When Does Closeness in Distribution Imply Representational Similarity? An Identifiability Perspective

When and why representations learned by different deep neural networks are similar is an active research topic. We choose to address these questions from the perspective of identifiability theory, which suggests that a measure of representational similarity should be invariant to transformations that leave the model distribution unchanged. Focusing on a model family which includes several popular pre-training approaches, e.g., autoregressive language models, we explore when models which generate distributions that are close have similar representations. We prove that a small Kullback-Leibler divergence between the model distributions does not guarantee that the corresponding representations are similar. This has the important corollary that models arbitrarily close to maximizing the likelihood can still learn dissimilar representations, a phenomenon mirrored in our empirical observations on models trained on CIFAR-10. We then define a distributional distance for which closeness implies representational similarity, and in synthetic experiments, we find that wider networks learn distributions which are closer with respect to our distance and have more similar representations. Our results establish a link between closeness in distribution and representational similarity.

Minimum-Excess-Work Guidance

We propose a regularization framework inspired by thermodynamic work for guiding pre-trained probability flow generative models (e.g., continuous normalizing flows or diffusion models) by minimizing excess work, a concept rooted in statistical mechanics and with strong conceptual connections to optimal transport. Our approach enables efficient guidance in sparse-data regimes common to scientific applications, where only limited target samples or partial density constraints are available. We introduce two strategies: Path Guidance for sampling rare transition states by concentrating probability mass on user-defined subsets, and Observable Guidance for aligning generated distributions with experimental observables while preserving entropy. We demonstrate the framework's versatility on a coarse-grained protein model, guiding it to sample transition configurations between folded/unfolded states and correct systematic biases using experimental data. The method bridges thermodynamic principles with modern generative architectures, offering a principled, efficient, and physics-inspired alternative to standard fine-tuning in data-scarce domains. Empirical results highlight improved sample efficiency and bias reduction, underscoring its applicability to molecular simulations and beyond.

Exploring the Effectiveness of Object-Centric Representations in Visual Question Answering: Comparative Insights with Foundation Models

Object-centric (OC) representations, which represent the state of a visual scene by modeling it as a composition of objects, have the potential to be used in various downstream tasks to achieve systematic compositional generalization and facilitate reasoning. However, these claims have not been thoroughly analyzed yet. Recently, foundation models have demonstrated unparalleled capabilities across diverse domains from language to computer vision, marking them as a potential cornerstone of future research for a multitude of computational tasks. In this paper, we conduct an extensive empirical study on representation learning for downstream Visual Question Answering (VQA), which requires an accurate compositional understanding of the scene. We thoroughly investigate the benefits and trade-offs of OC models and alternative approaches including large pre-trained foundation models on both synthetic and real-world data, and demonstrate a viable way to achieve the best of both worlds. The extensiveness of our study, encompassing over 800 downstream VQA models and 15 different types of upstream representations, also provides several additional insights that we believe will be of interest to the community at large.

Generating Multi-Modal and Multi-Attribute Single-Cell Counts with CFGen

Generative modeling of single-cell RNA-seq data has shown invaluable potential in community-driven tasks such as trajectory inference, batch effect removal and gene expression generation. However, most recent deep models generating synthetic single cells from noise operate on pre-processed continuous gene expression approximations, ignoring the inherently discrete and over-dispersed nature of single-cell data, which limits downstream applications and hinders the incorporation of robust noise models. Moreover, crucial aspects of deep-learning-based synthetic single-cell generation remain underexplored, such as controllable multi-modal and multi-label generation and its role in the performance enhancement of downstream tasks. This work presents Cell Flow for Generation (CFGen), a flow-based conditional generative model for multi-modal single-cell counts, which explicitly accounts for the discrete nature of the data. Our results suggest improved recovery of crucial biological data characteristics while accounting for novel generative tasks such as conditioning on multiple attributes and boosting rare cell type classification via data augmentation. By showcasing CFGen on a diverse set of biological datasets and settings, we provide evidence of its value to the fields of computational biology and deep generative models.

Diffusion Based Causal Representation Learning

Causal reasoning can be considered a cornerstone of intelligent systems. Having access to an underlying causal graph comes with the promise of cause-effect estimation and the identification of efficient and safe interventions. However, learning causal representations remains a major challenge, due to the complexity of many real-world systems. Previous works on causal representation learning have mostly focused on Variational Auto-Encoders (VAE). These methods only provide representations from a point estimate, and they are unsuitable to handle high dimensions. To overcome these problems, we proposed a new Diffusion-based Causal Representation Learning (DCRL) algorithm. This algorithm uses diffusion-based representations for causal discovery. DCRL offers access to infinite dimensional latent codes, which encode different levels of information in the latent code. In a first proof of principle, we investigate the use of DCRL for causal representation learning. We further demonstrate experimentally that this approach performs comparably well in identifying the causal structure and causal variables.

DiffEnc: Variational Diffusion with a Learned Encoder

Diffusion models may be viewed as hierarchical variational autoencoders (VAEs) with two improvements: parameter sharing for the conditional distributions in the generative process and efficient computation of the loss as independent terms over the hierarchy. We consider two changes to the diffusion model that retain these advantages while adding flexibility to the model. Firstly, we introduce a data- and depth-dependent mean function in the diffusion process, which leads to a modified diffusion loss. Our proposed framework, DiffEnc, achieves state-of-the-art likelihood on CIFAR-10. Secondly, we let the ratio of the noise variance of the reverse encoder process and the generative process be a free weight parameter rather than being fixed to 1. This leads to theoretical insights: For a finite depth hierarchy, the evidence lower bound (ELBO) can be used as an objective for a weighted diffusion loss approach and for optimizing the noise schedule specifically for inference. For the infinite-depth hierarchy, on the other hand, the weight parameter has to be 1 to have a well-defined ELBO.

On the Generalization of Learned Structured Representations

Despite tremendous progress over the past decade, deep learning methods generally fall short of human-level systematic generalization. It has been argued that explicitly capturing the underlying structure of data should allow connectionist systems to generalize in a more predictable and systematic manner. Indeed, evidence in humans suggests that interpreting the world in terms of symbol-like compositional entities may be crucial for intelligent behavior and high-level reasoning. Another common limitation of deep learning systems is that they require large amounts of training data, which can be expensive to obtain. In representation learning, large datasets are leveraged to learn generic data representations that may be useful for efficient learning of arbitrary downstream tasks. This thesis is about structured representation learning. We study methods that learn, with little or no supervision, representations of unstructured data that capture its hidden structure. In the first part of the thesis, we focus on representations that disentangle the explanatory factors of variation of the data. We scale up disentangled representation learning to a novel robotic dataset, and perform a systematic large-scale study on the role of pretrained representations for out-of-distribution generalization in downstream robotic tasks. The second part of this thesis focuses on object-centric representations, which capture the compositional structure of the input in terms of symbol-like entities, such as objects in visual scenes. Object-centric learning methods learn to form meaningful entities from unstructured input, enabling symbolic information processing on a connectionist substrate. In this study, we train a selection of methods on several common datasets, and investigate their usefulness for downstream tasks and their ability to generalize out of distribution.

Assessing Neural Network Robustness via Adversarial Pivotal Tuning

The ability to assess the robustness of image classifiers to a diverse set of manipulations is essential to their deployment in the real world. Recently, semantic manipulations of real images have been considered for this purpose, as they may not arise using standard adversarial settings. However, such semantic manipulations are often limited to style, color or attribute changes. While expressive, these manipulations do not consider the full capacity of a pretrained generator to affect adversarial image manipulations. In this work, we aim at leveraging the full capacity of a pretrained image generator to generate highly detailed, diverse and photorealistic image manipulations. Inspired by recent GAN-based image inversion methods, we propose a method called Adversarial Pivotal Tuning (APT). APT first finds a pivot latent space input to a pretrained generator that best reconstructs an input image. It then adjusts the weights of the generator to create small, but semantic, manipulations which fool a pretrained classifier. Crucially, APT changes both the input and the weights of the pretrained generator, while preserving its expressive latent editing capability, thus allowing the use of its full capacity in creating semantic adversarial manipulations. We demonstrate that APT generates a variety of semantic image manipulations, which preserve the input image class, but which fool a variety of pretrained classifiers. We further demonstrate that classifiers trained to be robust to other robustness benchmarks, are not robust to our generated manipulations and propose an approach to improve the robustness towards our generated manipulations. Code available at: https://captaine.github.io/apt/

DCI-ES: An Extended Disentanglement Framework with Connections to Identifiability

In representation learning, a common approach is to seek representations which disentangle the underlying factors of variation. Eastwood & Williams (2018) proposed three metrics for quantifying the quality of such disentangled representations: disentanglement (D), completeness (C) and informativeness (I). In this work, we first connect this DCI framework to two common notions of linear and nonlinear identifiability, thus establishing a formal link between disentanglement and the closely-related field of independent component analysis. We then propose an extended DCI-ES framework with two new measures of representation quality - explicitness (E) and size (S) - and point out how D and C can be computed for black-box predictors. Our main idea is that the functional capacity required to use a representation is an important but thus-far neglected aspect of representation quality, which we quantify using explicitness or ease-of-use (E). We illustrate the relevance of our extensions on the MPI3D and Cars3D datasets.

Assaying Out-Of-Distribution Generalization in Transfer Learning

Since out-of-distribution generalization is a generally ill-posed problem, various proxy targets (e.g., calibration, adversarial robustness, algorithmic corruptions, invariance across shifts) were studied across different research programs resulting in different recommendations. While sharing the same aspirational goal, these approaches have never been tested under the same experimental conditions on real data. In this paper, we take a unified view of previous work, highlighting message discrepancies that we address empirically, and providing recommendations on how to measure the robustness of a model and how to improve it. To this end, we collect 172 publicly available dataset pairs for training and out-of-distribution evaluation of accuracy, calibration error, adversarial attacks, environment invariance, and synthetic corruptions. We fine-tune over 31k networks, from nine different architectures in the many- and few-shot setting. Our findings confirm that in- and out-of-distribution accuracies tend to increase jointly, but show that their relation is largely dataset-dependent, and in general more nuanced and more complex than posited by previous, smaller scale studies.