When Do Language Models Endorse Limitations on Human Rights Principles?

As Large Language Models (LLMs) increasingly mediate global information access with the potential to shape public discourse, their alignment with universal human rights principles becomes important to ensure that these rights are abided by in high stakes AI-mediated interactions. In this paper, we evaluate how LLMs navigate trade-offs involving the Universal Declaration of Human Rights (UDHR), leveraging 1,152 synthetically generated scenarios across 24 rights articles and eight languages. Our analysis of eleven major LLMs reveals systematic biases where models: (1) accept limiting Economic, Social, and Cultural rights more often than Political and Civil rights, (2) demonstrate significant cross-linguistic variation with elevated endorsement rates of rights-limiting actions in Chinese and Hindi compared to English or Romanian, (3) show substantial susceptibility to prompt-based steering, and (4) exhibit noticeable differences between Likert and open-ended responses, highlighting critical challenges in LLM preference assessment.

Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles

Generative models have recently advanced $\textit{de novo}$ protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce $\textbf{RigidSSL}$ ($\textit{Rigidity-Aware Self-Supervised Learning}$), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43\% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8\% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling. The code is available at: https://github.com/ZhanghanNi/RigidSSL.git.

Use What You Know: Causal Foundation Models with Partial Graphs

Estimating causal quantities traditionally relies on bespoke estimators tailored to specific assumptions. Recently proposed Causal Foundation Models (CFMs) promise a more unified approach by amortising causal discovery and inference in a single step. However, in their current state, they do not allow for the incorporation of any domain knowledge, which can lead to suboptimal predictions. We bridge this gap by introducing methods to condition CFMs on causal information, such as the causal graph or more readily available ancestral information. When access to complete causal graph information is too strict a requirement, our approach also effectively leverages partial causal information. We systematically evaluate conditioning strategies and find that injecting learnable biases into the attention mechanism is the most effective method to utilise full and partial causal information. Our experiments show that this conditioning allows a general-purpose CFM to match the performance of specialised models trained on specific causal structures. Overall, our approach addresses a central hurdle on the path towards all-in-one causal foundation models: the capability to answer causal queries in a data-driven manner while effectively leveraging any amount of domain expertise.

Identifying Intervenable and Interpretable Features via Orthogonality Regularization

With recent progress on fine-tuning language models around a fixed sparse autoencoder, we disentangle the decoder matrix into almost orthogonal features. This reduces interference and superposition between the features, while keeping performance on the target dataset essentially unchanged. Our orthogonality penalty leads to identifiable features, ensuring the uniqueness of the decomposition. Further, we find that the distance between embedded feature explanations increases with stricter orthogonality penalty, a desirable property for interpretability. Invoking the $\textit{Independent Causal Mechanisms}$ principle, we argue that orthogonality promotes modular representations amenable to causal intervention. We empirically show that these increasingly orthogonalized features allow for isolated interventions. Our code is available under $\texttt{https://github.com/mrtzmllr/sae-icm}$.

LoRA and Privacy: When Random Projections Help (and When They Don't)

We introduce the (Wishart) projection mechanism, a randomized map of the form $S \mapsto M f(S)$ with $M \sim W_d(1/r I_d, r)$ and study its differential privacy properties. For vector-valued queries $f$, we prove non-asymptotic DP guarantees without any additive noise, showing that Wishart randomness alone can suffice. For matrix-valued queries, however, we establish a sharp negative result: in the noise-free setting, the mechanism is not DP, and we demonstrate its vulnerability by implementing a near perfect membership inference attack (AUC $> 0.99$). We then analyze a noisy variant and prove privacy amplification due to randomness and low rank projection, in both large- and small-rank regimes, yielding stronger privacy guarantees than additive noise alone. Finally, we show that LoRA-style updates are an instance of the matrix-valued mechanism, implying that LoRA is not inherently private despite its built-in randomness, but that low-rank fine-tuning can be more private than full fine-tuning at the same noise level. Preliminary experiments suggest that tighter accounting enables lower noise and improved accuracy in practice.

On the Emergence and Test-Time Use of Structural Information in Large Language Models

Learning structural information from observational data is central to producing new knowledge outside the training corpus. This holds for mechanistic understanding in scientific discovery as well as flexible test-time compositional generation. We thus study how language models learn abstract structures and utilize the learnt structural information at test-time. To ensure a controlled setup, we design a natural language dataset based on linguistic structural transformations. We empirically show that the emergence of learning structural information correlates with complex reasoning tasks, and that the ability to perform test-time compositional generation remains limited.

Latent Causal Diffusions for Single-Cell Perturbation Modeling

Perturbation screens hold the potential to systematically map regulatory processes at single-cell resolution, yet modeling and predicting transcriptome-wide responses to perturbations remains a major computational challenge. Existing methods often underperform simple baselines, fail to disentangle measurement noise from biological signal, and provide limited insight into the causal structure governing cellular responses. Here, we present the latent causal diffusion (LCD), a generative model that frames single-cell gene expression as a stationary diffusion process observed under measurement noise. LCD outperforms established approaches in predicting the distributional shifts of unseen perturbation combinations in single-cell RNA-sequencing screens while simultaneously learning a mechanistic dynamical system of gene regulation. To interpret these learned dynamics, we develop an approach we call causal linearization via perturbation responses (CLIPR), which yields an approximation of the direct causal effects between all genes modeled by the diffusion. CLIPR provably identifies causal effects under a linear drift assumption and recovers causal structure in both simulated systems and a genome-wide perturbation screen, where it clusters genes into coherent functional modules and resolves causal relationships that standard differential expression analysis cannot. The LCD-CLIPR framework bridges generative modeling with causal inference to predict unseen perturbation effects and map the underlying regulatory mechanisms of the transcriptome.

Generation is Required for Data-Efficient Perception

It has been hypothesized that human-level visual perception requires a generative approach in which internal representations result from inverting a decoder. Yet today's most successful vision models are non-generative, relying on an encoder that maps images to representations without decoder inversion. This raises the question of whether generation is, in fact, necessary for machines to achieve human-level visual perception. To address this, we study whether generative and non-generative methods can achieve compositional generalization, a hallmark of human perception. Under a compositional data generating process, we formalize the inductive biases required to guarantee compositional generalization in decoder-based (generative) and encoder-based (non-generative) methods. We then show theoretically that enforcing these inductive biases on encoders is generally infeasible using regularization or architectural constraints. In contrast, for generative methods, the inductive biases can be enforced straightforwardly, thereby enabling compositional generalization by constraining a decoder and inverting it. We highlight how this inversion can be performed efficiently, either online through gradient-based search or offline through generative replay. We examine the empirical implications of our theory by training a range of generative and non-generative methods on photorealistic image datasets. We find that, without the necessary inductive biases, non-generative methods often fail to generalize compositionally and require large-scale pretraining or added supervision to improve generalization. By comparison, generative methods yield significant improvements in compositional generalization, without requiring additional data, by leveraging suitable inductive biases on a decoder along with search and replay.

Scaling Behavior of Discrete Diffusion Language Models

Modern LLM pre-training consumes vast amounts of compute and training data, making the scaling behavior, or scaling laws, of different models a key distinguishing factor. Discrete diffusion language models (DLMs) have been proposed as an alternative to autoregressive language models (ALMs). However, their scaling behavior has not yet been fully explored, with prior work suggesting that they require more data and compute to match the performance of ALMs. We study the scaling behavior of DLMs on different noise types by smoothly interpolating between masked and uniform diffusion while paying close attention to crucial hyperparameters such as batch size and learning rate. Our experiments reveal that the scaling behavior of DLMs strongly depends on the noise type and is considerably different from ALMs. While all noise types converge to similar loss values in compute-bound scaling, we find that uniform diffusion requires more parameters and less data for compute-efficient training compared to masked diffusion, making them a promising candidate in data-bound settings. We scale our uniform diffusion model up to 10B parameters trained for $10^{22}$ FLOPs, confirming the predicted scaling behavior and making it the largest publicly known uniform diffusion model to date.

A Critical Perspective on Finite Sample Conformal Prediction Theory in Medical Applications

Machine learning (ML) is transforming healthcare, but safe clinical decisions demand reliable uncertainty estimates that standard ML models fail to provide. Conformal prediction (CP) is a popular tool that allows users to turn heuristic uncertainty estimates into uncertainty estimates with statistical guarantees. CP works by converting predictions of a ML model, together with a calibration sample, into prediction sets that are guaranteed to contain the true label with any desired probability. An often cited advantage is that CP theory holds for calibration samples of arbitrary size, suggesting that uncertainty estimates with practically meaningful statistical guarantees can be achieved even if only small calibration sets are available. We question this promise by showing that, although the statistical guarantees hold for calibration sets of arbitrary size, the practical utility of these guarantees does highly depend on the size of the calibration set. This observation is relevant in medical domains because data is often scarce and obtaining large calibration sets is therefore infeasible. We corroborate our critique in an empirical demonstration on a medical image classification task.