Cian Eastwood

Cian Eastwood, Alexander Robey, Shashank Singh et al. · eth-zurich

Domain generalization (DG) seeks predictors which perform well on unseen test distributions by leveraging data drawn from multiple related training distributions or domains. To achieve this, DG is commonly formulated as an average- or worst-case problem over the set of possible domains. However, predictors that perform well on average lack robustness while predictors that perform well in the worst case tend to be overly-conservative. To address this, we propose a new probabilistic framework for DG where the goal is to learn predictors that perform well with high probability. Our key idea is that distribution shifts seen during training should inform us of probable shifts at test time, which we realize by explicitly relating training and test domains as draws from the same underlying meta-distribution. To achieve probable DG, we propose a new optimization problem called Quantile Risk Minimization (QRM). By minimizing the $α$-quantile of predictor's risk distribution over domains, QRM seeks predictors that perform well with probability $α$. To solve QRM in practice, we propose the Empirical QRM (EQRM) algorithm and provide: (i) a generalization bound for EQRM; and (ii) the conditions under which EQRM recovers the causal predictor as $α\to 1$. In our experiments, we introduce a more holistic quantile-focused evaluation protocol for DG and demonstrate that EQRM outperforms state-of-the-art baselines on datasets from WILDS and DomainBed.

Cian Eastwood, Shashank Singh, Andrei Liviu Nicolicioiu et al. · eth-zurich, mila

To avoid failures on out-of-distribution data, recent works have sought to extract features that have an invariant or stable relationship with the label across domains, discarding "spurious" or unstable features whose relationship with the label changes across domains. However, unstable features often carry complementary information that could boost performance if used correctly in the test domain. In this work, we show how this can be done without test-domain labels. In particular, we prove that pseudo-labels based on stable features provide sufficient guidance for doing so, provided that stable and unstable features are conditionally independent given the label. Based on this theoretical insight, we propose Stable Feature Boosting (SFB), an algorithm for: (i) learning a predictor that separates stable and conditionally-independent unstable features; and (ii) using the stable-feature predictions to adapt the unstable-feature predictions in the test domain. Theoretically, we prove that SFB can learn an asymptotically-optimal predictor without test-domain labels. Empirically, we demonstrate the effectiveness of SFB on real and synthetic data.

Cian Eastwood, Andrei Liviu Nicolicioiu, Julius von Kügelgen et al. · eth-zurich, mila

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, thereby 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.

Cian Eastwood, Julius von Kügelgen, Linus Ericsson et al. · eth-zurich

Self-supervised representation learning often uses data augmentations to induce some invariance to "style" attributes of the data. However, with downstream tasks generally unknown at training time, it is difficult to deduce a priori which attributes of the data are indeed "style" and can be safely discarded. To deal with this, current approaches try to retain some style information by tuning the degree of invariance to some particular task, such as ImageNet object classification. However, prior work has shown that such task-specific tuning can lead to significant performance degradation on other tasks that rely on the discarded style. To address this, we introduce a more principled approach that seeks to disentangle style features rather than discard them. The key idea is to add multiple style embedding spaces where: (i) each is invariant to all-but-one augmentation; and (ii) joint entropy is maximized. We formalize our structured data-augmentation procedure from a causal latent-variable-model perspective, and prove identifiability of both content and individual style variables. We empirically demonstrate the benefits of our approach on both synthetic and real-world data.

Charles Jones, Emmanuel Noutahi, Jason Hartford et al.

Flow-matching generative models are increasingly used to simulate cell responses to biological perturbations. However, the design space for building such models is large and underexplored. We systematically analyse the design space of flow matching models for cell-microscopy images, finding that many popular techniques are unnecessary and can even hurt performance. We develop a simple, stable, and scalable recipe which we use to train our foundation model. We scale our model to two orders of magnitude larger than prior methods, achieving a two-fold FID and ten-fold KID improvement over prior methods. We then fine-tune our model with pre-trained molecular embeddings to achieve state-of-the-art performance simulating responses to unseen molecules. Code is available at https://github.com/valence-labs/microscopy-flow-matching

Cian Eastwood, Li Nanbo, Christopher K. I. Williams

Given two object images, how can we explain their differences in terms of the underlying object properties? To address this question, we propose Align-Deform-Subtract (ADS) -- an interventional framework for explaining object differences. By leveraging semantic alignments in image-space as counterfactual interventions on the underlying object properties, ADS iteratively quantifies and removes differences in object properties. The result is a set of "disentangled" error measures which explain object differences in terms of the underlying properties. Experiments on real and synthetic data illustrate the efficacy of the framework.

Michael Tschannen, Cian Eastwood, Fabian Mentzer

We introduce Generative Infinite-Vocabulary Transformers (GIVT) which generate vector sequences with real-valued entries, instead of discrete tokens from a finite vocabulary. To this end, we propose two surprisingly simple modifications to decoder-only transformers: 1) at the input, we replace the finite-vocabulary lookup table with a linear projection of the input vectors; and 2) at the output, we replace the logits prediction (usually mapped to a categorical distribution) with the parameters of a multivariate Gaussian mixture model. Inspired by the image-generation paradigm of VQ-GAN and MaskGIT, where transformers are used to model the discrete latent sequences of a VQ-VAE, we use GIVT to model the unquantized real-valued latent sequences of a $β$-VAE. In class-conditional image generation GIVT outperforms VQ-GAN (and improved variants thereof) as well as MaskGIT, and achieves performance competitive with recent latent diffusion models. Finally, we obtain strong results outside of image generation when applying GIVT to panoptic segmentation and depth estimation with a VAE variant of the UViM framework.

Frederik Wenkel, Wilson Tu, Cassandra Masschelein et al.

Accurately predicting cellular responses to genetic perturbations is essential for understanding disease mechanisms and designing effective therapies. Yet exhaustively exploring the space of possible perturbations (e.g., multi-gene perturbations or across tissues and cell types) is prohibitively expensive, motivating methods that can generalize to unseen conditions. In this work, we explore how knowledge graphs of gene-gene relationships can improve out-of-distribution (OOD) prediction across three challenging settings: unseen single perturbations; unseen double perturbations; and unseen cell lines. In particular, we present: (i) TxPert, a new state-of-the-art method that leverages multiple biological knowledge networks to predict transcriptional responses under OOD scenarios; (ii) an in-depth analysis demonstrating the impact of graphs, model architecture, and data on performance; and (iii) an expanded benchmarking framework that strengthens evaluation standards for perturbation modeling.

Konstantin Donhauser, Kristina Ulicna, Gemma Elyse Moran et al.

Sparse dictionary learning (DL) has emerged as a powerful approach to extract semantically meaningful concepts from the internals of large language models (LLMs) trained mainly in the text domain. In this work, we explore whether DL can extract meaningful concepts from less human-interpretable scientific data, such as vision foundation models trained on cell microscopy images, where limited prior knowledge exists about which high-level concepts should arise. We propose a novel combination of a sparse DL algorithm, Iterative Codebook Feature Learning (ICFL), with a PCA whitening pre-processing step derived from control data. Using this combined approach, we successfully retrieve biologically meaningful concepts, such as cell types and genetic perturbations. Moreover, we demonstrate how our method reveals subtle morphological changes arising from human-interpretable interventions, offering a promising new direction for scientific discovery via mechanistic interpretability in bioimaging.

Li Nanbo, Cian Eastwood, Robert B. Fisher

Learning object-centric representations of multi-object scenes is a promising approach towards machine intelligence, facilitating high-level reasoning and control from visual sensory data. However, current approaches for unsupervised object-centric scene representation are incapable of aggregating information from multiple observations of a scene. As a result, these "single-view" methods form their representations of a 3D scene based only on a single 2D observation (view). Naturally, this leads to several inaccuracies, with these methods falling victim to single-view spatial ambiguities. To address this, we propose The Multi-View and Multi-Object Network (MulMON) -- a method for learning accurate, object-centric representations of multi-object scenes by leveraging multiple views. In order to sidestep the main technical difficulty of the multi-object-multi-view scenario -- maintaining object correspondences across views -- MulMON iteratively updates the latent object representations for a scene over multiple views. To ensure that these iterative updates do indeed aggregate spatial information to form a complete 3D scene understanding, MulMON is asked to predict the appearance of the scene from novel viewpoints during training. Through experiments, we show that MulMON better-resolves spatial ambiguities than single-view methods -- learning more accurate and disentangled object representations -- and also achieves new functionality in predicting object segmentations for novel viewpoints.

Cian Eastwood, Ian Mason, Christopher K. I. Williams et al.

Source-free domain adaptation (SFDA) aims to adapt a model trained on labelled data in a source domain to unlabelled data in a target domain without access to the source-domain data during adaptation. Existing methods for SFDA leverage entropy-minimization techniques which: (i) apply only to classification; (ii) destroy model calibration; and (iii) rely on the source model achieving a good level of feature-space class-separation in the target domain. We address these issues for a particularly pervasive type of domain shift called measurement shift which can be resolved by restoring the source features rather than extracting new ones. In particular, we propose Feature Restoration (FR) wherein we: (i) store a lightweight and flexible approximation of the feature distribution under the source data; and (ii) adapt the feature-extractor such that the approximate feature distribution under the target data realigns with that saved on the source. We additionally propose a bottom-up training scheme which boosts performance, which we call Bottom-Up Feature Restoration (BUFR). On real and synthetic data, we demonstrate that BUFR outperforms existing SFDA methods in terms of accuracy, calibration, and data efficiency, while being less reliant on the performance of the source model in the target domain.