arXiv subjects

Niki Kilbertus

Publications and source records attributed to Niki Kilbertus.

At least 37 records · Page 2Linked to original sources

arXiv2025

Targeted Sequential Indirect Experiment Design

Scientific hypotheses typically concern specific aspects of complex, imperfectly understood or entirely unknown mechanisms, such as the effect of gene expression levels on phenotypes or how microbial communities influence environmental health. Such queries are inherently causal (rather than purely associational), but in many settings, experiments can not be conducted directly on the target variables of interest, but are indirect. Therefore, they perturb the target variable, but do not remove potential confounding factors. If, additionally, the resulting experimental measurements are multi-dimensional and the studied mechanisms nonlinear, the query of interest is generally not identified. We develop an adaptive strategy to design indirect experiments that optimally inform a targeted query about the ground truth mechanism in terms of sequentially narrowing the gap between an upper and lower bound on the query. While the general formulation consists of a bi-level optimization procedure, we derive an efficiently estimable analytical kernel-based estimator of the bounds for the causal effect, a query of key interest, and demonstrate the efficacy of our approach in confounded, multivariate, nonlinear synthetic settings.

stat.ME↗

arXiv2025

Beyond Predictions in Neural ODEs: Identification and Interventions

Spurred by tremendous success in pattern matching and prediction tasks, researchers increasingly resort to machine learning to aid original scientific discovery. Given large amounts of observational data about a system, can we uncover the rules that govern its evolution? Solving this task holds the great promise of fully understanding the causal interactions and being able to make reliable predictions about the system's behavior under interventions. We take a step towards answering this question for time-series data generated from systems of ordinary differential equations (ODEs). While the governing ODEs might not be identifiable from data alone, we show that combining simple regularization schemes with flexible neural ODEs can robustly recover the dynamics and causal structures from time-series data. Our results on a variety of (non)-linear first and second order systems as well as real data validate our method. We conclude by showing that we can also make accurate predictions under interventions on variables or the system itself.

cs.LG↗

arXiv2024

Towards Physically Consistent Deep Learning For Climate Model Parameterizations

Climate models play a critical role in understanding and projecting climate change. Due to their complexity, their horizontal resolution of about 40-100 km remains too coarse to resolve processes such as clouds and convection, which need to be approximated via parameterizations. These parameterizations are a major source of systematic errors and large uncertainties in climate projections. Deep learning (DL)-based parameterizations, trained on data from computationally expensive short, high-resolution simulations, have shown great promise for improving climate models in that regard. However, their lack of interpretability and tendency to learn spurious non-physical correlations result in reduced trust in the climate simulation. We propose an efficient supervised learning framework for DL-based parameterizations that leads to physically consistent models with improved interpretability and negligible computational overhead compared to standard supervised training. First, key features determining the target physical processes are uncovered. Subsequently, the neural network is fine-tuned using only those relevant features. We show empirically that our method robustly identifies a small subset of the inputs as actual physical drivers, therefore removing spurious non-physical relationships. This results in by design physically consistent and interpretable neural networks while maintaining the predictive performance of unconstrained black-box DL-based parameterizations.

cs.LG↗

arXiv2024

Learning Representations of Instruments for Partial Identification of Treatment Effects

Reliable estimation of treatment effects from observational data is important in many disciplines such as medicine. However, estimation is challenging when unconfoundedness as a standard assumption in the causal inference literature is violated. In this work, we leverage arbitrary (potentially high-dimensional) instruments to estimate bounds on the conditional average treatment effect (CATE). Our contributions are three-fold: (1) We propose a novel approach for partial identification through a mapping of instruments to a discrete representation space so that we yield valid bounds on the CATE. This is crucial for reliable decision-making in real-world applications. (2) We derive a two-step procedure that learns tight bounds using a tailored neural partitioning of the latent instrument space. As a result, we avoid instability issues due to numerical approximations or adversarial training. Furthermore, our procedure aims to reduce the estimation variance in finite-sample settings to yield more reliable estimates. (3) We show theoretically that our procedure obtains valid bounds while reducing estimation variance. We further perform extensive experiments to demonstrate the effectiveness across various settings. Overall, our procedure offers a novel path for practitioners to make use of potentially high-dimensional instruments (e.g., as in Mendelian randomization).

cs.LG↗

arXiv2024

Uncertainty-Aware Optimal Treatment Selection for Clinical Time Series

In personalized medicine, the ability to predict and optimize treatment outcomes across various time frames is essential. Additionally, the ability to select cost-effective treatments within specific budget constraints is critical. Despite recent advancements in estimating counterfactual trajectories, a direct link to optimal treatment selection based on these estimates is missing. This paper introduces a novel method integrating counterfactual estimation techniques and uncertainty quantification to recommend personalized treatment plans adhering to predefined cost constraints. Our approach is distinctive in its handling of continuous treatment variables and its incorporation of uncertainty quantification to improve prediction reliability. We validate our method using two simulated datasets, one focused on the cardiovascular system and the other on COVID-19. Our findings indicate that our method has robust performance across different counterfactual estimation baselines, showing that introducing uncertainty quantification in these settings helps the current baselines in finding more reliable and accurate treatment selection. The robustness of our method across various settings highlights its potential for broad applicability in personalized healthcare solutions.

cs.LG↗

arXiv2024

Causal machine learning for predicting treatment outcomes

Causal machine learning (ML) offers flexible, data-driven methods for predicting treatment outcomes including efficacy and toxicity, thereby supporting the assessment and safety of drugs. A key benefit of causal ML is that it allows for estimating individualized treatment effects, so that clinical decision-making can be personalized to individual patient profiles. Causal ML can be used in combination with both clinical trial data and real-world data, such as clinical registries and electronic health records, but caution is needed to avoid biased or incorrect predictions. In this Perspective, we discuss the benefits of causal ML (relative to traditional statistical or ML approaches) and outline the key components and steps. Finally, we provide recommendations for the reliable use of causal ML and effective translation into the clinic.

cs.LG↗

arXiv2024

Learning Counterfactually Invariant Predictors

Notions of counterfactual invariance (CI) have proven essential for predictors that are fair, robust, and generalizable in the real world. We propose graphical criteria that yield a sufficient condition for a predictor to be counterfactually invariant in terms of a conditional independence in the observational distribution. In order to learn such predictors, we propose a model-agnostic framework, called Counterfactually Invariant Prediction (CIP), building on the Hilbert-Schmidt Conditional Independence Criterion (HSCIC), a kernel-based conditional dependence measure. Our experimental results demonstrate the effectiveness of CIP in enforcing counterfactual invariance across various simulated and real-world datasets including scalar and multi-variate settings.

cs.LG↗

arXiv2024

Instrumental Variable Estimation for Compositional Treatments

Many scientific datasets are compositional in nature. Important biological examples include species abundances in ecology, cell-type compositions derived from single-cell sequencing data, and amplicon abundance data in microbiome research. Here, we provide a causal view on compositional data in an instrumental variable setting where the composition acts as the cause. First, we crisply articulate potential pitfalls for practitioners regarding the interpretation of compositional causes from the viewpoint of interventions and warn against attributing causal meaning to common summary statistics such as diversity indices in microbiome data analysis. We then advocate for and develop multivariate methods using statistical data transformations and regression techniques that take the special structure of the compositional sample space into account while still yielding scientifically interpretable results. In a comparative analysis on synthetic and real microbiome data we show the advantages and limitations of our proposal. We posit that our analysis provides a useful framework and guidance for valid and informative cause-effect estimation in the context of compositional data.

cs.LG↗

arXiv2024

Unbalancedness in Neural Monge Maps Improves Unpaired Domain Translation

In optimal transport (OT), a Monge map is known as a mapping that transports a source distribution to a target distribution in the most cost-efficient way. Recently, multiple neural estimators for Monge maps have been developed and applied in diverse unpaired domain translation tasks, e.g. in single-cell biology and computer vision. However, the classic OT framework enforces mass conservation, which makes it prone to outliers and limits its applicability in real-world scenarios. The latter can be particularly harmful in OT domain translation tasks, where the relative position of a sample within a distribution is explicitly taken into account. While unbalanced OT tackles this challenge in the discrete setting, its integration into neural Monge map estimators has received limited attention. We propose a theoretically grounded method to incorporate unbalancedness into any Monge map estimator. We improve existing estimators to model cell trajectories over time and to predict cellular responses to perturbations. Moreover, our approach seamlessly integrates with the OT flow matching (OT-FM) framework. While we show that OT-FM performs competitively in image translation, we further improve performance by incorporating unbalancedness (UOT-FM), which better preserves relevant features. We hence establish UOT-FM as a principled method for unpaired image translation.

cs.CV↗

arXiv2024

Stabilized Neural Differential Equations for Learning Dynamics with Explicit Constraints

Many successful methods to learn dynamical systems from data have recently been introduced. However, ensuring that the inferred dynamics preserve known constraints, such as conservation laws or restrictions on the allowed system states, remains challenging. We propose stabilized neural differential equations (SNDEs), a method to enforce arbitrary manifold constraints for neural differential equations. Our approach is based on a stabilization term that, when added to the original dynamics, renders the constraint manifold provably asymptotically stable. Due to its simplicity, our method is compatible with all common neural differential equation (NDE) models and broadly applicable. In extensive empirical evaluations, we demonstrate that SNDEs outperform existing methods while broadening the types of constraints that can be incorporated into NDE training.

cs.LG↗

arXiv2023

ODEFormer: Symbolic Regression of Dynamical Systems with Transformers

We introduce ODEFormer, the first transformer able to infer multidimensional ordinary differential equation (ODE) systems in symbolic form from the observation of a single solution trajectory. We perform extensive evaluations on two datasets: (i) the existing "Strogatz" dataset featuring two-dimensional systems; (ii) ODEBench, a collection of one- to four-dimensional systems that we carefully curated from the literature to provide a more holistic benchmark. ODEFormer consistently outperforms existing methods while displaying substantially improved robustness to noisy and irregularly sampled observations, as well as faster inference. We release our code, model and benchmark dataset publicly.

cs.LG↗

arXiv2023

Predicting Ordinary Differential Equations with Transformers

We develop a transformer-based sequence-to-sequence model that recovers scalar ordinary differential equations (ODEs) in symbolic form from irregularly sampled and noisy observations of a single solution trajectory. We demonstrate in extensive empirical evaluations that our model performs better or on par with existing methods in terms of accurate recovery across various settings. Moreover, our method is efficiently scalable: after one-time pretraining on a large set of ODEs, we can infer the governing law of a new observed solution in a few forward passes of the model.

cs.LG↗

arXiv2023

Modeling Content Creator Incentives on Algorithm-Curated Platforms

Content creators compete for user attention. Their reach crucially depends on algorithmic choices made by developers on online platforms. To maximize exposure, many creators adapt strategically, as evidenced by examples like the sprawling search engine optimization industry. This begets competition for the finite user attention pool. We formalize these dynamics in what we call an exposure game, a model of incentives induced by algorithms, including modern factorization and (deep) two-tower architectures. We prove that seemingly innocuous algorithmic choices, e.g., non-negative vs. unconstrained factorization, significantly affect the existence and character of (Nash) equilibria in exposure games. We proffer use of creator behavior models, like exposure games, for an (ex-ante) pre-deployment audit. Such an audit can identify misalignment between desirable and incentivized content, and thus complement post-hoc measures like content filtering and moderation. To this end, we propose tools for numerically finding equilibria in exposure games, and illustrate results of an audit on the MovieLens and LastFM datasets. Among else, we find that the strategically produced content exhibits strong dependence between algorithmic exploration and content diversity, and between model expressivity and bias towards gender-based user and creator groups.

cs.GT↗

arXiv2023

Sequential Underspecified Instrument Selection for Cause-Effect Estimation

Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e.g., the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e.g., drugs or antibiotics). In such underspecified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

stat.ME↗

arXiv2023

Stochastic Causal Programming for Bounding Treatment Effects

Causal effect estimation is important for many tasks in the natural and social sciences. We design algorithms for the continuous partial identification problem: bounding the effects of multivariate, continuous treatments when unmeasured confounding makes identification impossible. Specifically, we cast causal effects as objective functions within a constrained optimization problem, and minimize/maximize these functions to obtain bounds. We combine flexible learning algorithms with Monte Carlo methods to implement a family of solutions under the name of stochastic causal programming. In particular, we show how the generic framework can be efficiently formulated in settings where auxiliary variables are clustered into pre-treatment and post-treatment sets, where no fine-grained causal graph can be easily specified. In these settings, we can avoid the need for fully specifying the distribution family of hidden common causes. Monte Carlo computation is also much simplified, leading to algorithms which are more computationally stable against alternatives.

stat.ML↗

arXiv2022

Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution

Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains a challenge due to technical limitations and, more importantly, the cost of such multiplexed experiments. Thus, transferring information from routinely performed bulk RNA HTS is required to enrich single-cell data meaningfully. We introduce chemCPA, a new encoder-decoder architecture to study the perturbational effects of unseen drugs. We combine the model with an architecture surgery for transfer learning and demonstrate how training on existing bulk RNA HTS datasets can improve generalisation performance. Better generalisation reduces the need for extensive and costly screens at single-cell resolution. We envision that our proposed method will facilitate more efficient experiment designs through its ability to generate in-silico hypotheses, ultimately accelerating drug discovery.

cs.LG↗

arXiv2022

Supervised Learning and Model Analysis with Compositional Data

The compositionality and sparsity of high-throughput sequencing data poses a challenge for regression and classification. However, in microbiome research in particular, conditional modeling is an essential tool to investigate relationships between phenotypes and the microbiome. Existing techniques are often inadequate: they either rely on extensions of the linear log-contrast model (which adjusts for compositionality, but is often unable to capture useful signals), or they are based on black-box machine learning methods (which may capture useful signals, but ignore compositionality in downstream analyses). We propose KernelBiome, a kernel-based nonparametric regression and classification framework for compositional data. It is tailored to sparse compositional data and is able to incorporate prior knowledge, such as phylogenetic structure. KernelBiome captures complex signals, including in the zero-structure, while automatically adapting model complexity. We demonstrate on par or improved predictive performance compared with state-of-the-art machine learning methods. Additionally, our framework provides two key advantages: (i) We propose two novel quantities to interpret contributions of individual components and prove that they consistently estimate average perturbation effects of the conditional mean, extending the interpretability of linear log-contrast models to nonparametric models. (ii) We show that the connection between kernels and distances aids interpretability and provides a data-driven embedding that can augment further analysis. Finally, we apply the KernelBiome framework to two public microbiome studies and illustrate the proposed model analysis. KernelBiome is available as an open-source Python package at https://github.com/shimenghuang/KernelBiome.

stat.ML↗

arXiv2022

Discovering ordinary differential equations that govern time-series

Natural laws are often described through differential equations yet finding a differential equation that describes the governing law underlying observed data is a challenging and still mostly manual task. In this paper we make a step towards the automation of this process: we propose a transformer-based sequence-to-sequence model that recovers scalar autonomous ordinary differential equations (ODEs) in symbolic form from time-series data of a single observed solution of the ODE. Our method is efficiently scalable: after one-time pretraining on a large set of ODEs, we can infer the governing laws of a new observed solution in a few forward passes of the model. Then we show that our model performs better or on par with existing methods in various test cases in terms of accurate symbolic recovery of the ODE, especially for more complex expressions.

cs.LG↗