Dominik Meier

Kia-Jüng Yang, Dominik Meier, Jiachen Zhao et al.

Large reasoning models (LRMs) generate chain-of-thought (CoT) traces before producing final outputs, introducing a dynamic internal state that may complicate control mechanisms such as refusal. Unlike instruction-tuned LLMs, where refusal is mediated by a single directional subspace, refusal in large reasoning models (LRMs) additionally depends on the CoT. In DeepSeek-R1-Distill-LLaMA-8B, activation steering reverses refusal in only 39% of cases when the CoT is kept fixed, but removing the CoT entirely increases this to 70%, indicating that the CoT actively reinforces refusal. In a two-stage intervention where the model regenerates its CoT under activation steering, refusal is reversed in 94% of cases, while the resulting CoT alone retains 48% of this effect even after steering is removed. This suggests that the CoT can carry and reconstruct the compliance signal independently. These findings indicate that refusal in LRMs is jointly encoded in residual stream activations and CoT. This joint activation makes LRM more robust against activation-level interventions alone, but exposes CoT to a possible alternative surface attack.

Dominik Meier, Ipek Ensari, Stefan Konigorski

Personalized adaptive interventions offer the opportunity to increase patient benefits, however, there are challenges in their planning and implementation. Once implemented, it is an important question whether personalized adaptive interventions are indeed clinically more effective compared to a fixed gold standard intervention. In this paper, we present an innovative N-of-1 trial study design testing whether implementing a personalized intervention by an online reinforcement learning agent is feasible and effective. Throughout, we use a new study on physical exercise recommendations to reduce pain in endometriosis for illustration. We describe the design of a contextual bandit recommendation agent and evaluate the agent in simulation studies. The results show that, first, implementing a personalized intervention by an online reinforcement learning agent is feasible. Second, such adaptive interventions have the potential to improve patients' benefits even if only few observations are available. As one challenge, they add complexity to the design and implementation process. In order to quantify the expected benefit, data from previous interventional studies is required. We expect our approach to be transferable to other interventions and clinical interventions.

Dominik Meier, Jan Philip Wahle, Terry Ruas et al.

Paraphrases represent a human's intuitive ability to understand expressions presented in various different ways. Current paraphrase evaluations of language models primarily use binary approaches, offering limited interpretability of specific text changes. Atomic paraphrase types (APT) decompose paraphrases into different linguistic changes and offer a granular view of the flexibility in linguistic expression (e.g., a shift in syntax or vocabulary used). In this study, we assess the human preferences towards ChatGPT in generating English paraphrases with ten APTs and five prompting techniques. We introduce APTY (Atomic Paraphrase TYpes), a dataset of 800 sentence-level and word-level annotations by 15 annotators. The dataset also provides a human preference ranking of paraphrases with different types that can be used to fine-tune models with RLHF and DPO methods. Our results reveal that ChatGPT and a DPO-trained LLama 7B model can generate simple APTs, such as additions and deletions, but struggle with complex structures (e.g., subordination changes). This study contributes to understanding which aspects of paraphrasing language models have already succeeded at understanding and what remains elusive. In addition, we show how our curated datasets can be used to develop language models with specific linguistic capabilities.

Brian Cho, Dominik Meier, Kyra Gan et al.

In multi-armed bandits, the tasks of reward maximization and pure exploration are often at odds with each other. The former focuses on exploiting arms with the highest means, while the latter may require constant exploration across all arms. In this work, we focus on good arm identification (GAI), a practical bandit inference objective that aims to label arms with means above a threshold as quickly as possible. We show that GAI can be efficiently solved by combining a reward-maximizing sampling algorithm with a novel nonparametric anytime-valid sequential test for labeling arm means. We first establish that our sequential test maintains error control under highly nonparametric assumptions and asymptotically achieves the minimax optimal e-power, a notion of power for anytime-valid tests. Next, by pairing regret-minimizing sampling schemes with our sequential test, we provide an approach that achieves minimax optimal stopping times for labeling arms with means above a threshold, under an error probability constraint. Our empirical results validate our approach beyond the minimax setting, reducing the expected number of samples for all stopping times by at least 50% across both synthetic and real-world settings.

Dominik Meier, Shixing Yu, Sagnik Nandy et al.

Single-cell RNA sequencing (scRNA-seq) enables the study of cellular heterogeneity. Yet, clustering accuracy, and with it downstream analyses based on cell labels, remain challenging due to measurement noise and biological variability. In standard latent spaces (e.g., obtained through PCA), data from different cell types can be projected close together, making accurate clustering difficult. We introduce a latent plug-and-play diffusion framework that separates the observation and denoising space. This separation is operationalized through a novel Gibbs sampling procedure: the learned diffusion prior is applied in a low-dimensional latent space to perform denoising, while to steer this process, noise is reintroduced into the original high-dimensional observation space. This unique "input-space steering" ensures the denoising trajectory remains faithful to the original data structure. Our approach offers three key advantages: (1) adaptive noise handling via a tunable balance between prior and observed data; (2) uncertainty quantification through principled uncertainty estimates for downstream analysis; and (3) generalizable denoising by leveraging clean reference data to denoise noisier datasets, and via averaging, improve quality beyond the training set. We evaluate robustness on both synthetic and real single-cell genomics data. Our method improves clustering accuracy on synthetic data across varied noise levels and dataset shifts. On real-world single-cell data, our method demonstrates improved biological coherence in the resulting cell clusters, with cluster boundaries that better align with known cell type markers and developmental trajectories.

Dominik Meier, Sujai Hiremath, Promit Ghosal et al.

Distinguishing cause and effect from bivariate observational data is a foundational problem in many disciplines, but challenging without additional assumptions. Additive noise models (ANMs) are widely used to enable sample-efficient bivariate causal discovery. However, conventional ANM-based methods fail when unobserved mediators corrupt the causal relationship between variables. This paper makes three key contributions: first, we rigorously characterize why standard ANM approaches break down in the presence of unmeasured mediators. Second, we demonstrate that prior solutions for hidden mediation are brittle in finite sample settings, limiting their practical utility. To address these gaps, we propose Bivariate Denoising Diffusion (BiDD) for causal discovery, a method designed to handle latent noise introduced by unmeasured mediators. Unlike prior methods that infer directionality through mean squared error loss comparisons, our approach introduces a novel independence test statistic: during the noising and denoising processes for each variable, we condition on the other variable as input and evaluate the independence of the predicted noise relative to this input. We prove asymptotic consistency of BiDD under the ANM, and conjecture that it performs well under hidden mediation. Experiments on synthetic and real-world data demonstrate consistent performance, outperforming existing methods in mediator-corrupted settings while maintaining strong performance in mediator-free settings.