Predicting cancer dynamics under treatment is challenging due to high inter-patient heterogeneity, lack of predictive biomarkers, and sparse and noisy longitudinal data. Mathematical models can summarize cancer dynamics by a few interpretable parameters per patient. Machine learning methods can then be trained to predict the model parameters from baseline covariates, but do not account for uncertainty in the parameter estimates. Instead, hierarchical Bayesian modeling can model the relationship between baseline covariates to longitudinal measurements via mechanistic parameters while accounting for uncertainty in every part of the model. The mapping from baseline covariates to model parameters can be modeled in several ways. A linear mapping simplifies inference but fails to capture nonlinear covariate effects and scale poorly for interaction modeling when the number of covariates is large. In contrast, Bayesian neural networks can potentially discover interactions between covariates automatically, but at a substantial cost in computational complexity. In this work, we develop a hierarchical Bayesian model of subpopulation dynamics that uses baseline covariate information to predict cancer dynamics under treatment, inspired by cancer dynamics in multiple myeloma (MM), where serum M protein is a well-known proxy of tumor burden. As a working example, we apply the model to a simulated dataset and compare its ability to predict M protein trajectories to a model with linear covariate effects. Our results show that the Bayesian neural network covariate effect model predicts cancer dynamics more accurately than a linear covariate effect model when covariate interactions are present. The framework can also be applied to other types of cancer or other time series prediction problems that can be described with a parametric model.

The process of calibrating computer models of natural phenomena is essential for applications in the physical sciences, where plenty of domain knowledge can be embedded into simulations and then calibrated against real observations. Current machine learning approaches, however, mostly rely on rerunning simulations over a fixed set of designs available in the observed data, potentially neglecting informative correlations across the design space and requiring a large amount of simulations. Instead, we consider the calibration process from the perspective of Bayesian adaptive experimental design and propose a data-efficient algorithm to run maximally informative simulations within a batch-sequential process. At each round, the algorithm jointly estimates the parameters of the posterior distribution and optimal designs by maximising a variational lower bound of the expected information gain. The simulator is modelled as a sample from a Gaussian process, which allows us to correlate simulations and observed data with the unknown calibration parameters. We show the benefits of our method when compared to related approaches across synthetic and real-data problems.

Bayesian Optimization (BO) has proven to be very successful at optimizing a static, noisy, costly-to-evaluate black-box function $f : \mathcal{S} \to \mathbb{R}$. However, optimizing a black-box which is also a function of time (i.e., a dynamic function) $f : \mathcal{S} \times \mathcal{T} \to \mathbb{R}$ remains a challenge, since a dynamic Bayesian Optimization (DBO) algorithm has to keep track of the optimum over time. This changes the nature of the optimization problem in at least three aspects: (i) querying an arbitrary point in $\mathcal{S} \times \mathcal{T}$ is impossible, (ii) past observations become less and less relevant for keeping track of the optimum as time goes by and (iii) the DBO algorithm must have a high sampling frequency so it can collect enough relevant observations to keep track of the optimum through time. In this paper, we design a Wasserstein distance-based criterion able to quantify the relevancy of an observation with respect to future predictions. Then, we leverage this criterion to build W-DBO, a DBO algorithm able to remove irrelevant observations from its dataset on the fly, thus maintaining simultaneously a good predictive performance and a high sampling frequency, even in continuous-time optimization tasks with unknown horizon. Numerical experiments establish the superiority of W-DBO, which outperforms state-of-the-art methods by a comfortable margin.

Continuous normalizing flows (CNFs) learn the probability path between a reference and a target density by modeling the vector field generating said path using neural networks. Recently, Lipman et al. (2022) introduced a simple and inexpensive method for training CNFs in generative modeling, termed flow matching (FM). In this paper, we re-purpose this method for probabilistic inference by incorporating Markovian sampling methods in evaluating the FM objective and using the learned probability path to improve Monte Carlo sampling. We propose a sequential method, which uses samples from a Markov chain to fix the probability path defining the FM objective. We augment this scheme with an adaptive tempering mechanism that allows the discovery of multiple modes in the target. Under mild assumptions, we establish convergence to a local optimum of the FM objective, discuss improvements in the convergence rate, and illustrate our methods on synthetic and real-world examples.

Fairness is a critical objective in policy design and algorithmic decision-making. Identifying the causal pathways of unfairness requires knowledge of the underlying structural causal model, which may be incomplete or unavailable. This limits the practicality of causal fairness analysis in complex or low-knowledge domains. To mitigate this practicality gap, we advocate for developing efficient causal discovery methods for fairness applications. To this end, we introduce local discovery for direct discrimination (LD3): a polynomial-time algorithm that recovers structural evidence of direct discrimination. LD3 performs a linear number of conditional independence tests with respect to variable set size. Moreover, we propose a graphical criterion for identifying the weighted controlled direct effect (CDE), a qualitative measure of direct discrimination. We prove that this criterion is satisfied by the knowledge returned by LD3, increasing the accessibility of the weighted CDE as a causal fairness measure. Taking liver transplant allocation as a case study, we highlight the potential impact of LD3 for modeling fairness in complex decision systems. Results on real-world data demonstrate more plausible causal relations than baselines, which took 197x to 5870x longer to execute.

We re-examine the problem of reconstructing a high-dimensional signal from a small set of linear measurements, in combination with image prior from a diffusion probabilistic model. Well-established methods for optimizing such measurements include principal component analysis (PCA), independent component analysis (ICA) and compressed sensing (CS), all of which rely on axis- or subspace-aligned statistical characterization. But many naturally occurring signals, including photographic images, contain richer statistical structure. To exploit such structure, we introduce a general method for obtaining an optimized set of linear measurements, assuming a Bayesian inverse solution that leverages the prior implicit in a neural network trained to perform denoising. We demonstrate that these measurements are distinct from those of PCA and CS, with significant improvements in minimizing squared reconstruction error. In addition, we show that optimizing the measurements for the SSIM perceptual loss leads to perceptually improved reconstruction. Our results highlight the importance of incorporating the specific statistical regularities of natural signals when designing effective linear measurements.

I generalize acyclic deterministic structural equation models to the nondeterministic case and argue that it offers an improved semantics for counterfactuals. The standard, deterministic, semantics developed by Halpern (and based on the initial proposal of Galles & Pearl) assumes that for each assignment of values to parent variables there is a unique assignment to their child variable, and it assumes that the actual world (an assignment of values to all variables of a model) specifies a unique counterfactual world for each intervention. Both assumptions are unrealistic, and therefore I drop both of them in my proposal. I do so by allowing multi-valued functions in the structural equations. In addition, I adjust the semantics so that the solutions to the equations that obtained in the actual world are preserved in any counterfactual world. I motivate the resulting logic by comparing it to the standard one by Halpern and to more recent proposals that are closer to mine. Finally, I extend these models to the probabilistic case and show that they open up the way to identifying counterfactuals even in Causal Bayesian Networks.

The varying significance of distinct primitive behaviors during the policy learning process has been overlooked by prior model-free RL algorithms. Leveraging this insight, we explore the causal relationship between different action dimensions and rewards to evaluate the significance of various primitive behaviors during training. We introduce a causality-aware entropy term that effectively identifies and prioritizes actions with high potential impacts for efficient exploration. Furthermore, to prevent excessive focus on specific primitive behaviors, we analyze the gradient dormancy phenomenon and introduce a dormancy-guided reset mechanism to further enhance the efficacy of our method. Our proposed algorithm, ACE: Off-policy Actor-critic with Causality-aware Entropy regularization, demonstrates a substantial performance advantage across 29 diverse continuous control tasks spanning 7 domains compared to model-free RL baselines, which underscores the effectiveness, versatility, and efficient sample efficiency of our approach. Benchmark results and videos are available at https://ace-rl.github.io/.

Anomaly detection is the task of identifying examples that do not behave as expected. Because anomalies are rare and unexpected events, collecting real anomalous examples is often challenging in several applications. In addition, learning an anomaly detector with limited (or no) anomalies often yields poor prediction performance. One option is to employ auxiliary synthetic anomalies to improve the model training. However, synthetic anomalies may be of poor quality: anomalies that are unrealistic or indistinguishable from normal samples may deteriorate the detector's performance. Unfortunately, no existing methods quantify the quality of auxiliary anomalies. We fill in this gap and propose the expected anomaly posterior (EAP), an uncertainty-based score function that measures the quality of auxiliary anomalies by quantifying the total uncertainty of an anomaly detector. Experimentally on 40 benchmark datasets of images and tabular data, we show that EAP outperforms 12 adapted data quality estimators in the majority of cases.

Causal structure discovery from observations can be improved by integrating background knowledge provided by an expert to reduce the hypothesis space. Recently, Large Language Models (LLMs) have begun to be considered as sources of prior information given the low cost of querying them relative to a human expert. In this work, firstly, we propose a set of metrics for assessing LLM judgments for causal graph discovery independently of the downstream algorithm. Secondly, we systematically study a set of prompting designs that allows the model to specify priors about the structure of the causal graph. Finally, we present a general methodology for the integration of LLM priors in graph discovery algorithms, finding that they help improve performance on common-sense benchmarks and especially when used for assessing edge directionality. Our work highlights the potential as well as the shortcomings of the use of LLMs in this problem space.