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01.
arXiv (CS.AI) 2026-06-16

MBABench: Evaluating LLM Agents on End-to-End Spreadsheet Tasks in Finance

arXiv:2605.22664v3 Announce Type: replace Abstract: LLM agents are increasingly expected to carry out end-to-end workflows, producing complete artifacts from high-level user instructions. To meet enterprise needs, frontier AI labs have developed agents that can construct entire spreadsheets from scratch. This is especially relevant in finance, where core workflows such as financial modeling, forecasting, and scenario analysis are commonly conducted through spreadsheets. Yet, existing spreadsheet benchmarks do not measure this advanced capability, focusing instead on question-answering or single-formula edits. To address this gap, we provide one of the first evaluations of agents on end-to-end spreadsheet tasks, focusing on economically critical financial workflows such as modeling and scenario analysis. Since deliverables therein are routinely reviewed and revised by multiple stakeholders, judging their quality necessarily involves high-level criteria such as readability or ease of modification. To reflect the multidimensional nature of solution quality, we develop an evaluation taxonomy comprising three dimensions: Accuracy, Formula, and Format, each comprising fine-grained criteria that reflect professional standards. The Claude family leads the benchmark and produces the most professional-looking outputs in our qualitative review, but even the strongest agents frequently fall short of professional finance standards and degrade sharply as the difficulty increases beyond a few chained calculations. This suggests that current agents are not yet able to reliably produce professional-quality spreadsheets at the level of complexity real-world workflows demand.

02.
arXiv (CS.AI) 2026-06-11

The Impossibility of Eliciting Latent Knowledge

arXiv:2606.12268v1 Announce Type: new Abstract: Advanced AI systems have extensive knowledge of their environments; in fact, their knowledge may (far) exceed that of their developers or users. Consequently, a desirable property for an AI system is that it is honest – that it accurately reports its beliefs about the world. Designing an AI system to be honest may be difficult, especially if we want to ask it questions about latent variables in the environment – variables which are hidden from the human interacting with it. This gives rise to the problem of eliciting latent knowledge (ELK): the problem of training an AI agent to honestly report its beliefs. In this paper, we make ELK formally precise using Causal Influence Diagrams (CIDs). CIDs can be used to describe the relationship between an agent's training environment and its subjective representation of the world. We use CIDs to formalise the distinction between observable and latent variables, to specify what exactly it means for an agent to be honest, and to formally define goal misgeneralisation. We show that, under certain circumstances, developers can incentivise an agent to honestly answer questions by providing correct feedback during training. However, a natural, but undesirable, way for an agent to generalise is to provide answers which humans would evaluate as true, rather than honest answers. We prove an impossibility theorem stating: There is no feedback-based training strategy that depends only on agent behaviour and with certainty produces an honest agent, even if feedback is perfect during training.

04.
arXiv (math.PR) 2026-06-11

Sample Path Properties of the Fractional Wiener–Weierstrass Bridge II

arXiv:2606.11994v1 Announce Type: new Abstract: Fractional Wiener–Weierstrass bridges are a class of Gaussian processes obtained by replacing trigonometric functions in the construction of classical Weierstrass functions by fractional Brownian bridges. A number of their sample path properties were derived in Schied–Zhang (2024,2026). The analysis in these papers left several open questions, most of which are addressed here. Specifically, we prove that, in the regime in which the Weierstrass mechanism dominates the underlying fractional Brownian bridge, the limiting $b$-adic variation coefficient has an absolutely continuous distribution and is therefore genuinely random. At the critical point between the two roughness regimes, we establish the power-variation formula and the critical $\Phi$-variation limit conjectured in Schied–Zhang (2024). Finally, we derive the Hausdorff dimension for the graphs of the sample paths by proving a conjecture from Schied–Zhang (2026) for the missing high-Hurst case.

05.
arXiv (CS.AI) 2026-06-18

Surrogate Benchmarks for Model Merging Optimization

arXiv:2509.02555v2 Announce Type: replace-cross Abstract: Model merging techniques aim to integrate the abilities of multiple models into a single model. Most model merging techniques have hyperparameters, and their setting affects the performance of the merged model. Because several existing works show that tuning hyperparameters in model merging can enhance the merging outcome, developing hyperparameter optimization algorithms for model merging is a promising direction. However, its optimization process is computationally expensive, particularly in merging LLMs. In this work, we develop surrogate benchmarks for optimization of the merging hyperparameters to realize algorithm development and performance comparison at low cost. We define two search spaces and collect data samples to construct surrogate models to predict the performance of a merged model from a hyperparameter. We demonstrate that our benchmarks can predict the performance of merged models well and simulate optimization algorithm behaviors.

06.
arXiv (quant-ph) 2026-06-16

Quantifying Coherence-to-Entanglement Conversion Efficiency under Noisy Operations

arXiv:2606.16916v1 Announce Type: new Abstract: We investigate the noise-limited conversion of local quantum coherence into bipartite entanglement in a minimal two-qubit protocol comprising a coherent single-qubit input, an incoherent ancilla, an ideal CNOT operation, and subsequent environmental noise. Employing the $l_1$-norm of coherence and the entanglement negativity as resource quantifiers, we establish an exact closed-form correspondence between local single-qubit input coherence and the two-qubit entanglement generated in the noiseless limit, showing that the output negativity is precisely one half of the initial $l_1$-coherence. We then derive analytic expressions for the surviving entanglement and the associated coherence-to-entanglement conversion efficiency under two representative noise mechanisms: independent phase damping and global two-qubit depolarizing noise. The two channels exhibit qualitatively distinct degradation behavior. Phase damping induces a universal multiplicative suppression of the generated entanglement, yielding a coherence-independent conversion efficiency and no finite-noise entanglement sudden death. In contrast, global depolarization introduces an isotropic mixing contribution that shifts the partial-transpose spectrum, producing coherence-dependent degradation and a finite sudden-death threshold. We show that maximally coherent inputs not only maximize the entanglement generated by the CNOT protocol but also optimize its robustness against depolarizing noise. Direct density-matrix simulations validate the analytic results to numerical precision. These findings provide a compact analytic benchmark for assessing how different noise mechanisms constrain coherence-to-entanglement conversion in elementary quantum-information protocols and near-term quantum devices.

07.
arXiv (CS.CL) 2026-06-16

LoLA: Low-Rank Linear Attention With Sparse Caching

The per-token cost of transformer inference scales with context length, preventing its application to lifelong in-context learning. Linear attention is an efficient alternative that maintains a constant memory footprint, even on infinite context lengths. While this is a potential candidate for lifelong learning, it falls short in memory capacity. In this paper, we propose LoLA, a training-free augmentation to linear attention that boosts associative recall. LoLA distributes past key-value pairs from context into three memory systems: (i) recent pairs in a local sliding window cache; (ii) difficult-to-memorize pairs in a sparse, global cache; and (iii) generic pairs in the recurrent hidden state of linear attention. We show through ablations that our self-recall error metric is crucial to efficiently manage long-term associative memories. On pass-key retrieval tasks, LoLA improves the base model's performance from 0.6% to 97.4% accuracy. This is achieved with a 4.6x smaller cache than Llama-3.1 8B on 4K context length. LoLA also outperforms other 1B and 8B parameter subquadratic models on zero-shot commonsense reasoning tasks.

08.
medRxiv (Medicine) 2026-06-24

Self-administered computerized cognitive training for cognitive deficits in individuals with metabolic syndrome: a randomized controlled trial

Background: Metabolic syndrome (MetS) has been associated with cognitive decline. Considering its increasing prevalence worldwide, the goal of this study was to evaluate the feasibility and efficacy of a short-term, self-administered computerized cognitive training programme in individuals with metabolic syndrome and low cognitive performances. Methods: Thirty six participants, aged 40-72 years (mean age: 57.8 years), were randomly assigned to the cognitive training or the passive control group. The cognitive training component of Long Lasting Memories (LLM) Care was used as an interactive software to enhance participants' cognitive functions. Up to 24 sessions, each lasting 45 minutes, were self-administered at home twice per week for 3 months. Thorough cognitive assessments with were performed at baseline (randomization), at the end of intervention, and 12 months after baseline. The primary outcome was performance at nine neuropsychological tests, and the secondary outcome was a self-reported questionnaire assessing everyday functional abilities. Primary analyses were performed employing mixed-effect models using the intention-to-treat principle. Results: Low adherence was observed in the study, as only 9 participants (50%) completed at least 8 sessions of the cognitive training programme (range 9-24 sessions, median 15 sessions). No statistically significant effect of the cognitive training programme on performance in neuropsychological tests or everyday functioning was found. At the end of the 3-month intervention programme, effect for visual memory enhancement in immediate ({beta} = 1.58, 95% CI = -1.84 to 4.99, Cohen's d = 0.39) and delayed recall ({beta} = 2.17, 95% CI = -1.68 to 6.01, Cohen's d = 0.45) was moderate in favour of the intervention group, and at 12-month follow-up, semantic verbal fluency gains for the intervention group were detected ({beta} = 2.78, 95% CI = -0.92 to 6.49, Cohen's d = 0.70), though with wide confidence intervals. Conclusions: Despite some small effects observed in memory and verbal fluency, cognitive training did not yield statistically significant improvements. The observed low adherence and limited benefits on mild cognitive deficits in mostly middle-aged individuals with MetS are likely associated with the self-administered and short-term nature of the computerized intervention. This highlights the need for more intensive and clinician-delivered approaches to enhance engagement. Registry: ClinicalTrials.gov, TRN: NCT05658354, Registration date: 08 December 2022. Keywords: Metabolic syndrome, cognitive deficits, cognitive training, computerized, adults

09.
arXiv (quant-ph) 2026-06-17

Impulse Decoding of Quantum LDPC Codes: Equivalence of Degeneracy and Code-Shortening

arXiv:2606.18240v1 Announce Type: new Abstract: Quantum error correction is essential for building scalable quantum computers. Within the stabilizer formalism, the Calderbank-Shor-Steane framework constructs quantum codes from pairs of classical linear codes. A distinctive feature in this setting is degeneracy, where multiple equivalent error estimates exist-a phenomenon that has no classical counterpart, and the lack of a meaningful classical coding-theoretic interpretation of which has remained a gap in the literature. In this paper, we demonstrate that degeneracy is closely related to the classical operation of shortening of a linear block code. Interestingly, the shortening here takes place at the decoder rather than at the encoder. Leveraging this insight, we present a parallel decoding scheme for quantum low-density parity-check codes, which we term impulse decoding, that significantly outperforms belief propagation with ordered statistics decoding, as well as several other existing techniques, under both code-capacity and circuit-level noise, with significantly lesser complexity. We then present another algorithm based on decoding of residual errors, which when combined with impulse decoding achieves further performance improvement under circuit-level noise.

10.
medRxiv (Medicine) 2026-06-15

Natural Language Processing Based Solution for Labeling Brain Metastasis Identified in Radiology Reports

Abstract Purpose: Brain metastases (BM) far exceed primary CNS tumours and constitute the majority workload for neuro-oncology care providers. Currently, the cancer registries only capture synchronous BMs, which is only a small proportion of all BMs. We aim to develop and validate a natural language processing (NLP) algorithm that identifies brain metastases in radiology reports, enabling scalable surveillance of asynchronous BMs. Methods: Using population-based cancer registry data in Alberta, Canada, we identified a cancer cohort diagnosed between 2012–2019 with follow-up to 2022. All brain/head radiology reports at and post-cancer diagnosis were identified. Reports were sampled through a multi-phase approach and manually labeled for BM presence. We trained two Bio_ClinicalBERT models on the "Findings" and "Impressions" sections, respectively, and took the maximum predicted probability as the report-level prediction. Internal and external validation used reports from the Canadian provinces of Alberta, Ontario, and British Columbia. Results: The models were trained on 1,879 samples. For internal validation, 1,833 reports from 357 patients were tested. At a probability threshold of 0.4, the model achieved a sensitivity of 0.888 and precision of 0.499. The ensemble substantially outperformed single-section models, which achieved sensitivities of only 67.8% (Findings) and 74.2% (Impressions). On external validation, sensitivity was 0.918 in Ontario and 0.726 in British Columbia, demonstrating robustness across diverse data distributions. Conclusions: An NLP-based pipeline processing both Findings and Impressions sections has been developed and validated in three Canadian provinces. It meets cancer registry operational requirements and to be implemented into the surveillance workflow in Alberta and British Columbia, providing a foundation for population-level BM surveillance.

11.
arXiv (quant-ph) 2026-06-15

Quantum geometrical description of hole spin qubits far away from the $\Gamma$-point

arXiv:2606.14683v1 Announce Type: cross Abstract: Hole spin qubits provide one of the leading platforms for spin-based quantum computing due to their large intrinsic spin-orbit interaction (SOI), which enables fast electrical manipulation. The SOI of planar quantum dots has mostly been investigated in theoretical studies by examining the SOI already present in the two-dimensional hole gas (2DHG). Here, we study the SOI created by the in-plane confinement by deriving non-perturbative effective Hamiltonians numerically for hole spin qubits. We find that the quantum geometry of the 2DHG naturally emerges, leading to a meaningful non-perturbative definition of pseudospin valid far away from the $\Gamma$-point. The SOI of the 2DHG and of the in-plane confinement have different forms; therefore, they cannot be turned off simultaneously, ruining the perfect spin-orbit switch functionality of spin qubits. We construct effective Hamiltonians using the symmetry approach for various low-dimensional hole systems: (i) a heavy-hole confined in a SiGe/Ge/SiGe heterostructure, (ii) a light-hole confined in SnGe/Ge, (iii) a gate-defined nanowire in SiGe/Ge/SiGe, and (iv) a hole confined in a Ge/Si core/shell nanowire. The non-perturbative effective Hamiltonians provide results with excellent agreement with the full Hamiltonians.

12.
arXiv (math.PR) 2026-06-18

A random recursive tree model with doubling events

arXiv:2501.18466v3 Announce Type: replace Abstract: We introduce a new model of random tree that grows like a random recursive tree, except at some exceptional "doubling events" when the tree is replaced by two copies of itself attached to a new root. We prove asymptotic results for the size of this tree at large times, its degree distribution, and its height profile. We also prove a lower bound for its height. Because of the doubling events that affect the tree globally, the proofs are all much more intricate than in the case of the random recursive tree in which the growing operation is always local.

13.
arXiv (CS.CL) 2026-06-25

Robustness assessment of large audio language models in multiple-choice evaluation

Recent advances in large audio language models (LALMs) have primarily been assessed using a multiple-choice question answering (MCQA) framework. However, subtle changes, such as shifting the order of choices, result in substantially different results. Existing MCQA frameworks do not account for this variability and report a single accuracy number per benchmark or category. We dive into the MCQA evaluation framework and conduct a systematic study spanning three benchmarks (MMAU, MMAR and MMSU) and four models: Audio Flamingo 2, Audio Flamingo 3, Qwen2.5-Omni-7B-Instruct, and Kimi-Audio-7B-Instruct. Our findings indicate that models are sensitive not only to the ordering of choices, but also to the paraphrasing of the question and the choices. Finally, we propose a simpler evaluation protocol and metric that account for subtle variations and provide a more detailed evaluation report of LALMs within the MCQA framework.

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

Geometric Action Model for Robot Policy Learning

Generalist robot policies must follow user instructions while reasoning about how objects, cameras, and robot actions interact in the 3D physical world. Recent vision-language-action models (VLAs) and video world-action models (WAMs) inherit strong semantic or temporal priors from large-scale foundation models, but they still operate primarily on 2D image frames or 2D-derived latent spaces, leaving implicit the 3D geometry required for contact-rich manipulation. We propose the Geometric Action Model (GAM), a language-conditioned manipulation policy that directly repurposes a pretrained geometric foundation model (GFM) as a shared substrate for perception, temporal prediction, and action decoding. GAM splits the GFM at an intermediate layer: the shallow layers serve as an observation encoder, and a causal future predictor inserted at the split layer forecasts future latent tokens conditioned on language, proprioception, and action history. The predicted future tokens are then routed through the remaining GFM blocks for feature propagation and decoding, allowing a single backbone to produce both future geometry and actions. This design equips the GFM with language-conditioned temporal world modeling through minimal architectural modification while preserving its rich geometric priors. Across a broad suite of simulation and real-robot manipulation benchmarks, GAM is more accurate, more robust, faster, and lighter than current foundation-model-scale baselines.

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

History of the Muddy Children Puzzle

arXiv:2606.13703v1 Announce Type: new Abstract: The Muddy Children Puzzle is a puzzle about knowledge and ignorance that has been inspiring for the development of epistemic logic. Who came up with it first? This is unclear. We trace the origin of the Muddy Children Puzzle through logical and literary publications over the past two centuries. The puzzle inspired a numerous variations such as involving numbers or coloured hats. We also present a novel hats puzzle involving self-reference.

16.
Nature (Science) 2026-06-18

Daily briefing: The proteins that protect us from deadly mutations

作者:

Proteins that ‘buffer’ the effects of mutations could help to treat diseases such as cancers. Plus, goats can follow human voices and the battle over a key ocean observatory project in the United States. Proteins that ‘buffer’ the effects of mutations could help to treat diseases such as cancers. Plus, goats can follow human voices and the battle over a key ocean observatory project in the United States.

17.
arXiv (CS.AI) 2026-06-16

Agentic Framework for Deep Learning workload migration via In-Context Learning

arXiv:2606.15994v1 Announce Type: new Abstract: Translating deep learning models from PyTorch's flexible, object-oriented design to JAX's functional, stateless setup is usually a manual and error-prone task. Automated migration is challenging because Large Language Models (LLMs) struggle with strict and dynamic API alignment and are prone to mistakes for exacting operations. We propose a fully autonomous system that combines In-Context Learning (ICL) with oracle-driven self-debugging. First, we curated an ICL context that serves as a strict reference for idiomatic JAX styling and test case generation. Second, instead of depending on the LLM to deduce mathematical outputs, we run the source PyTorch modules to get their actual dynamic tensor states. This creates an unchangeable execution oracle. We then use an autonomous agentic loop to synthesize tests based on the oracle data. The test cases are executed repeatedly, and the traceback is sent back to the LLM for self-correction. Ablations show that combining ICL references with oracle grounding and self-debugging greatly outperforms pure instructional and basic agentic baselines. This improvement does not add an excessive computational overhead. Our lightweight pipeline achieves 91% numerical equivalence (compared to baseline: 9%, instruction + self-debugging: 27%) on neural modules, providing a highly reliable, scalable blueprint for cross-framework migration. This has been validated across several state-of-the-art models including SAM (segment anything), T5, Code Whisper amongst others showing high numerical equivalency. Code: https://github.com/AI-Hypercomputer/accelerator-agents/tree/main/MaxCode

18.
arXiv (CS.CV) 2026-06-17

Contrastive Action-Image Pre-training for Visuomotor Control

Existing vision encoders for robotics face a fundamental bottleneck: robotic datasets lack the scale necessary for large-scale pre-training. Prior work circumvents this data scarcity by turning to internet-scale image and language data or egocentric human video. While these models show promise, neither paradigm learns from paired vision and action data, which downstream visuomotor control policies require. However, robot trajectories, the most direct source of this paired signal, are not available at pre-training scale, motivating us to extract action signals from abundant human video instead. To this end, we introduce CAIP (Contrastive Action-Image Pre-training), a vision encoder that treats human hand poses from large-scale egocentric video as a proxy for end-effector actions. By extracting 3D hand keypoints, a representation that aligns naturally with downstream robot action spaces, CAIP learns a unified action-image representation through a contrastive objective. Leveraging 32,041 hours of egocentric human video and only 88 hours of robotic manipulation data, CAIP outperforms state-of-the-art vision encoders including DINOv2, SigLIP, MVP, and R3M. Evaluated on a challenging real-world dexterous manipulation setup using Dexmate Vega and Sharpa Wave hands, CAIP yields performance gains of more than 30% on tasks involving folding, pouring, and fine-grained manipulation. Our results show that our method of contrastive action-centric pre-training yields a scalable path to achieving robust visual representations better suited for physical interaction.

19.
bioRxiv (Bioinfo) 2026-06-18

A Two-Stage Interpretable Framework for Predicting Plant-Derived Small RNA Targets on Human 3'UTRs

作者:

Can plant-derived small RNAs target human mRNA 3'UTRs via complementary base pairing and produce experimentally detectable regulatory effects? This question concerns not only the fundamental feasibility of cross-kingdom RNA regulation but also the technological pathway for screening plant-derived active small nucleic acids. Existing miRNA target prediction tools are predominantly designed for endogenous miRNA-mRNA systems, exhibiting notable limitations when applied to cross-species small RNA inputs and small-sample wet-lab experimental adaptation. In this study, we developed a two-layer prediction framework, MetaLulu-AI. The first layer builds upon publicly available human miRNA-mRNA 3'UTR interaction data, utilizing XGBoost to learn foundational binding rules on human 3'UTRs based on 41 interpretable computational features, including seed region pairing types, local context sequence composition, site positioning, and RNA secondary structures. The second layer is tailored to the experimental system of plant-derived small RNAs and human target genes. It introduces 40 experimental samples using significant changes in endogenous protein expression as the regulatory standard (determined by Western blot or ELISA 48 hours post-transfection of small RNAs via Lipo3000). Using 52-dimensional computational features and the optimal transcript scores from the first layer as inputs, this layer employs TabPFN for experimental label adaptation. The first-layer dataset consists of 38,752 training samples, 5,536 validation samples, and 11,073 testing samples (totaling 55,361), with a positive-to-negative sample ratio of approximately 1:5.4. On the randomly split test set, the model achieved an AUC of 0.9686, a recall of 0.8523, a precision of 0.8080, and an accuracy of 0.9452 (at a decision threshold of 0.4797). Group-based splitting revealed that the model maintains high discriminative power for unseen genes (AUC = 0.9541), though its generalization ability for completely unseen miRNAs decreases (AUC = 0.7390). For the 40 experimental samples in the second layer, the TabPFN model achieved an average AUC of 0.7406 {+/-} 0.092 across ten repeated 70/30 random splits, outperforming the baseline of directly using the first-layer scores (0.3563 {+/-} 0.149); the average AUC in a 5-fold cross-validation was 0.770 {+/-} 0.177. SHAP analysis demonstrated a clear divergence in the discriminative basis of the two models: the first layer relies more heavily on the thermodynamics of the small RNA itself and the quality of canonical seed sites, whereas the second layer focuses more on the local UTR environment and statistical site features. Although the current second-layer results are constrained by sample size and gene coverage, this framework serves as a preliminary observation of the adaptation mechanism for cross-kingdom regulation experiments, and motivating future large-scale validation. Under stricter leave-one-gene-out and leave-one-small-RNA-out evaluation, the adapter exceeded the first-layer score baseline but only matched the majority-class baseline, underscoring that entity-level generalization is not yet established.

21.
Nature (Science) 2026-06-24

The mutational landscape of STING-induced immunity

作者:

Stimulator of interferon genes (STING) is an evolutionary conserved immune signalling protein with key roles in host defence, cancer, senescence and inflammation1–3. Downstream of STING, type I interferon, inflammatory cytokine signalling and non-canonical autophagy are governed by a multilayered mechanism integrating ligand-induced structural transitions, protein–protein interactions and coordinated intracellular trafficking4–13. Despite its central role in immunity and relevance as therapeutic target14, the sequence elements that govern STING (in)activation in cells remain incompletely understood. Here we developed a massively parallel assay to systematically chart the sequence-function landscape of STING. Profiling thousands of single amino-acid variants, we identified structural and functional determinants that shape the immunostimulatory capacity of STING and its ability to translate ligand recognition into distinct signalling outputs. Cryogenic-electron microscopy structures of select STING hyperactive variants revealed new regulatory principles dictating conformational transition from inactive to signalling-competent states of STING. Mutational effects are widespread across the functional landscape and can sensitize STING towards the natural ligand 2′3′-cGAMP15–18 or decouple interferon induction from non-canonical autophagy, demonstrating a diversity of possible responses that can be accessed through single point substitutions. Finally, our data showed the clinical and evolutionary relevance of naturally occurring STING protein variants. Collectively, these findings define molecular principles that tune STING activity and chart the landscape of its functional potential across immune contexts. A massively parallel assay systematically charts the sequence-function landscape of the STING signalling protein, and the findings define molecular principles that tune STING activity and show its functional potential across immune contexts.

22.
medRxiv (Medicine) 2026-06-24

Allostatic load modifies neuropsychiatric risk following traumatic brain injury

Importance: Outcomes following traumatic brain injury (TBI) vary substantially, with a subset of individuals experiencing neuropsychiatric morbidity and worse prognosis. Exposure to psychosocial and environmental stressors may be an important, yet understudied, modifier of TBI trajectory. Allostatic load (AL) represents the cumulative physiological burden of chronic stress and provides a useful framework for evaluating pre-injury vulnerability. Objective: To assess the relationship between pre-injury AL burden and risk of mortality and incident neuropsychiatric diagnosis following TBI. Design, Setting, and Participants: This cohort study leveraged electronic health record, survey, and laboratory data from the All of Us Research Program, version 8. Participants aged 18 years or older enrolled between May 6, 2018, and October 1, 2023, were queried for TBI diagnosis using clinical diagnostic codes. Data were analyzed between November 11, 2024, and January 7, 2026. Exposure: The physiological burden of pre-injury chronic stress exposure was estimated using an AL index (pALI) derived from anthropometric and laboratory biomarkers collected before index TBI. Main Outcomes and Measures: Post-TBI mortality and incident neuropsychiatric diagnosis clusters. Mortality risk was assessed using Cox proportional hazards models (hazard ratio [HR] with 95% CI), and risk of incident neuropsychiatric diagnosis was modeled using competing-risk regression with death as a competing event (sub-distribution HR with 95% CI). Results: The primary cohort included 4,552 individuals with an established TBI diagnosis and sufficient biomarker data to estimate pALI. The pALI measure differed across sociodemographic groups and was positively correlated with perceived stress (r=.08, p=.002). Higher pALI was associated with increased post-TBI mortality risk (adjusted HR=1.71; 95%CI, 1.36-2.14). Elevated pALI was also associated with greater risk of incident post-traumatic stress disorder (PTSD; adjusted HR=1.28; 95%CI, 1.10-1.50) and sleep disorder (adjusted HR=1.42 95%CI, 1.29-1.57) diagnoses. Conclusions and Relevance: Higher pre-injury ALI was associated with increased risk of mortality and select neuropsychiatric outcomes following TBI, suggesting that AL burden may shape post-injury trajectories. Pre-injury chronic stress exposure and underlying stress biology may represent underrecognized determinants of vulnerability and resilience in brain injury recovery.

23.
arXiv (CS.LG) 2026-06-16

Learning Hybrid Biophysical Neuron Models with Neural ODEs

arXiv:2606.16693v1 Announce Type: cross Abstract: Biophysical neuron models link measurements of neural activity to underlying cellular mechanisms. Yet, a central challenge is that the kinetics of many ion channels are poorly characterized, and practical simplifications – omitting channels or reducing morphological detail – introduce systematic gaps between model and biology. Bridging these gaps requires approaches that can flexibly discover unmodeled dynamics while preserving mechanistic interpretability. Here, we introduce a hybrid modeling framework that embeds neural ordinary differential equations into conductance-based biophysical models to capture unknown currents or mis-specified channel kinetics. By parameterizing the neural ODE in terms of voltage-dependent steady-state and time-constant functions, we recover interpretable gating dynamics directly from voltage recordings without assuming a functional form. We show that the hybrid model fits the gating kinetics of 2400 ion channel models and recovers unknown gating dynamics from single current-clamp recordings, generalizing to out-of-distribution stimulus regimes under realistic inputs and parameter misspecification. We also use our method to reduce a multicompartment model of a cortical neuron into a single-compartment hybrid model with a learned axial current, yielding up to an order of magnitude lower computational cost. Together, our results establish a plug-and-play framework for selectively replacing unknown components of conductance-based models with neural ODEs while preserving their mechanistic structure.

24.
arXiv (CS.LG) 2026-06-25

KIGNet: Physics-Motivated Multi-Graph Representation Learning for Explainable Jet Tagging

arXiv:2512.07420v3 Announce Type: replace-cross Abstract: Jet identification plays a central role in analyzing data from high-energy collider experiments. While deep learning has improved jet classification, it often lacks interpretability. We introduce the Kinematic Interaction Graph Network (KIGNet), a graph neural network that integrates kinematic variables into jet classification by constructing four graph representations per jet, each weighted by a distinct variable: angular separation ($\Delta$), relative transverse momentum ($k_T$), momentum fraction ($z$), and invariant mass squared ($m^2$). Three of these ($\Delta$, $k_T$, $z$) are motivated by the Lund jet plane, grounded in perturbative QCD factorization; the fourth ($m^2$) adds complementary mass-scale sensitivity for heavy-flavor identification. Using Gradient-weighted Class Activation Mapping (Grad-CAM), we determine which variables dominate classification. Angular separation and relative transverse momentum account for about 76% of the total Grad-CAM attribution (40.72% and 35.67%), with momentum fraction and invariant mass contributing the remaining 24%. This hierarchy is consistent with the soft-collinear structure of QCD radiation in the training data, showing that the network learns physically interpretable representations rather than spurious correlations. On the JetClass dataset, KIGNet achieves a macro-accuracy of 95.07%, macro-AUC of 96.61%, and macro-AUPR of 81.52%, relative improvements of 2.45%, 3.40%, and 19.11% over the state-of-the-art baseline. On the Aspen Open Jets dataset of real CMS collision data, KIGNet produces substantially more structured latent representations than the baseline, reducing the Davies-Bouldin Index by 52.15% ($0.8395 \rightarrow 0.4017$) and increasing the Dunn Index by 42.33% ($0.0189 \rightarrow 0.0269$), confirming that physics-informed kinematic encoding generalizes beyond idealized simulation to experimental detector conditions.

25.
arXiv (CS.AI) 2026-06-16

Beyond Scalars: Evaluating and Understanding LLM Reasoning via Geometric Progress and Stability

arXiv:2603.10384v3 Announce Type: replace Abstract: Evaluating LLM reliability via scalar probabilities often fails to capture the structural dynamics of reasoning. We introduce TRACED, a framework that assesses reasoning quality through theoretically grounded geometric kinematics. By decomposing reasoning traces into Progress (displacement) and Stability (curvature), we reveal a distinct topological divergence: correct reasoning manifests as high-progress, stable trajectories, whereas hallucinations are characterized by low-progress, unstable patterns (stalled displacement with high curvature fluctuations). Leveraging these signatures, our probabilistic framework achieves competitive performance and superior robustness across diverse benchmarks. Crucially, TRACED bridges geometry and cognition by mapping high curvature to ''Hesitation Loops'' and displacement to ''Certainty Accumulation'', offering a physical lens to decode the internal dynamics of machine thought.