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.

The interpretability of deep neural networks has become a subject of great interest within the medical and healthcare domain. This attention stems from concerns regarding transparency, legal and ethical considerations, and the medical significance of predictions generated by these deep neural networks in clinical decision support systems. To address this matter, our study delves into the application of four well-established interpretability methods: Local Interpretable Model-agnostic Explanations (LIME), Shapley Additive exPlanations (SHAP), Gradient-weighted Class Activation Mapping (Grad-CAM), and Layer-wise Relevance Propagation (LRP). Leveraging the approach of transfer learning with a multi-label-multi-class chest radiography dataset, we aim to interpret predictions pertaining to specific pathology classes. Our analysis encompasses both single-label and multi-label predictions, providing a comprehensive and unbiased assessment through quantitative and qualitative investigations, which are compared against human expert annotation. Notably, Grad-CAM demonstrates the most favorable performance in quantitative evaluation, while the LIME heatmap score segmentation visualization exhibits the highest level of medical significance. Our research underscores both the outcomes and the challenges faced in the holistic approach adopted for assessing these interpretability methods and suggests that a multimodal-based approach, incorporating diverse sources of information beyond chest radiography images, could offer additional insights for enhancing interpretability in the medical domain.

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/.

With the increasing availability and affordability of personal robots, they will no longer be confined to large corporate warehouses or factories but will instead be expected to operate in less controlled environments alongside larger groups of people. In addition to ensuring safety and efficiency, it is crucial to minimize any negative psychological impact robots may have on humans and follow unwritten social norms in these situations. Our research aims to develop a model that can predict the movements of pedestrians and perceptually-social groups in crowded environments. We introduce a new Social Group Long Short-term Memory (SG-LSTM) model that models human groups and interactions in dense environments using a socially-aware LSTM to produce more accurate trajectory predictions. Our approach enables navigation algorithms to calculate collision-free paths faster and more accurately in crowded environments. Additionally, we also release a large video dataset with labeled pedestrian groups for the broader social navigation community. We show comparisons with different metrics on different datasets (ETH, Hotel, MOT15) and different prediction approaches (LIN, LSTM, O-LSTM, S-LSTM) as well as runtime performance.

Vision language tasks, such as answering questions about or generating captions that describe an image, are difficult tasks for computers to perform. A relatively recent body of research has adapted the pretrained transformer architecture introduced in \citet{vaswani2017attention} to vision language modeling. Transformer models have greatly improved performance and versatility over previous vision language models. They do so by pretraining models on a large generic datasets and transferring their learning to new tasks with minor changes in architecture and parameter values. This type of transfer learning has become the standard modeling practice in both natural language processing and computer vision. Vision language transformers offer the promise of producing similar advancements in tasks which require both vision and language. In this paper, we provide a broad synthesis of the currently available research on vision language transformer models and offer some analysis of their strengths, limitations and some open questions that remain.

Driver gaze plays an important role in different gaze-based applications such as driver attentiveness detection, visual distraction detection, gaze behavior understanding, and building driver assistance system. The main objective of this study is to perform a comprehensive summary of driver gaze fundamentals, methods to estimate driver gaze, and it's applications in real world driving scenarios. We first discuss the fundamentals related to driver gaze, involving head-mounted and remote setup based gaze estimation and the terminologies used for each of these data collection methods. Next, we list out the existing benchmark driver gaze datasets, highlighting the collection methodology and the equipment used for such data collection. This is followed by a discussion of the algorithms used for driver gaze estimation, which primarily involves traditional machine learning and deep learning based techniques. The estimated driver gaze is then used for understanding gaze behavior while maneuvering through intersections, on-ramps, off-ramps, lane changing, and determining the effect of roadside advertising structures. Finally, we have discussed the limitations in the existing literature, challenges, and the future scope in driver gaze estimation and gaze-based applications.

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.

Classification of whole-brain functional connectivity MRI data with convolutional neural networks (CNNs) has shown promise, but the complexity of these models impedes understanding of which aspects of brain activity contribute to classification. While visualization techniques have been developed to interpret CNNs, bias inherent in the method of encoding abstract input data, as well as the natural variance of deep learning models, detract from the accuracy of these techniques. We introduce a stochastic encoding method in an ensemble of CNNs to classify functional connectomes by gender. We applied our method to resting-state and task data from the UK BioBank, using two visualization techniques to measure the salience of three brain networks involved in task- and resting-states, and their interaction. To regress confounding factors such as head motion, age, and intracranial volume, we introduced a multivariate balancing algorithm to ensure equal distributions of such covariates between classes in our data. We achieved a final AUROC of 0.8459. We found that resting-state data classifies more accurately than task data, with the inner salience network playing the most important role of the three networks overall in classification of resting-state data and connections to the central executive network in task data.