Daily Papers

Conversational tutoring systems (CTSs) offer learning experiences driven by natural language interaction. They are known to promote high levels of cognitive engagement and benefit learning outcomes, particularly in reasoning tasks. Nonetheless, the time and cost required to author CTS content is a major obstacle to widespread adoption. In this paper, we introduce a novel type of CTS that leverages the recent advances in large language models (LLMs) in two ways: First, the system induces a tutoring script automatically from a lesson text. Second, the system automates the script orchestration via two LLM-based agents (Ruffle&Riley) with the roles of a student and a professor in a learning-by-teaching format. The system allows a free-form conversation that follows the ITS-typical inner and outer loop structure. In an initial between-subject online user study (N = 100) comparing Ruffle&Riley to simpler QA chatbots and reading activity, we found no significant differences in post-test scores. Nonetheless, in the learning experience survey, Ruffle&Riley users expressed higher ratings of understanding and remembering and further perceived the offered support as more helpful and the conversation as coherent. Our study provides insights for a new generation of scalable CTS technologies.

Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial intelligence-driven protein design. However, we lack a sufficient understanding of how very large-scale models and data play a role in effective protein model development. We introduce a suite of protein language models, named ProGen2, that are scaled up to 6.4B parameters and trained on different sequence datasets drawn from over a billion proteins from genomic, metagenomic, and immune repertoire databases. ProGen2 models show state-of-the-art performance in capturing the distribution of observed evolutionary sequences, generating novel viable sequences, and predicting protein fitness without additional finetuning. As large model sizes and raw numbers of protein sequences continue to become more widely accessible, our results suggest that a growing emphasis needs to be placed on the data distribution provided to a protein sequence model. We release the ProGen2 models and code at https://github.com/salesforce/progen.

Objective: While recent advances in text-conditioned generative models have enabled the synthesis of realistic medical images, progress has been largely confined to 2D modalities such as chest X-rays. Extending text-to-image generation to volumetric Computed Tomography (CT) remains a significant challenge, due to its high dimensionality, anatomical complexity, and the absence of robust frameworks that align vision-language data in 3D medical imaging. Methods: We introduce a novel architecture for Text-to-CT generation that combines a latent diffusion model with a 3D contrastive vision-language pretraining scheme. Our approach leverages a dual-encoder CLIP-style model trained on paired CT volumes and radiology reports to establish a shared embedding space, which serves as the conditioning input for generation. CT volumes are compressed into a low-dimensional latent space via a pretrained volumetric VAE, enabling efficient 3D denoising diffusion without requiring external super-resolution stages. Results: We evaluate our method on the CT-RATE dataset and conduct a comprehensive assessment of image fidelity, clinical relevance, and semantic alignment. Our model achieves competitive performance across all tasks, significantly outperforming prior baselines for text-to-CT generation. Moreover, we demonstrate that CT scans synthesized by our framework can effectively augment real data, improving downstream diagnostic performance. Conclusion: Our results show that modality-specific vision-language alignment is a key component for high-quality 3D medical image generation. By integrating contrastive pretraining and volumetric diffusion, our method offers a scalable and controllable solution for synthesizing clinically meaningful CT volumes from text, paving the way for new applications in data augmentation, medical education, and automated clinical simulation.

Deep-learning (DL) compilers such as TVM and TensorRT are increasingly being used to optimize deep neural network (DNN) models to meet performance, resource utilization and other requirements. Bugs in these compilers can result in models whose semantics differ from the original ones, producing incorrect results that corrupt the correctness of downstream applications. However, finding bugs in these compilers is challenging due to their complexity. In this work, we propose a new fuzz testing approach for finding bugs in deep-learning compilers. Our core approach consists of (i) generating diverse yet valid DNN test models that can exercise a large part of the compiler's transformation logic using light-weight operator specifications; (ii) performing gradient-based search to find model inputs that avoid any floating-point exceptional values during model execution, reducing the chance of missed bugs or false alarms; and (iii) using differential testing to identify bugs. We implemented this approach in NNSmith which has found 72 new bugs for TVM, TensorRT, ONNXRuntime, and PyTorch to date. Of these 58 have been confirmed and 51 have been fixed by their respective project maintainers.

As recently demonstrated, Deep Neural Networks (DNN), usually trained using single precision IEEE 754 floating point numbers (binary32), can also work using lower precision. Therefore, 16-bit and 8-bit compressed format have attracted considerable attention. In this paper, we focused on two families of formats that have already achieved interesting results in compressing binary32 numbers in machine learning applications, without sensible degradation of the accuracy: bfloat and posit. Even if 16-bit and 8-bit bfloat/posit are routinely used for reducing the storage of the weights/biases of trained DNNs, the inference still often happens on the 32-bit FPU of the CPU (especially if GPUs are not available). In this paper we propose a way to decompress a tensor of bfloat/posits just before computations, i.e., after the compressed operands have been loaded within the vector registers of a vector capable CPU, in order to save bandwidth usage and increase cache efficiency. Finally, we show the architectural parameters and considerations under which this solution is advantageous with respect to the uncompressed one.

Histopathology plays a central role in clinical medicine and biomedical research. While artificial intelligence shows promising results on many pathological tasks, generalization and dealing with rare diseases, where training data is scarce, remains a challenge. Distilling knowledge from unlabeled data into a foundation model before learning from, potentially limited, labeled data provides a viable path to address these challenges. In this work, we extend the state of the art of foundation models for digital pathology whole slide images by semi-automated data curation and incorporating pathologist domain knowledge. Specifically, we combine computational and pathologist domain knowledge (1) to curate a diverse dataset of 103k slides corresponding to 750 million image patches covering data from different fixation, staining, and scanning protocols as well as data from different indications and labs across the EU and US, (2) for grouping semantically similar slides and tissue patches, and (3) to augment the input images during training. We evaluate the resulting model on a set of public and internal benchmarks and show that although our foundation model is trained with an order of magnitude less slides, it performs on par or better than competing models. We expect that scaling our approach to more data and larger models will further increase its performance and capacity to deal with increasingly complex real world tasks in diagnostics and biomedical research.

Pathology foundation models substantially advanced the possibilities in computational pathology -- yet tradeoffs in terms of performance, robustness, and computational requirements remained, which limited their clinical deployment. In this report, we present Atlas 2, Atlas 2-B, and Atlas 2-S, three pathology vision foundation models which bridge these shortcomings by showing state-of-the-art performance in prediction performance, robustness, and resource efficiency in a comprehensive evaluation across eighty public benchmarks. Our models were trained on the largest pathology foundation model dataset to date comprising 5.5 million histopathology whole slide images, collected from three medical institutions Charité - Universtätsmedizin Berlin, LMU Munich, and Mayo Clinic.

Biomedical Foundation Models (FMs) are rapidly transforming AI-enabled healthcare research and entering clinical validation. However, their susceptibility to learning non-biological technical features -- including variations in surgical/endoscopic techniques, laboratory procedures, and scanner hardware -- poses risks for clinical deployment. We present the first systematic investigation of pathology FM robustness to non-biological features. Our work (i) introduces measures to quantify FM robustness, (ii) demonstrates the consequences of limited robustness, and (iii) proposes a framework for FM robustification to mitigate these issues. Specifically, we developed PathoROB, a robustness benchmark with three novel metrics, including the robustness index, and four datasets covering 28 biological classes from 34 medical centers. Our experiments reveal robustness deficits across all 20 evaluated FMs, and substantial robustness differences between them. We found that non-robust FM representations can cause major diagnostic downstream errors and clinical blunders that prevent safe clinical adoption. Using more robust FMs and post-hoc robustification considerably reduced (but did not yet eliminate) the risk of such errors. This work establishes that robustness evaluation is essential for validating pathology FMs before clinical adoption and demonstrates that future FM development must integrate robustness as a core design principle. PathoROB provides a blueprint for assessing robustness across biomedical domains, guiding FM improvement efforts towards more robust, representative, and clinically deployable AI systems that prioritize biological information over technical artifacts.

Understanding how deep learning models predict oncology patient risk can provide critical insights into disease progression, support clinical decision-making, and pave the way for trustworthy and data-driven precision medicine. Building on recent advances in the spatial modeling of the tumor microenvironment using graph neural networks, we present an explainable cell graph (xCG) approach for survival prediction. We validate our model on a public cohort of imaging mass cytometry (IMC) data for 416 cases of lung adenocarcinoma. We explain survival predictions in terms of known phenotypes on the cell level by computing risk attributions over cell graphs, for which we propose an efficient grid-based layer-wise relevance propagation (LRP) method. Our ablation studies highlight the importance of incorporating the cancer stage and model ensembling to improve the quality of risk estimates. Our xCG method, together with the IMC data, is made publicly available to support further research.

Medical foundation models, pre-trained with large-scale clinical data, demonstrate strong performance in diverse clinically relevant applications. RETFound, trained on nearly one million retinal images, exemplifies this approach in applications with retinal images. However, the emergence of increasingly powerful and multifold larger generalist foundation models such as DINOv2 and DINOv3 raises the question of whether domain-specific pre-training remains essential, and if so, what gap persists. To investigate this, we systematically evaluated the adaptability of DINOv2 and DINOv3 in retinal image applications, compared to two specialist RETFound models, RETFound-MAE and RETFound-DINOv2. We assessed performance on ocular disease detection and systemic disease prediction using two adaptation strategies: fine-tuning and linear probing. Data efficiency and adaptation efficiency were further analysed to characterise trade-offs between predictive performance and computational cost. Our results show that although scaling generalist models yields strong adaptability across diverse tasks, RETFound-DINOv2 consistently outperforms these generalist foundation models in ocular-disease detection and oculomics tasks, demonstrating stronger generalisability and data efficiency. These findings suggest that specialist retinal foundation models remain the most effective choice for clinical applications, while the narrowing gap with generalist foundation models suggests that continued data and model scaling can deliver domain-relevant gains and position them as strong foundations for future medical foundation models.

Language identification (LID) is a fundamental step in curating multilingual corpora. However, LID models still perform poorly for many languages, especially on the noisy and heterogeneous web data often used to train multilingual language models. In this paper, we introduce CommonLID, a community-driven, human-annotated LID benchmark for the web domain, covering 109 languages. Many of the included languages have been previously under-served, making CommonLID a key resource for developing more representative high-quality text corpora. We show CommonLID's value by using it, alongside five other common evaluation sets, to test eight popular LID models. We analyse our results to situate our contribution and to provide an overview of the state of the art. In particular, we highlight that existing evaluations overestimate LID accuracy for many languages in the web domain. We make CommonLID and the code used to create it available under an open, permissive license.

Young exoplanets provide a critical link between understanding planet formation and atmospheric evolution. Direct imaging spectroscopy allows us to infer the properties of young, wide orbit, giant planets with high signal-to-noise. This allows us to compare this young population to exoplanets characterized with transmission spectroscopy, which has indirectly revealed the presence of clouds, photochemistry, and a diversity of atmospheric compositions. Direct detections have also been made for brown dwarfs, but direct studies of young giant planets in the mid-infrared were not possible prior to JWST. With two exoplanets around a solar type star, the YSES-1 system is an ideal laboratory for studying this early phase of exoplanet evolution. We report the first direct observations of silicate clouds in the atmosphere of the exoplanet YSES-1 c through its 9-11 micron absorption feature, and the first circumplanetary disk silicate emission around its sibling planet, YSES-1 b. The clouds of YSES-1 c are composed of either amorphous iron-enriched pyroxene or a combination of amorphous MgSiO3 and Mg2SiO4, with particle sizes of less than or equal to 0.1 micron at 1 millibar of pressure. We attribute the emission from the disk around YSES-1 b to be from submicron olivine dust grains, which may have formed through collisions of planet-forming bodies in the disk.