We present Apertus, a fully open suite of large language models (LLMs) designed to address two systemic shortcomings in today's open model ecosystem: data compliance and multilingual representation. Unlike many prior models that release weights without reproducible data pipelines or regard for content-owner rights, Apertus models are pretrained exclusively on openly available data, retroactively respecting `robots.txt` exclusions and filtering for non-permissive, toxic, and personally identifiable content. To mitigate risks of memorization, we adopt the Goldfish objective during pretraining, strongly suppressing verbatim recall of data while retaining downstream task performance. The Apertus models also expand multilingual coverage, training on 15T tokens from over 1800 languages, with ~40% of pretraining data allocated to non-English content. Released at 8B and 70B scales, Apertus approaches state-of-the-art results among fully open models on multilingual benchmarks, rivalling or surpassing open-weight counterparts. Beyond model weights, we release all scientific artifacts from our development cycle with a permissive license, including data preparation scripts, checkpoints, evaluation suites, and training code, enabling transparent audit and extension.

Stellarators are magnetic confinement devices under active development to deliver steady-state carbon-free fusion energy. Their design involves a high-dimensional, constrained optimization problem that requires expensive physics simulations and significant domain expertise. Recent advances in plasma physics and open-source tools have made stellarator optimization more accessible. However, broader community progress is currently bottlenecked by the lack of standardized optimization problems with strong baselines and datasets that enable data-driven approaches, particularly for quasi-isodynamic (QI) stellarator configurations, considered as a promising path to commercial fusion due to their inherent resilience to current driven disruptions. Here, we release an open dataset of diverse QI-like stellarator plasma boundary shapes, paired with their ideal magnetohydrodynamic (MHD) equilibria and performance metrics. We generated this dataset by sampling a variety of QI fields and optimizing corresponding stellarator plasma boundaries. We introduce three optimization benchmarks of increasing complexity: (1) a single objective geometric optimization problem, (2) a "simple-to-build" QI stellarator, and (3) a multi-objective ideal-MHD stable QI stellarator that investigates trade-offs between compactness and coil simplicity. For every benchmark, we provide reference code, evaluation scripts, and strong baselines based on classical optimization techniques. Finally, we show how learned models trained on our dataset can efficiently generate novel, feasible configurations without querying expensive physics oracles. By openly releasing the dataset along with benchmark problems and baselines, we aim to lower the entry barrier for optimization and machine learning researchers to engage in stellarator design and to accelerate cross-disciplinary progress toward bringing fusion energy to the grid.

Variant effect predictors (VEPs) aim to assess the functional impact of protein variants, traditionally relying on multiple sequence alignments (MSAs). This approach assumes that naturally occurring variants are fit, an assumption challenged by pharmacogenomics, where some pharmacogenes experience low evolutionary pressure. Deep mutational scanning (DMS) datasets provide an alternative by offering quantitative fitness scores for variants. In this work, we propose a transformer-based matrix variational auto-encoder (matVAE) with a structured prior and evaluate its performance on 33 DMS datasets corresponding to 26 drug target and ADME proteins from the ProteinGym benchmark. Our model trained on MSAs (matVAE-MSA) outperforms the state-of-the-art DeepSequence model in zero-shot prediction on DMS datasets, despite using an order of magnitude fewer parameters and requiring less computation at inference time. We also compare matVAE-MSA to matENC-DMS, a model of similar capacity trained on DMS data, and find that the latter performs better on supervised prediction tasks. Additionally, incorporating AlphaFold-generated structures into our transformer model further improves performance, achieving results comparable to DeepSequence trained on MSAs and finetuned on DMS. These findings highlight the potential of DMS datasets to replace MSAs without significant loss in predictive performance, motivating further development of DMS datasets and exploration of their relationships to enhance variant effect prediction.

As machine learning technology gets applied to actual products and solutions, new challenges have emerged. Models unexpectedly fail to generalize to small changes in the distribution, tend to be confident on novel data they have never seen, or cannot communicate the rationale behind their decisions effectively with the end users. Collectively, we face a trustworthiness issue with the current machine learning technology. This textbook on Trustworthy Machine Learning (TML) covers a theoretical and technical background of four key topics in TML: Out-of-Distribution Generalization, Explainability, Uncertainty Quantification, and Evaluation of Trustworthiness. We discuss important classical and contemporary research papers of the aforementioned fields and uncover and connect their underlying intuitions. The book evolved from the homonymous course at the University of T\"ubingen, first offered in the Winter Semester of 2022/23. It is meant to be a stand-alone product accompanied by code snippets and various pointers to further sources on topics of TML. The dedicated website of the book is https://trustworthyml.io/.

Differentially private gradient descent (DP-GD) has been extremely effective both theoretically, and in practice, for solving private empirical risk minimization (ERM) problems. In this paper, we focus on understanding the impact of the clipping norm, a critical component of DP-GD, on its convergence. We provide the first formal convergence analysis of clipped DP-GD. More generally, we show that the value which one sets for clipping really matters: done wrong, it can dramatically affect the resulting quality; done properly, it can eliminate the dependence of convergence on the model dimensionality. We do this by showing a dichotomous behavior of the clipping norm. First, we show that if the clipping norm is set smaller than the optimal, even by a constant factor, the excess empirical risk for convex ERMs can increase from $O(1/n)$ to $\Omega(1)$, where $n$ is the number of data samples. Next, we show that, regardless of the value of the clipping norm, clipped DP-GD minimizes a well-defined convex objective over an unconstrained space, as long as the underlying ERM is a generalized linear problem. Furthermore, if the clipping norm is set within at most a constant factor higher than the optimal, then one can obtain an excess empirical risk guarantee that is independent of the dimensionality of the model space. Finally, we extend our result to non-convex generalized linear problems by showing that DP-GD reaches a first-order stationary point as long as the loss is smooth, and the convergence is independent of the dimensionality of the model space.

Filial imprinting in domestic chicks is of interest in psychology, biology, and computational modeling because it exemplifies simple, rapid, innately programmedlearning which is biased toward learning about some objects. Hom et al. have recently discovered a naive visual preference for heads and necks which develops over the course of the first three days of life. The neurological basis of this predisposition is almost entirely unknown;that of imprinting-related learning is fairly clear. This project is the first model of the predisposition consistent with what is known about learning in imprinting. The model develops the predisposition appropriately,learns to "approach" a training object, and replicates one interaction between the two processes. Future work will replicate more interactions between imprinting and the predisposition in chicks, and analyze why the system works.