Generative pretraining (the "GPT" in ChatGPT) enables language models to learn from vast amounts of internet text without human supervision. This approach has driven breakthroughs across AI by allowing deep neural networks to learn from massive, unstructured datasets. We use the term foundation models to refer to large pretrained systems that can be adapted to a wide range of tasks within and across domains, and these models are increasingly applied beyond language to the brain sciences. These models achieve strong predictive accuracy, raising hopes that they might illuminate computational principles. But predictive success alone does not guarantee scientific understanding. Here, we outline how foundation models can be productively integrated into the brain sciences, highlighting both their promise and their limitations. The central challenge is to move from prediction to explanation: linking model computations to mechanisms underlying neural activity and cognition.

Training large language models (LLMs) from scratch can yield models with unique functionalities and strengths, but it is costly and often leads to redundant capabilities. A more cost-effective alternative is to fuse existing pre-trained LLMs with different architectures into a more powerful model. However, a key challenge in existing model fusion is their dependence on manually predefined vocabulary alignment, which may not generalize well across diverse contexts, leading to performance degradation in several evaluation. To solve this, we draw inspiration from distribution learning and propose the probabilistic token alignment method as a general and soft mapping for alignment, named as PTA-LLM. Our approach innovatively reformulates token alignment into a classic mathematical problem: optimal transport, seamlessly leveraging distribution-aware learning to facilitate more coherent model fusion. Apart from its inherent generality, PTA-LLM exhibits interpretability from a distributional perspective, offering insights into the essence of the token alignment. Empirical results demonstrate that probabilistic token alignment enhances the target model's performance across multiple capabilities. Our code is avaliable at https://runjia.tech/neurips_pta-llm/.

As the industry increasingly adopts agentic AI systems, understanding their unique vulnerabilities becomes critical. Prior research suggests that security flaws at the model level do not fully capture the risks present in agentic deployments, where models interact with tools and external environments. This paper investigates this gap by conducting a comparative red teaming analysis of GPT-OSS-20B, a 20-billion parameter open-source model. Using our observability framework AgentSeer to deconstruct agentic systems into granular actions and components, we apply iterative red teaming attacks with harmful objectives from HarmBench at two distinct levels: the standalone model and the model operating within an agentic loop. Our evaluation reveals fundamental differences between model level and agentic level vulnerability profiles. Critically, we discover the existence of agentic-only vulnerabilities, attack vectors that emerge exclusively within agentic execution contexts while remaining inert against standalone models. Agentic level iterative attacks successfully compromise objectives that completely failed at the model level, with tool-calling contexts showing 24\% higher vulnerability than non-tool contexts. Conversely, certain model-specific exploits work exclusively at the model level and fail when transferred to agentic contexts, demonstrating that standalone model vulnerabilities do not always generalize to deployed systems.

We present the first language-model-driven agentic artificial intelligence (AI) system to autonomously execute multi-stage physics experiments on a production synchrotron light source. Implemented at the Advanced Light Source particle accelerator, the system translates natural language user prompts into structured execution plans that combine archive data retrieval, control-system channel resolution, automated script generation, controlled machine interaction, and analysis. In a representative machine physics task, we show that preparation time was reduced by two orders of magnitude relative to manual scripting even for a system expert, while operator-standard safety constraints were strictly upheld. Core architectural features, plan-first orchestration, bounded tool access, and dynamic capability selection, enable transparent, auditable execution with fully reproducible artifacts. These results establish a blueprint for the safe integration of agentic AI into accelerator experiments and demanding machine physics studies, as well as routine operations, with direct portability across accelerators worldwide and, more broadly, to other large-scale scientific infrastructures.

Despite Large Language Models (LLMs) demonstrating superior translation performance and long-context capabilities, evaluation methodologies remain constrained to sentence-level assessment due to dataset limitations, token number restrictions in metrics, and rigid sentence boundary requirements. We introduce SEGALE, an evaluation scheme that extends existing automatic metrics to long-document translation by treating documents as continuous text and applying sentence segmentation and alignment methods. Our approach enables previously unattainable document-level evaluation, handling translations of arbitrary length generated with document-level prompts while accounting for under-/over-translations and varied sentence boundaries. Experiments show our scheme significantly outperforms existing long-form document evaluation schemes, while being comparable to evaluations performed with groundtruth sentence alignments. Additionally, we apply our scheme to book-length texts and newly demonstrate that many open-weight LLMs fail to effectively translate documents at their reported maximum context lengths.

Clinical notes contain rich patient information, such as diagnoses or medications, making them valuable for patient representation learning. Recent advances in large language models have further improved the ability to extract meaningful representations from clinical texts. However, clinical notes are often missing. For example, in our analysis of the MIMIC-IV dataset, 24.5% of patients have no available discharge summaries. In such cases, representations can be learned from other modalities such as structured data, chest X-rays, or radiology reports. Yet the availability of these modalities is influenced by clinical decision-making and varies across patients, resulting in modality missing-not-at-random (MMNAR) patterns. We propose a causal representation learning framework that leverages observed data and informative missingness in multimodal clinical records. It consists of: (1) an MMNAR-aware modality fusion component that integrates structured data, imaging, and text while conditioning on missingness patterns to capture patient health and clinician-driven assignment; (2) a modality reconstruction component with contrastive learning to ensure semantic sufficiency in representation learning; and (3) a multitask outcome prediction model with a rectifier that corrects for residual bias from specific modality observation patterns. Comprehensive evaluations across MIMIC-IV and eICU show consistent gains over the strongest baselines, achieving up to 13.8% AUC improvement for hospital readmission and 13.1% for ICU admission.

Alignment plays a crucial role in Large Language Models (LLMs) in aligning with human preferences on a specific task/domain. Traditional alignment methods suffer from catastrophic forgetting, where models lose previously acquired knowledge when adapting to new preferences or domains. We introduce LifeAlign, a novel framework for lifelong alignment that enables LLMs to maintain consistent human preference alignment across sequential learning tasks without forgetting previously learned knowledge. Our approach consists of two key innovations. First, we propose a focalized preference optimization strategy that aligns LLMs with new preferences while preventing the erosion of knowledge acquired from previous tasks. Second, we develop a short-to-long memory consolidation mechanism that merges denoised short-term preference representations into stable long-term memory using intrinsic dimensionality reduction, enabling efficient storage and retrieval of alignment patterns across diverse domains. We evaluate LifeAlign across multiple sequential alignment tasks spanning different domains and preference types. Experimental results demonstrate that our method achieves superior performance in maintaining both preference alignment quality and knowledge retention compared to existing lifelong learning approaches. The codes and datasets will be released on GitHub.

We introduce MaskVCT, a zero-shot voice conversion (VC) model that offers multi-factor controllability through multiple classifier-free guidances (CFGs). While previous VC models rely on a fixed conditioning scheme, MaskVCT integrates diverse conditions in a single model. To further enhance robustness and control, the model can leverage continuous or quantized linguistic features to enhance intellgibility and speaker similarity, and can use or omit pitch contour to control prosody. These choices allow users to seamlessly balance speaker identity, linguistic content, and prosodic factors in a zero-shot VC setting. Extensive experiments demonstrate that MaskVCT achieves the best target speaker and accent similarities while obtaining competitive word and character error rates compared to existing baselines. Audio samples are available at https://maskvct.github.io/.

These limitations lead to reduced robustness and generalization, making it difficult to meet the stringent demands of intelligent manufacturing for high accuracy, adaptability, and real-time responsiveness [8]. For these challenges, Multimodal Large Language Models (MLLMs) have recently attracted significant attention as a promising paradigm for industrial vision inspection [9]. By integrating heterogeneous modalities such as images and text, MLLMs exhibit enhanced semantic understanding and cross-modal reasoning capabilities [10], which are crucial for accurately interpreting intricate industrial scenes. This capability enables them to identify subtle defect patterns that would otherwise be overlooked by unimodal vision systems [11]. However, the adoption of MLLMs in real-world industrial environments is hindered by their massive parameter scale, high computational cost, and substantial memory footprint [12]. Deploying these models directly on resource-constrained edge devices often proves infeasible [13], while cloud-only processing introduces latency that disrupts the stringent real-time requirements of industrial pipelines [14]. To address these issues, we propose SAEC, a scene-aware enhanced edge-cloud collaborative industrial vision inspection framework with MLLM. The central idea of SAEC is to integrate scene-aware mechanisms with an edge-cloud collaborative architecture in order to balance accuracy and efficiency. By harmonizing multimodal reasoning with adaptive task scheduling across edge and cloud resources, SAEC achieves robust defect detection under complex scenarios, while maintaining scalability, resource efficiency, and practicality for deployment in real-world manufacturing systems.

Relational object rearrangement (ROR) tasks (e.g., insert flower to vase) require a robot to manipulate objects with precise semantic and geometric reasoning. Existing approaches either rely on pre-collected demonstrations that struggle to capture complex geometric constraints or generate goal-state observations to capture semantic and geometric knowledge, but fail to explicitly couple object transformation with action prediction, resulting in errors due to generative noise. To address these limitations, we propose Imagine2Act, a 3D imitation-learning framework that incorporates semantic and geometric constraints of objects into policy learning to tackle high-precision manipulation tasks. We first generate imagined goal images conditioned on language instructions and reconstruct corresponding 3D point clouds to provide robust semantic and geometric priors. These imagined goal point clouds serve as additional inputs to the policy model, while an object-action consistency strategy with soft pose supervision explicitly aligns predicted end-effector motion with generated object transformation. This design enables Imagine2Act to reason about semantic and geometric relationships between objects and predict accurate actions across diverse tasks. Experiments in both simulation and the real world demonstrate that Imagine2Act outperforms previous state-of-the-art policies. More visualizations can be found at https://sites.google.com/view/imagine2act.