar visualization examples without a guided tutorial in the study. Feedback from a post-study qualitative questionnaire further suggests that blending interfaces enabled participants to learn the system easily and assisted them in confidently editing unfamiliar visualization grammar in the code editor, enabling expressive customization. Reflecting on our study results and the design of our system, we discuss the different interaction patterns that we identified and design implications for blending visualization authoring interfaces.