Having a unified, coherent taxonomy is essential for effective knowledge representation in domain-specific applications as diverse terminologies need to be mapped to underlying concepts. Traditional manual approaches to taxonomy alignment rely on expert review of concept pairs, but this becomes prohibitively expensive and time-consuming at scale, while subjective interpretations often lead to expert disagreements. Existing automated methods for taxonomy alignment have shown promise but face limitations in handling nuanced semantic relationships and maintaining consistency across different domains. These approaches often struggle with context-dependent concept mappings and lack transparent reasoning processes. We propose a novel framework that combines large language models (LLMs) with expert calibration and iterative prompt optimization to automate taxonomy alignment. Our method integrates expert-labeled examples, multi-stage prompt engineering, and human validation to guide LLMs in generating both taxonomy linkages and supporting rationales. In evaluating our framework on a domain-specific mapping task of concept essentiality, we achieved an F1-score of 0.97, substantially exceeding the human benchmark of 0.68. These results demonstrate the effectiveness of our approach in scaling taxonomy alignment while maintaining high-quality mappings and preserving expert oversight for ambiguous cases.

Explicit noise-level conditioning is widely regarded as essential for the effective operation of Graph Diffusion Models (GDMs). In this work, we challenge this assumption by investigating whether denoisers can implicitly infer noise levels directly from corrupted graph structures, potentially eliminating the need for explicit noise conditioning. To this end, we develop a theoretical framework centered on Bernoulli edge-flip corruptions and extend it to encompass more complex scenarios involving coupled structure-attribute noise. Extensive empirical evaluations on both synthetic and real-world graph datasets, using models such as GDSS and DiGress, provide strong support for our theoretical findings. Notably, unconditional GDMs achieve performance comparable or superior to their conditioned counterparts, while also offering reductions in parameters (4-6%) and computation time (8-10%). Our results suggest that the high-dimensional nature of graph data itself often encodes sufficient information for the denoising process, opening avenues for simpler, more efficient GDM architectures.

This book offers a hands-on introduction to building and understanding federated learning (FL) systems. FL enables multiple devices -- such as smartphones, sensors, or local computers -- to collaboratively train machine learning (ML) models, while keeping their data private and local. It is a powerful solution when data cannot or should not be centralized due to privacy, regulatory, or technical reasons. The book is designed for students, engineers, and researchers who want to learn how to design scalable, privacy preserving FL systems. Our main focus is on personalization: enabling each device to train its own model while still benefiting from collaboration with relevant devices. This is achieved by leveraging similarities between (the learning tasks associated with) devices that are encoded by the weighted edges (or links) of a federated learning network (FL network). The key idea is to represent real-world FL systems as networks of devices, where nodes correspond to device and edges represent communication links and data similarities between them. The training of personalized models for these devices can be naturally framed as a distributed optimization problem. This optimization problem is referred to as generalized total variation minimization (GTVMin) and ensures that devices with similar learning tasks learn similar model parameters. Our approach is both mathematically principled and practically motivated. While we introduce some advanced ideas from optimization theory and graph-based learning, we aim to keep the book accessible. Readers are guided through the core ideas step by step, with intuitive explanations.

Inferring causal relationships between variable pairs is crucial for understanding multivariate interactions in complex systems. Knowledge-based causal discovery -- which involves inferring causal relationships by reasoning over the metadata of variables (e.g., names or textual context) -- offers a compelling alternative to traditional methods that rely on observational data. However, existing methods using Large Language Models (LLMs) often produce unstable and inconsistent results, compromising their reliability for causal inference. To address this, we introduce a novel approach that integrates Knowledge Graphs (KGs) with LLMs to enhance knowledge-based causal discovery. Our approach identifies informative metapath-based subgraphs within KGs and further refines the selection of these subgraphs using Learning-to-Rank-based models. The top-ranked subgraphs are then incorporated into zero-shot prompts, improving the effectiveness of LLMs in inferring the causal relationship. Extensive experiments on biomedical and open-domain datasets demonstrate that our method outperforms most baselines by up to 44.4 points in F1 scores, evaluated across diverse LLMs and KGs. Our code and datasets are available on GitHub: https://github.com/susantiyuni/path-to-causality

Causal effect estimation from observational data is fundamental across various applications. However, selecting an appropriate estimator from dozens of specialized methods demands substantial manual effort and domain expertise. We present CausalPFN, a single transformer that amortizes this workflow: trained once on a large library of simulated data-generating processes that satisfy ignorability, it infers causal effects for new observational datasets out-of-the-box. CausalPFN combines ideas from Bayesian causal inference with the large-scale training protocol of prior-fitted networks (PFNs), learning to map raw observations directly to causal effects without any task-specific adjustment. Our approach achieves superior average performance on heterogeneous and average treatment effect estimation benchmarks (IHDP, Lalonde, ACIC). Moreover, it shows competitive performance for real-world policy making on uplift modeling tasks. CausalPFN provides calibrated uncertainty estimates to support reliable decision-making based on Bayesian principles. This ready-to-use model does not require any further training or tuning and takes a step toward automated causal inference (https://github.com/vdblm/CausalPFN).

Latent Gaussian variables have been popularised in probabilistic machine learning. In turn, gradient estimators are the machinery that facilitates gradient-based optimisation for models with latent Gaussian variables. The reparameterisation trick is often used as the default estimator as it is simple to implement and yields low-variance gradients for variational inference. In this work, we propose the R2-G2 estimator as the Rao-Blackwellisation of the reparameterisation gradient estimator. Interestingly, we show that the local reparameterisation gradient estimator for Bayesian MLPs is an instance of the R2-G2 estimator and Rao-Blackwellisation. This lets us extend benefits of Rao-Blackwellised gradients to a suite of probabilistic models. We show that initial training with R2-G2 consistently yields better performance in models with multiple applications of the reparameterisation trick.

We study the problem of likelihood maximization when the likelihood function is intractable but model simulations are readily available. We propose a sequential, gradient-based optimization method that directly models the Fisher score based on a local score matching technique which uses simulations from a localized region around each parameter iterate. By employing a linear parameterization to the surrogate score model, our technique admits a closed-form, least-squares solution. This approach yields a fast, flexible, and efficient approximation to the Fisher score, effectively smoothing the likelihood objective and mitigating the challenges posed by complex likelihood landscapes. We provide theoretical guarantees for our score estimator, including bounds on the bias introduced by the smoothing. Empirical results on a range of synthetic and real-world problems demonstrate the superior performance of our method compared to existing benchmarks.

Long Short-Term Memory (LSTM) neural network models have become the cornerstone for sequential data modeling in numerous applications, ranging from natural language processing to time series forecasting. Despite their success, the problem of model selection, including hyperparameter tuning, architecture specification, and regularization choice remains largely heuristic and computationally expensive. In this paper, we propose a unified statistical framework for systematic model selection in LSTM networks. Our framework extends classical model selection ideas, such as information criteria and shrinkage estimation, to sequential neural networks. We define penalized likelihoods adapted to temporal structures, propose a generalized threshold approach for hidden state dynamics, and provide efficient estimation strategies using variational Bayes and approximate marginal likelihood methods. Several biomedical data centric examples demonstrate the flexibility and improved performance of the proposed framework.

In many settings in science and industry, such as drug discovery and clinical trials, a central challenge is designing experiments under time and budget constraints. Bayesian Optimal Experimental Design (BOED) is a paradigm to pick maximally informative designs that has been increasingly applied to such problems. During training, BOED selects inputs according to a pre-determined acquisition criterion. During testing, the model learned during training encounters a naturally occurring distribution of test samples. This leads to an instance of covariate shift, where the train and test samples are drawn from different distributions. Prior work has shown that in the presence of model misspecification, covariate shift amplifies generalization error. Our first contribution is to provide a mathematical decomposition of generalization error that reveals key contributors to generalization error in the presence of model misspecification. We show that generalization error under misspecification is the result of, in addition to covariate shift, a phenomenon we term error (de-)amplification which has not been identified or studied in prior work. Our second contribution is to provide a detailed empirical analysis to show that methods that result in representative and de-amplifying training data increase generalization performance. Our third contribution is to develop a novel acquisition function that mitigates the effects of model misspecification by including a term for representativeness and implicitly inducing de-amplification. Our experimental results demonstrate that our method outperforms traditional BOED in the presence of misspecification.

Off-policy learning and evaluation leverage logged bandit feedback datasets, which contain context, action, propensity score, and feedback for each data point. These scenarios face significant challenges due to high variance and poor performance with low-quality propensity scores and heavy-tailed reward distributions. We address these issues by introducing a novel estimator based on the log-sum-exponential (LSE) operator, which outperforms traditional inverse propensity score estimators. Our LSE estimator demonstrates variance reduction and robustness under heavy-tailed conditions. For off-policy evaluation, we derive upper bounds on the estimator's bias and variance. In the off-policy learning scenario, we establish bounds on the regret -- the performance gap between our LSE estimator and the optimal policy -- assuming bounded $(1+ε)$-th moment of weighted reward. Notably, we achieve a convergence rate of $O(n^{-ε/(1+ ε)})$ for the regret bounds, where $ε\in [0,1]$ and $n$ is the size of logged bandit feedback dataset. Theoretical analysis is complemented by comprehensive empirical evaluations in both off-policy learning and evaluation scenarios, confirming the practical advantages of our approach. The code for our estimator is available at the following link: https://github.com/armin-behnamnia/lse-offpolicy-learning.