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01.
medRxiv (Medicine) 2026-06-11

Two modes of aversive control in suicidality: joint computational modelling exposes regime-specific clinical signatures invisible to symptom-based stratification

Suicidal thoughts and behaviours (STBs) are heterogeneous in their proximal dynamics, planning, and stress-sensitivity, yet most subtyping efforts remain symptom-driven and rarely validated across independent datasets. Computational mixture modelling offers a principled alternative: by fitting explicit models of learning and action selection and partitioning individuals by their latent parameter profiles, it can identify mechanistically distinct control strategies invisible to cross-sectional symptom measurement. We applied this approach to aversive Go/NoGo performance, jointly clustering two independently collected STB-enriched samples (N = 50 and N = 184) using tasks with the same structure but different duration, reversal timing, and clinical instrumentation. Two recurrent behavioural regimes emerged: a fast/adaptive regime characterised by rapid policy updating and elevated feedback reactivity, and a slow/perseverative regime characterised by slow updating, high choice determinism, and a pronounced cost following contingency reversal. These regimes were stable across initialisations, recovered more parsimoniously in joint than independent solutions, and were largely orthogonal to symptom-based stratification. Critically, stratification by regime exposed clinical-computational coupling structures substantially attenuated in pooled analyses. Pooled, population-level associations were modest and anchored by a broad affective burden axis. Within the slow/perseverative regime, coupling reorganised around learning dynamics and internalizing burden (depression, hopelessness, and active suicidal ideation) with markedly larger effect sizes. Within the fast/adaptive regime, a dissociation between anxious-compulsive and antisocial-disinhibitory profiles emerged along the same computational axis, invisible at the population level. These findings support a view of suicidality heterogeneity in which clinically similar individuals differ in the control strategies they recruit under aversive uncertainty - variation that symptom measurement alone cannot capture.

02.
arXiv (CS.AI) 2026-06-12

Boosting Direct Preference Optimization with Penalization

作者:

arXiv:2606.12505v1 Announce Type: cross Abstract: Offline preference optimization has become a practical substitute for reinforcement learning from human feedback, but pairwise objectives such as Direct Preference Optimization (DPO) and its variants use only the chosen and rejected responses stored in a static dataset. This leaves a useful signal unused: the response that the reference model itself would generate for the same prompt. We propose Direct Preference Optimization with Penalization (DPOP), a simple extension of DPO that augments the base preference loss with a gated penalty on reference-greedy responses. DPOP activates this penalty only when the current policy still assigns a lower likelihood to the preferred response than to the rejected response. On AlpacaEval 2.0, DPOP improves length-controlled win rate over DPO, SimPO, and AlphaDPO on both Llama-3-8b-it and Gemma-2-9b-it, achieving relative gains of 5.3\% and 4.4\% over baselines on the two models, respectively. Ablations further show that a SimNPO-style length-normalized penalty is stronger than NPO and token-level unlikelihood in this setting.

03.
arXiv (CS.AI) 2026-06-11

READER: Robust Evidence-based Authorship Decoding via Extracted Representations

arXiv:2606.10794v2 Announce Type: replace Abstract: As agentic applications increasingly route user tasks through official and third-party LLM APIs, provenance becomes an operational question: which model generated a given black-box response? We study Dynamic Black-Box LLM Provenance: identifying the source LLM from generations elicited by query-varying, non-predefined prompts rather than a fixed input set or benchmark suite. This setting is difficult because prompt semantics dominate the text, while model-specific authorship traces are weak and inconsistent at the surface level. We introduce READER (Robust Evidence-based Authorship Decoding via Extracted Representations), a lightweight provenance framework that treats a frozen proxy LLM as a reader of hidden authorship evidence. READER maps black-box outputs into proxy activation space, temporally filters token states within each response, and performs Bayesian Evidence Accumulation by summing single-response log-posterior evidence across independently sampled prompts. This avoids fragile mean-pooling of prompt-specific representations while preserving the query-wise evidence needed for calibrated confidence. On Agent500, a 50-target dataset built from agent-style prompts, READER reaches $31.0$-$42.4\%$ top-1 accuracy from a single response and $70.0$-$84.0\%$ from 50 responses, substantially outperforming sentence-encoder fingerprints. Scaling across nine proxy readers further shows that stronger LLMs expose more linearly decodable authorship structure, suggesting that authorship perception is already present in frozen LLM representations and can be converted into reliable multi-query attribution.

04.
arXiv (CS.LG) 2026-06-11

Projected random forests and conformal prediction of circular data

arXiv:2410.24145v3 Announce Type: replace-cross Abstract: We apply conformal prediction techniques to regression problems with circular responses, producing prediction sets with adaptive arc length and finite-sample coverage guarantees for any circular predictive model under the assumption of data exchangeability. Leveraging the high performance of existing predictive models designed for linear responses, we analyze a general projection procedure that converts any linear-response regression model into one suitable for circular responses. When random forests are used as base models in this projection procedure, we leverage the random forest out-of-bag mechanism to eliminate the need for a separate calibration sample in the construction of prediction sets. On synthetic and real datasets, the resulting projected random forest model produces more efficient out-of-bag conformal prediction sets, with shorter median arc length, than the split conformal prediction sets generated by two existing alternative models.

05.
arXiv (CS.AI) 2026-06-19

TerraMind: Large-Scale Generative Multimodality for Earth Observation

arXiv:2504.11171v5 Announce Type: replace-cross Abstract: We present TerraMind, the first any-to-any generative, multimodal foundation model for Earth observation (EO). Unlike other multimodal models, TerraMind is pretrained on dual-scale representations combining both token-level and pixel-level data across modalities. On a token level, TerraMind encodes high-level contextual information to learn cross-modal relationships, while on a pixel level, TerraMind leverages fine-grained representations to capture critical spatial nuances. We pretrained TerraMind on nine geospatial modalities of a global, large-scale dataset. In this paper, we demonstrate that (i) TerraMind's dual-scale early fusion approach unlocks a range of zero-shot and few-shot applications for Earth observation, (ii) TerraMind introduces "Thinking-in-Modalities" (TiM) – the capability of generating additional artificial data during finetuning and inference to improve the model output – and (iii) TerraMind achieves beyond state-of-the-art performance in community-standard benchmarks for EO like PANGAEA. The pretraining dataset, the model weights, and our code are open-sourced under a permissive license.

06.
arXiv (CS.CV) 2026-06-15

HULFSynth : An INR based Super-Resolution and Ultra Low-Field MRI Synthesis via Contrast factor estimation

We present an unsupervised single image bidirectional Magnetic Resonance Image (MRI) synthesizer that synthesizes an Ultra-Low Field (ULF) like image from a High-Field (HF) magnitude image and vice-versa. Unlike existing MRI synthesis models, our approach is inspired by the physics that drives contrast changes between HF and ULF MRIs. Our forward model simulates a HF to ULF transformation by estimating the tissue-type Signal-to-Noise ratio (SNR) values based on target contrast values. For the Super-Resolution task, we used an Implicit Neural Representation (INR) network to synthesize HF image by simultaneously predicting tissue-type segmentations and image intensity without observed HF data. The proposed method is evaluated using synthetic ULF-like data from generated from standard 3T T$_1$-weighted images for qualitative assessments and paired 3T-64mT T$_1$-weighted images for validation experiments. WM-GM contrast improved by 52% in synthetic ULF-like images and 37% in 64mT images. Sensitivity experiments demonstrated the robustness of our forward model to variations in target contrast, noise and initial seeding.

07.
medRxiv (Medicine) 2026-06-11

A global cross-sectional survey of health professionals' interest-confidence gaps in value-based health care implementation: a learning needs assessment

Abstract Objectives Value-Based Health Care (VBHC) increasingly guides health system redesign internationally. Despite the increasing availability of VBHC education, gaps remain between health professionals' conceptual understanding of VBHC and their confidence to implement it in practice. This study assessed perceived learning needs and preferences of healthcare professionals across foundational topics essential to VBHC implementation. Design Cross-sectional online survey study Setting and participants The survey was distributed to the global VBHC community and yielded 518 responses. Most respondents were based in the UK and Ireland (51%) and 65% had more than 10 years of experience in the health sector. Participants represented a variety of professional backgrounds, including clinicians (34%), operational or executive managers and leaders (22%), and life sciences or procurement professionals (13%). Primary and secondary outcome measures Primary outcome measures included self-reported interest and confidence across 15 VBHC domains and the magnitude of the gap between them. Secondary outcomes included perceived implementation challenges and preferred VBHC learning approaches, including prior engagement with VBHC-related learning. Results Respondents identified substantial VBHC implementation challenges, including implementing outcome measurement (62.4%), conflicting priorities (57.7%), and resistance to change (56.8%). Interest in all VBHC domains was high (median >= 80/10), while confidence to implement remained substantially lower across most domains (median

08.
arXiv (CS.LG) 2026-06-17

Geometrical fairness in graph neural networks

arXiv:2606.17684v1 Announce Type: cross Abstract: Graph-based learning methods have become increasingly prominent due to their strong performance across diverse applications. Among these, recent frameworks grounded in diffusion processes provide a unifying perspective that extends traditional graph neural network formulations while addressing limitations of standard message-passing mechanisms. Despite these advances, concerns remain regarding the fairness of such models, as they may propagate or amplify biases present in the data. In this work, we introduce a fairness-aware adaptation of graph-based diffusion by modifying the underlying Laplacian operator. Our approach incorporates multiple complementary transformations, including subspace projections, spectral adjustments, and frequency-based filtering, to mitigate bias-related components. Leveraging the intrinsic smoothing properties of graph diffusion, we provide a principled analysis of the resulting behavior and establish theoretical insights into fairness properties. We evaluate the proposed framework on both synthetic and real-world datasets, demonstrating that it achieves competitive performance while improving fairness metrics with limited additional computational cost.

09.
arXiv (CS.CV) 2026-06-15

Visual Quality Score Assessment of Large White Goods in Remanufacture with Multi-View Deformable-DETR

Remanufacturing large white goods is essential for a circular economy, yet visual quality assessment remains a manual bottleneck for training and pricing. Conventional detection methods require extensive annotation and struggle with small defects in high-resolution multi-view data. We present a multi-view framework based on Deformable-DETR for automated quality scoring that aggregates information across redundant views to extract fine-grained features. To enhance robustness with limited labels, we employ self-supervised pretraining followed by supervised fine-tuning on expert-annotated scores. Additionally, a linear projection over frozen feature maps identifies regions of interest to explain model decisions. Evaluated on an industrial multi-view dataset, our approach delivers precise quality assessments while reducing reliance on manual annotation and per-part customization, enabling scalable and transparent inspection for remanufacturing lines.

10.
arXiv (CS.LG) 2026-06-12

PLaID++: A Preference Aligned Language Model for Targeted Inorganic Materials Design

arXiv:2509.07150v4 Announce Type: replace Abstract: Reinforcement Learning from Verifiable Rewards (RLVR) has emerged as a promising approach to improve correctness in LLMs, however, in many scientific problems, the objective is not necessarily to produce the correct answer, but instead to produce a diverse array of candidates which satisfy a set of constraints. We study this challenge in the context of materials generation. To this end, we introduce PLaID++, an LLM post-trained for stable and property-guided crystal generation. We find that performance hinges on our crystallographic representation and reward formulation. First, we introduce a compact, symmetry-informed Wyckoff text representation which improves computational efficiency and encourages generalization from physical priors. Second, we demonstrate that temperature scaling acts as an entropy regularizer which counteracts mode collapse and encourages exploration. By encoding symmetry constraints directly into text and guiding model outputs towards desirable chemical space, PLaID++ generates structures that are thermodynamically stable, unique, and novel at a $\sim$50\% greater rate than prior methods and conditionally generates structures with desired space group properties. Our work demonstrates the potential of adapting post-training techniques from natural language processing to materials design, paving the way for targeted and efficient discovery of novel materials.

11.
arXiv (CS.AI) 2026-06-11

Sustainability assessment using multimodal AI agents

arXiv:2507.17012v2 Announce Type: replace Abstract: Reducing the rapidly growing environmental impact of the computing industry requires assessing the emissions of electronics at scale. However, a traditional life cycle assessment (LCA) of an electronic device, which maps materials and processes to environmental impacts, often requires proprietary or unavailable data. Here, we reimagine conventional sustainability assessment by introducing a multimodal multi-agent AI system that emulates the collaborative process between LCA professionals and stakeholders (such as product managers and engineers) to automatically estimate the carbon footprint of electronic devices. The agents iteratively construct a complete life-cycle inventory by leveraging a structured data abstraction and software tools that mine information from the public internet, including repair communities and government regulatory databases. This reduces data gaps and data collection from weeks or months of expert time to under one minute. The system can calculate carbon footprint within 19% of expert LCAs with zero proprietary data (typical of the variation between human LCAs). We also show that by encoding domain-specific knowledge, environmental impact estimation can be reframed as a data-driven prediction task, in which both unknown products and emission factors are represented as weighted combinations of similar ones with known emissions.

12.
arXiv (CS.AI) 2026-06-16

Unifying Acoustic Features and Text with Multimodal LLMs for Neurodegenerative Screening

arXiv:2606.14788v1 Announce Type: cross Abstract: Voice-based screening offers a scalable and non-invasive way to assess neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD), but their staging remains challenging due to the difficulty of integrating heterogeneous data. This paper presents NeurMLLM, an efficient multimodal generative framework for neurodegenerative disease staging. NeurMLLM first encodes the spectrograms and Mel-frequency cepstral coefficients of audio data with vision transformers and projects their representations into the embedding space of a large language model (LLM), where they are concatenated with transcript and demographic instruction tokens as a single unified sequence. The LLM is then instruction-tuned via Low-Rank Adaptation using task prompts to autoregressively predict a constrained label token, enabling a generative classification. By evaluating on the Bridge2AI-Voice dataset for fine-grained staging of AD and PD, we observe that NeurMLLM achieves strong performance, consistently outperforming classical machine learning methods and existing LLM-based approaches. The results show the high potential of multimodal LLMs in neurodegenerative disease staging, improving staging accuracy and supporting accessible deployment.

13.
medRxiv (Medicine) 2026-06-22

AFFORDABILITY OF INTOXICATION FROM CHEAP ETHANOL: EVIDENCE FROM RETAIL ALCOHOL MARKETS IN UGANDA

Background: Alcohol affordability is a determinant of consumption and alcohol-related harm. In many low- and middle-income countries (LMICs), informal production, variable alcohol strength, and non-standard packaging complicate conventional affordability measures, limiting evidence on the economic accessibility of alcohol and the cost of intoxication. Objective: To assess the affordability of intoxication in Uganda by estimating the cost of obtaining ethanol to reach intoxication across alcohol products, packaging types, and retail contexts. Methods: Data were collected on 824 alcoholic beverages from urban, rural, and urban-slum retail markets. Ethanol-standardized pricing (price per gram of alcohol) was calculated, and the cost of consuming 60 g of ethanol was estimated. Multivariate regression identified determinants of ethanol affordability. Results: Affordability varied by product type and packaging. Opaque beers and illicit spirits provided the cheapest pathways to intoxication, with median costs of UGX 1,200-1,500 per 60 g of ethanol. Plastic packaging was associated with lower ethanol costs than glass packaging. Ethanol prices differed across formal and informal markets (p < 0.01), while rural areas and urban informal settlements had 20-25% lower costs than urban areas. Regulatory status alone did not predict affordability. Conclusions: In Ugandas diverse alcohol market, affordability is driven by access to ethanol rather than beverage price alone. Low-cost, high-strength alcohol sold through informal channels enables intoxication at minimal expense, among disadvantaged populations. Implications: Alcohol policies should target ethanol content through minimum unit pricing, alcohol-content-based taxation, and regulation of informal markets and packaging practices to reduce harmful consumption and inequities.

14.
arXiv (CS.LG) 2026-06-16

Test-Time Compute Scaling for ASR with Depth-Conditioned Looped Transformers

arXiv:2606.04678v2 Announce Type: replace Abstract: End-to-end ASR systems typically use fixed-depth acoustic encoders at inference, making it difficult to trade additional test-time computation for improved recognition without training a larger model. A natural approach is to reuse a shared Transformer block recurrently, but we find that naive looping does not fully exploit additional recurrent compute. We introduce LARM, a depth-conditioned looped Transformer that turns recurrent encoder depth into a controllable test-time compute axis. LARM combines sparse CTC checkpoints, supervision-clock embeddings, FiLM depth conditioning, and delayed soft-posterior feedback. These components structure the loop into recognition checkpoints separated by latent refinement phases and allow shared weights to specialize across recurrent steps. On LibriSpeech, LARM improves WER as the number of inference loops increases and achieves performance competitive with deeper unshared-parameter baselines. Our results show that test-time compute scaling can extend beyond autoregressive language-model reasoning to continuous non-autoregressive speech recognition.

15.
medRxiv (Medicine) 2026-06-15

A More-Than-Human Approach to Designing for Mental Health: Remixing Prototypes for the Contexts of Complex Healthcare Infrastructures

Digital mental health tools (DMHTs) often fail to be successfully implemented in clinical settings. While user- and human-centred design frameworks are frequently proposed for developing effective tools, they are insufficient to address the sociotechnical complexity of healthcare environments. This paper addresses this limitation by detailing the application of a more-than-human design framework to incorporate wider contextual factors into design decisions. To demonstrate the application of this more-than-human design framework, we present a case study showcasing the design of one specific feature within a DMHT intended to support Health Improvement Practitioners (HIPs) in New Zealand's Integrated Primary Mental Health and Addictions (IPMHA) service. Our process blends usage-context storyboards with interface prototypes, using think-aloud interviews to test the contextual fit of our prototypes. The initial design concept failed due to contextual factors such as inconsistent wait times and the administrative burden on clients and clinic staff. This led to a pivot to a more context-appropriate, practitioner-focused, in-session concept for digital psychometric administration and automated scoring. This case study demonstrates that for DMHTs to be viable within complex healthcare environments, design must focus on more than the needs of a single user, incorporating multiple stakeholders and contextual variables across the wider service-delivery context.

16.
arXiv (math.PR) 2026-06-16

Experimentation for Different Scheduling Policies on Queues: Mixed Differences-in-Q Estimators Based on Little's Law

arXiv:2605.29641v2 Announce Type: replace-cross Abstract: In data centers, tasks are dispatched to various servers to evenly distribute the workload. When a data center considers implementing a new scheduling algorithm, it typically conducts an A/B test prior to deployment to assess the real-world impact of this new method. However, a straightforward A/B test might be interfered with so-called ``Markovian'' interference. We utilized the Differences-in-Q estimator, as developed by Farias et al. (2022), and introduced mixed Differences-in-Q estimators grounded in Little's Law. We show that our A/B testing methods significantly reduce bias and variance when testing various scheduling policies. Extensive simulations were conducted under scenarios like non-stationary arrival rates, heterogeneous service rates, and communication delays. These simulations highlight the robustness and efficacy of our A/B testing approach.

17.
arXiv (CS.AI) 2026-06-12

Neuro-Symbolic Agents for Regulated Process Automation: Challenges and Research Agenda

arXiv:2606.13405v1 Announce Type: new Abstract: LLM-based agents are entering regulated industries where they automate judgment intensive quality management processes. We argue that symbolic structures already embedded in these domains, including regulations, typed process models, and compliance constraints, should be treated not merely as external monitoring mechanisms but as core architectural components that shape the agent's decision-making and behavior. We propose compliance-by-construction as a complementary paradigm to guardrail-based monitoring: a structural foundation that prevents control-flow violations, while guardrails remain essential for catching semantic errors. We identify a structured set of neuro-symbolic research challenges on foundational and capability level and show that addressing them jointly enables compliance-by-construction. We call on the neuro-symbolic community to engage with regulated process automation as a high impact research domain.

18.
arXiv (CS.CV) 2026-06-16

Learning Sparse Latent Predictive Foundation Model for Multimodal Neuroimaging

Brain MRIs are routinely acquired as multiple complementary sequences with unique contrast weighting, including T1-weighed imaging (T1w) anatomic and fluid-sensitive T2-weighted (T2w) contrasts. However, methods for learning unified representations across the multitude of MRI contrast mechanisms at health-system scale are lacking. In this study, we introduce Neuro-JEPA, a sparse multimodal neuroimaging foundation model that combines a latent predictive objective with a Mixture-of-Experts architecture to encode brain MRI across core T1w, T2w, and fluid-suppressed FLAIR imaging (FLAIR). We further provide a systematic methodological study of architectural, masking, objective, and sparsity design choices beneficial for robust neuroimaging multimodal representation learning. Neuro-JEPA was pretrained on 1,551,862 scans from 428,647 studies after modality-specific preprocessing with data curation across three core structural brain MRI sequences. We evaluated the learned representations across clinical and research settings, including 25 tasks from three health systems: NYU Langone, NYU Long Island, and Massachusetts General Hospital, and 22 tasks from 12 public datasets, covering unimodal, multimodal and cross-domain evaluation configurations. Across these benchmarks, existing neuroimaging foundation models showed inconsistent gains over a simple convolutional neural network (CNN) baseline, whereas Neuro-JEPA achieved stronger and more consistent performance across all evaluated settings. These results establish a scalable methodological framework for multimodal neuroimaging representation learning and highlight the need for foundation model evaluation protocols that include simple baselines, clinically heterogeneous cohorts and controlled multimodal comparisons.

19.
arXiv (CS.LG) 2026-06-16

Scalar-pathway fidelity improves physical accuracy in short-range equivariant interatomic potentials

arXiv:2606.15892v1 Announce Type: new Abstract: Accurate interatomic potentials enable molecular dynamics of materials, molecules, and interfaces beyond density-functional-theory length and time scales. Equivariant neural network potentials have improved the representation of local geometry. However, their deployable energy surfaces ultimately manifest through invariant scalar channels, whose aggregation and spectral resolution remain comparatively underexamined. Here we use Physics-Aware Neighborhood (PAN) pooling and Physics-Guided Spectral (PGS) mixers as controlled scalar-pathway probes: lightweight, symmetry-preserving modifications that act only on \(\ell=0\) channels while leaving the equivariant tensor backbone unchanged. Using MACE as a high-body-order mechanistic scaffold, PAN adds coordination-sensitive amplitude modulation, whereas PGS augments edge and readout scalar features with radial and tapered spectral bases. Across metallic Ag, covalent Si, a short-range ionic LiF/Li–F subset, and MD17/rMD17 molecules, this scalar-pathway correction reduces MACE force errors by 22–27\% and energy errors by 19–22\%; on systems with stress labels, stress errors decrease by 27–28\%, at approximately 5\% additional inference-FLOPs cost. Directionally consistent gains in Allegro and NequIP further indicate that the correction is portable across distinct short-range equivariant backbones, although effect sizes remain architecture-dependent. These results identify scalar-pathway fidelity as a practical design dimension for short-range equivariant interatomic potentials.

20.
arXiv (CS.AI) 2026-06-16

AI Supply Chain Galaxy: 3D Visual Analytics for License Compliance

arXiv:2606.16292v1 Announce Type: cross Abstract: The rapid proliferation of machine learning model reuse has transformed the AI ecosystem into a highly interconnected supply chain. Traditional compliance tools and static reports struggle to navigate these massive, multi-hop dependency networks. To address this, we present AI Supply Chain Galaxy (AISCG), an interactive 3D visual analytics system for model provenance and compliance auditing. AISCG maps models into a 3D spatial layout, integrating explicit structural dependencies with a rule-based compliance engine. It supports multi-scale exploration, from global community detection to localized, path-aware lineage tracing. We demonstrate its efficacy through an ecosystem-scale empirical analysis of 908,449 models from Hugging Face. Our findings reveal a concerning landscape: 55.46% of models exhibit compliance risks or metadata conflicts/omissions. We also identified distinct risk patterns, including a 56.67% license omission rate in adapter derivations and an 8.05% "license drift" rate in fine-tuning. Through a case study on the complex Llama model family, we show how AISCG empowers analysts to intuitively trace inherited restrictive terms and identify root causes across deep topological networks, significantly reducing the cognitive load of compliance auditing.

21.
arXiv (CS.LG) 2026-06-12

Earth Science Foundation Models: From Perception to Reasoning and Discovery

arXiv:2605.12542v2 Announce Type: replace-cross Abstract: Large foundation models (FMs) are transforming Earth science by integrating heterogeneous multimodal data, such as multi-platform imagery, gridded reanalysis data, diverse geophysical and geochemical observations, and domain-specific text, to support tasks ranging from basic perception to advanced scientific discovery. This paper provides a unified review of Earth science foundation models (Earth FMs) through two complementary dimensions: depth, which traces the evolution of model capabilities from perception to multimodal reasoning and agentic scientific workflows, and breadth, which summarizes their expanding applications across the atmosphere, hydrosphere, lithosphere, biosphere, anthroposphere, and cryosphere, as well as coupled Earth system processes. Using this framework, we review representative multimodal Earth foundation models and compile more than 200 datasets and benchmarks spanning diverse Earth science tasks and modalities. We further discuss key challenges in multimodal data heterogeneity, scientific reliability and continual updating, scalability and sustainability, and the transition from foundation models to agentic and embodied Earth intelligence, and outline future directions toward more integrated, trustworthy, and actionable AI Earth scientists. Overall, this paper offers a structured roadmap for understanding the development of Earth foundation models from both capability depth and application breadth.

22.
arXiv (CS.AI) 2026-06-12

HD-Prot: A Protein Language Model for Joint Sequence-Structure Modeling with Continuous Structure Tokens

arXiv:2512.15133v3 Announce Type: replace-cross Abstract: Proteins inherently possess a consistent sequence-structure duality. The abundance of protein sequence data, which can be readily represented as discrete tokens, has driven fruitful developments in protein language models (pLMs). A key remaining challenge, however, is how to effectively integrate continuous structural knowledge into pLMs. Current methods often discretize protein structures to accommodate the language modeling framework, which inevitably results in the loss of fine-grained information and limits the performance potential of multimodal pLMs. In this paper, we argue that such concerns can be circumvented: a sequence-based pLM can be extended to incorporate the structure modality through continuous tokens, i.e., high-fidelity protein structure latents that avoid vector quantization. Specifically, we propose a hybrid diffusion protein language model, HD-Prot, which embeds a continuous-valued diffusion head atop a discrete pLM, enabling seamless operation with both discrete and continuous tokens for joint sequence-structure modeling. It captures inter-token dependencies across modalities through a unified absorbing diffusion process, and estimates per-token distributions via categorical prediction for sequences and continuous diffusion for structures. Extensive results demonstrate that HD-Prot achieves competitive performance in unconditional sequence-structure co-generation, motif-scaffolding, protein structure prediction, and inverse folding tasks. Furthermore, our method can perform on par with state-of-the-art multimodal pLMs, despite being developed under limited computational resources (i.e., less than one-tenth the budget for modality extension fine-tuning). It highlights the viability of simultaneously estimating categorical and continuous distributions within a unified language model architecture, offering a promising alternative direction for multimodal pLMs.

23.
bioRxiv (Bioinfo) 2026-06-16

Orion: Towards Lab Automation with Computer-Using Agents

Laboratory discovery increasingly depends on computational workflows that connect experimental data to analysis, interpretation and follow-up hypotheses. Yet these workflows remain constrained by labor-intensive use of specialized software, visual inspection through graphical user interfaces, and integration of knowledge across multiple sources. Here, we present Orion, a computer-using AI agent for biomedical image analysis and interpretation that moves towards lab automation by automating this computational layer of laboratory work. Orion combines large language models with terminal execution, GUI control and adaptive multi-step reasoning in a shared computing environment. It can inspect visual data, operate standard scientific software, mine web resources and conduct end-to-end analysis and interpretation workflows without requiring bespoke software integrations. Across benchmarks, Orion achieved over 90% accuracy on biomedical database and literature retrieval tasks, learned to use the popular tools CellProfiler and QuPath for quantitative analysis of cellular and tissue images, respectively, and facilitated autonomous discovery in experimental imaging data. In 100 hours of autonomous exploration of a large-scale perturbation imaging dataset, Orion generated 52 research reports, of which human scientist review prioritized 22 plausible mechanistic hypotheses. These results show that computer-using AI agents can substantially expand the reach of laboratory automation, providing a scalable and auditable route from experimental imaging data to quantitative analysis, reports and biologically grounded hypotheses.

24.
medRxiv (Medicine) 2026-06-15

Using wastewater surveillance to explore community-level dietary intake in sewered and non-sewered sanitation systems in Malawi, Africa

Wastewater can be used to measure biomarkers that reflect population-level dietary intake and diversity; however, how this approach may apply in a low-income country remains a knowledge gap. This study aims to evaluate whether select dietary-related metabolites can be detected in wastewater and environmental surveillance (WES) samples from both sewered and non-sewered sanitation systems in Malawi, Africa. Fourteen WES samples were collected and analyzed from two university campuses in Mzuzu and Thyolo, Malawi. Four targets were analyzed: N-methyl-2-pyridone-5-carboxamide (2PY; a biomarker of vitamin B3), 4-pyridoxic acid (4-PA; a biomarker of vitamin B6), as well as enterodiol and enterolactone (biomarkers of dietary fiber and polyphenol consumption). An 18-question survey, paired spatiotemporally with the WES measurements, assessed self-reported daily dietary intake, food insecurity, and nutrient deficiency symptoms among 500 respondents. Among the 14 WES samples, 2PY, 4-PA, and enterolactone were detected, while enterodiol was not detected above the method limit (

25.
arXiv (CS.CV) 2026-06-17

Do We Really Need Diffusion? A Fast U-Net for Paired Medical Image Translation

Magnetic resonance imaging-signal fat fraction (MRI-SFF) quantifies tissue fat and serves as an established biomarker for metabolic and musculoskeletal disorders. The acquisition requires, however, specialized MRI sequences, which are not available routinely. We investigate whether SFF can be estimated from widely available T2-weighted (T2w) MRI via image-to-image translation (I2I). We further compare a lightweight 4-level U-Net to a state-of-the-art Denoising Diffusion Probabilistic Model (DDPM) using a dataset of 230 048 paired 2D images (183 517 train, 23 621 val, 22 910 test) from the German National Cohort (NAKO). Both models clearly outperform the identity baseline (Pearson correlation r = 0.769, mean absolute error MAE = 0.070 +/- 0.054), which confirms that the models learn a non-trivial cross-modal mapping. Interestingly, the lightweight U-Net outperforms the DDPM in both correlation (r = 0.975 vs. 0.962) and error (MAE = 0.014 +/- 0.015 vs. 0.019 +/- 0.019), while reducing inference time by a factor of 208 (25.2 ms vs. 5 227.2 ms per image using 50 Denoising Diffusion Implicit Model (DDIM) steps). The strong clinical performance at substantially reduced computational cost enables real-time clinical use.