Related papers: Towards Interpretable Protein Structure Prediction…
Sparse autoencoders (SAEs) have recently emerged as a powerful tool for interpreting the internal representations of large language models (LLMs), revealing latent latent features with semantical meaning. This interpretability has also…
Predicting protein function from amino acid sequence remains a central challenge in data-scarce (low-$N$) regimes, limiting machine learning-guided protein design when only small amounts of assay-labeled sequence-function data are…
The rapid advancements in transformer-based language models have revolutionized natural language processing, yet understanding the internal mechanisms of these models remains a significant challenge. This paper explores the application of…
Sparse autoencoders (SAEs) are a mechanistic interpretability technique that have been used to provide insight into learned concepts within large protein language models. Here, we employ TopK and Ordered SAEs to investigate autoregressive…
Sparse Autoencoder (SAE) has emerged as a powerful tool for mechanistic interpretability of large language models. Recent works apply SAE to protein language models (PLMs), aiming to extract and analyze biologically meaningful features from…
Sparse autoencoders (SAEs) have emerged as a powerful tool for interpreting neural networks by extracting the concepts represented in their activations. However, choosing the size of the SAE dictionary (i.e. number of learned concepts)…
Interpretability can improve the safety, transparency and trust of AI models, which is especially important in healthcare applications where decisions often carry significant consequences. Mechanistic interpretability, particularly through…
Deep learning, particularly with the advancement of Large Language Models, has transformed biomolecular modeling, with protein language models such as ESM inspiring emerging RNA language models such as RiNALMo. Recent work has begun…
Protein language models (PLMs) have demonstrated remarkable success in protein modeling and design, yet their internal mechanisms for predicting structure and function remain poorly understood. Here we present a systematic approach to…
Sparse autoencoders (SAEs) are a popular technique for interpreting language model activations, and there is extensive recent work on improving SAE effectiveness. However, most prior work evaluates progress using unsupervised proxy metrics…
Sparse autoencoders (SAEs) \citep{bricken2023monosemanticity,gao2024scalingevaluatingsparseautoencoders} rely on dictionary learning to extract interpretable features from neural networks at scale in an unsupervised manner, with…
Large Language Models (LLMs) have transformed natural language processing, yet their internal mechanisms remain largely opaque. Recently, mechanistic interpretability has attracted significant attention from the research community as a…
Sparse autoencoders (SAEs) have lately been used to uncover interpretable latent features in large language models. By projecting dense embeddings into a much higher-dimensional and sparse space, learned features become disentangled and…
Analyzing large-scale text corpora is a core challenge in machine learning, crucial for tasks like identifying undesirable model behaviors or biases in training data. Current methods often rely on costly LLM-based techniques (e.g.…
RFdiffusion is a popular and well-established model for generation of protein structures. However, this generative process offers limited insight into its internal representations and how they contribute to the final protein structure.…
Pathology plays an important role in disease diagnosis, treatment decision-making and drug development. Previous works on interpretability for machine learning models on pathology images have revolved around methods such as attention value…
Sparse Autoencoders (SAEs) have emerged as a popular tool for interpreting the hidden states of large language models (LLMs). By learning to reconstruct activations from a sparse bottleneck layer, SAEs discover interpretable features from…
Vision foundation models (FMs) achieve state-of-the-art performance in medical imaging. However, they encode information in abstract latent representations that clinicians cannot interrogate or verify. The goal of this study is to…
Sparse autoencoders (SAEs) are useful for detecting and steering interpretable features in neural networks, with particular potential for understanding complex multimodal representations. Given their ability to uncover interpretable…
Translating the internal representations and computations of models into concepts that humans can understand is a key goal of interpretability. While recent dictionary learning methods such as Sparse Autoencoders (SAEs) provide a promising…