Related papers: Modelling Cellular Perturbations with the Sparse A…

Latent variable models such as the Variational Auto-Encoder (VAE) have become a go-to tool for analyzing biological data, especially in the field of single-cell genomics. One remaining challenge is the interpretability of latent variables…

Single-cell perturbation prediction aims to infer how cells respond to unseen interventions and to achieve out-of-distribution (OOD) generalization, providing a computational route to understanding how perturbations reshape cellular…

Single-cell perturbation modeling is fundamental for understanding and predicting cellular responses to genetic perturbations. However, existing approaches, from causal representation learning to foundation models, often struggle with an…

Sparse autoencoders (SAEs) improve interpretability in multimodal models, but it remains unclear whether SAE features form modular, composable units for reasoning-an assumption underlying many intervention-based steering methods. We test…

Is there really much more to say about sparse autoencoders (SAEs)? Autoencoders in general, and SAEs in particular, represent deep architectures that are capable of modeling low-dimensional latent structure in data. Such structure could…

Variational Autoencoders (VAEs) are powerful generative models for learning latent representations. Standard VAEs generate dispersed and unstructured latent spaces by utilizing all dimensions, which limits their interpretability, especially…

Variational autoencoders (VAEs) employ Bayesian inference to interpret sensory inputs, mirroring processes that occur in primate vision across both ventral (Higgins et al., 2021) and dorsal (Vafaii et al., 2023) pathways. Despite their…

To truly understand vision models, we must not only interpret their learned features but also validate these interpretations through controlled experiments. While earlier work offers either rich semantics or direct control, few post-hoc…

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…

Many current state-of-the-art models for sequential recommendations are based on transformer architectures. Interpretation and explanation of such black box models is an important research question, as a better understanding of their…

In the following short article we adapt a new and popular machine learning model for inference on medical data sets. Our method is based on the Variational AutoEncoder (VAE) framework that we adapt to survival analysis on small data sets…

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…

Learning interpretable latent representations from tabular data remains a challenge in deep generative modeling. We introduce SE-VAE (Structural Equation-Variational Autoencoder), a novel architecture that embeds measurement structure…

Although artificial neural networks are often described as brain-inspired, their representations typically rely on continuous activations, such as the continuous latent variables in variational autoencoders (VAEs), which limits their…

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…

Unsupervised approaches to large language model (LLM) interpretability, such as sparse autoencoders (SAEs), offer a way to decode LLM activations into interpretable and, ideally, controllable concepts. On the one hand, these approaches…

As in many fields of medical research, survival analysis has witnessed a growing interest in the application of deep learning techniques to model complex, high-dimensional, heterogeneous, incomplete, and censored medical data. Current…

Sparse Autoencoders (SAEs) have emerged as a promising approach for interpreting neural network representations by learning sparse, human-interpretable features from dense activations. We investigate whether incorporating variational…

Predicting cellular responses to various perturbations is a critical focus in drug discovery and personalized therapeutics, with deep learning models playing a significant role in this endeavor. Single-cell datasets contain technical…

We propose a variational autoencoder (VAE) approach for parameter estimation in nonlinear mixed-effects models based on ordinary differential equations (NLME-ODEs) using longitudinal data from multiple subjects. In moderate dimensions,…