The rapid proliferation of large language models (LLMs) has fundamentally transformed scientific computing, enabling breakthroughs across domains from computational biology to materials science. As these models scale to hundreds of billions of parameters, high-performance computing (HPC) facilities face mounting challenges in providing sustainable, cost-effective inference capabilities to diverse research communities. Traditional GPU-centric approaches, while delivering exceptional throughput, present significant barriers in terms of power consumption, cooling requirements, and capital investment, particularly problematic for shared research cyberinfrastructures serving hundreds of concurrent users. The National Research Platform (NRP) exemplifies these challenges and opportunities. As a federated Kubernetes-based infrastructure supporting over 300 research groups across over 100 sites, the NRP must balance competing demands: delivering high-performance AI capabilities while managing constrained power budgets, enabling fine-grained resource allocation for multi-tenant workloads, and providing cost-effective access to emerging AI models for diverse scientific applications [1, 2]. 1

Trustworthy language models should provide both correct and verifiable answers. However, citations generated directly by standalone LLMs are often unreliable. As a result, current systems insert citations by querying an external retriever at inference time, introducing latency, infrastructure dependence, and vulnerability to retrieval noise. We explore whether LLMs can be made to reliably attribute to the documents seen during continual pretraining without test-time retrieval, by revising the training process. To study this, we construct CitePretrainBench, a benchmark that mixes real-world corpora (Wikipedia, Common Crawl, arXiv) with novel documents and probes both short-form (single-fact) and long-form (multi-fact) citation tasks. Our approach follows a two-stage process: (1) continual pretraining to index factual knowledge by binding it to persistent document identifiers; and (2) instruction tuning to elicit citation behavior. We introduce Active Indexing for the first stage, which creates generalizable, source-anchored bindings by augmenting training with synthetic data that (i) restate each fact in diverse, compositional forms and (ii) enforce bidirectional training (source-to-fact and fact-to-source). This equips the model to both generate content from a cited source and attribute its own answers, improving robustness to paraphrase and composition. Experiments with Qwen-2.5-7B&3B show that Active Indexing consistently outperforms a Passive Indexing baseline, which simply appends an identifier to each document, achieving citation precision gains of up to 30.2% across all tasks and models. Our ablation studies reveal that performance continues to improve as we scale the amount of augmented data, showing a clear upward trend even at 16x the original token count. Finally, we show that internal citations complement external ones by making the model more robust to retrieval noise.

Generative models in function spaces, situated at the intersection of generative modeling and operator learning, are attracting increasing attention due to their immense potential in diverse scientific and engineering applications. While functional generative models are theoretically domain- and discretization-agnostic, current implementations heavily rely on the Fourier Neural Operator (FNO), limiting their applicability to regular grids and rectangular domains. To overcome these critical limitations, we introduce the Mesh-Informed Neural Operator (MINO). By leveraging graph neural operators and cross-attention mechanisms, MINO offers a principled, domain- and discretization-agnostic backbone for generative modeling in function spaces. This advancement significantly expands the scope of such models to more diverse applications in generative, inverse, and regression tasks. Furthermore, MINO provides a unified perspective on integrating neural operators with general advanced deep learning architectures. Finally, we introduce a suite of standardized evaluation metrics that enable objective comparison of functional generative models, addressing another critical gap in the field.

Training reasoning language models (LMs) with reinforcement learning (RL) for one-hot correctness inherently relies on the LM being able to explore and solve its task with some chance at initialization. Furthermore, a key use case of reasoning LMs is to act as teachers for distilling new students and cold-starting future RL iterations rather than being deployed themselves. From these considerations, we introduce a new framework that avoids RL's exploration challenge by training a new class of Reinforcement-Learned Teachers (RLTs) focused on yielding the most effective downstream distillation. RLTs are prompted with both the question and solution to each problem, and tasked to simply "connect-the-dots" with detailed explanations tailored for their students. We train RLTs with dense rewards obtained by feeding each explanation to the student and testing its understanding of the problem's solution. In practice, the raw outputs of a 7B RLT provide higher final performance on competition and graduate-level tasks than existing distillation and cold-starting pipelines that collect and postprocess the reasoning traces of orders of magnitude larger LMs. Furthermore, RLTs maintain their effectiveness when training larger students and when applied zero-shot to out-of-distribution tasks, unlocking new levels of efficiency and re-usability for the RL reasoning framework. Code available at: https://github.com/SakanaAI/RLT

Machine learning techniques offer an effective approach to modeling dynamical systems solely from observed data. However, without explicit structural priors -- built-in assumptions about the underlying dynamics -- these techniques typically struggle to generalize to aspects of the dynamics that are poorly represented in the training data. Here, we demonstrate that reservoir computing -- a simple, efficient, and versatile machine learning framework often used for data-driven modeling of dynamical systems -- can generalize to unexplored regions of state space without explicit structural priors. First, we describe a multiple-trajectory training scheme for reservoir computers that supports training across a collection of disjoint time series, enabling effective use of available training data. Then, applying this training scheme to multistable dynamical systems, we show that RCs trained on trajectories from a single basin of attraction can achieve out-of-domain generalization by capturing system behavior in entirely unobserved basins.

Finite-sum Coupled Compositional Optimization (FCCO), characterized by its coupled compositional objective structure, emerges as an important optimization paradigm for addressing a wide range of machine learning problems. In this paper, we focus on a challenging class of non-convex non-smooth FCCO, where the outer functions are non-smooth weakly convex or convex and the inner functions are smooth or weakly convex. Existing state-of-the-art result face two key limitations: (1) a high iteration complexity of $O(1/ε^6)$ under the assumption that the stochastic inner functions are Lipschitz continuous in expectation; (2) reliance on vanilla SGD-type updates, which are not suitable for deep learning applications. Our main contributions are two fold: (i) We propose stochastic momentum methods tailored for non-smooth FCCO that come with provable convergence guarantees; (ii) We establish a new state-of-the-art iteration complexity of $O(1/ε^5)$. Moreover, we apply our algorithms to multiple inequality constrained non-convex optimization problems involving smooth or weakly convex functional inequality constraints. By optimizing a smoothed hinge penalty based formulation, we achieve a new state-of-the-art complexity of $O(1/ε^5)$ for finding an (nearly) $ε$-level KKT solution. Experiments on three tasks demonstrate the effectiveness of the proposed algorithms.

In-context learning (ICL) enables large language models (LLMs) to perform new tasks using only a few demonstrations. However, in Named Entity Recognition (NER), existing ICL methods typically rely on task-agnostic semantic similarity for demonstration retrieval, which often yields less relevant examples and leads to inferior results. We introduce DEER, a training-free ICL approach that enables LLMs to make more informed entity predictions through the use of label-grounded statistics. DEER leverages token-level statistics from training labels to identify tokens most informative for entity recognition, enabling entity-focused demonstrations. It further uses these statistics to detect and refine error-prone tokens through a targeted reflection step. Evaluated on five NER datasets across four LLMs, DEER consistently outperforms existing ICL methods and achieves performance comparable to supervised fine-tuning. Further analyses demonstrate that DEER improves example retrieval, remains effective on both seen and unseen entities, and exhibits strong robustness in low-resource settings.

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or are deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against deep learning models and a naive SMARTS pattern based classifier. C3PO outperforms the naive classifier, but does not reach the performance of state of the art deep learning methods. However, C3PO has a number of strengths that complement deep learning methods, including explainability and reduced data dependence. C3PO can be used alongside deep learning classifiers to provide an explanation of the classification, where both methods agree. The programs can be used as part of the ontology development process, and iteratively refined by expert human curators.

Recent studies indicate that deep neural networks degrade in generalization performance under noisy supervision. Existing methods focus on isolating clean subsets or correcting noisy labels, facing limitations such as high computational costs, heavy hyperparameter tuning process, and coarse-grained optimization. To address these challenges, we propose a novel two-stage noisy learning framework that enables instance-level optimization through a dynamically weighted loss function, avoiding hyperparameter tuning. To obtain stable and accurate information about noise modeling, we introduce a simple yet effective metric, termed wrong event, which dynamically models the cleanliness and difficulty of individual samples while maintaining computational costs. Our framework first collects wrong event information and builds a strong base model. Then we perform noise-robust training on the base model, using a probabilistic model to handle the wrong event information of samples. Experiments on five synthetic and real-world LNL benchmarks demonstrate our method surpasses state-of-the-art methods in performance, achieves a nearly 75% reduction in computational time and improves model scalability.

We propose a method for variable selection in the intensity function of spatial point processes that combines sparsity-promoting estimation with noise-robust model selection. As high-resolution spatial data becomes increasingly available through remote sensing and automated image analysis, identifying spatial covariates that influence the localization of events is crucial to understand the underlying mechanism. However, results from automated acquisition techniques are often noisy, for example due to measurement uncertainties or detection errors, which leads to spurious displacements and missed events. We study the impact of such noise on sparse point-process estimation across different models, including Poisson and Thomas processes. To improve noise robustness, we propose to use stability selection based on point-process subsampling and to incorporate a non-convex best-subset penalty to enhance model-selection performance. In extensive simulations, we demonstrate that such an approach reliably recovers true covariates under diverse noise scenarios and improves both selection accuracy and stability. We then apply the proposed method to a forestry data set, analyzing the distribution of trees in relation to elevation and soil nutrients in a tropical rain forest. This shows the practical utility of the method, which provides a systematic framework for robust variable selection in spatial point-process models under noise, without requiring additional knowledge of the process.