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01.
medRxiv (Medicine) 2026-06-15

Multi-domain AD risk burden and plasma biomarkers in cognitively unimpaired adults

Authors:
Li↗M. Y↗Tolosa-Tort↗Heston↗M. B↗Insel↗Andrews↗S. J↗

Introduction: Alzheimer's disease (AD) pathology accumulates decades before symptom onset, yet how the cumulative effect of genetic, familial, and modifiable lifestyle risk burden jointly affects plasma biomarker levels and trajectories in cognitively unimpaired older adults remains unknown. Methods: We analyzed data from 261 participants in the PREVENT-AD cohort. A composite risk score integrating APOE e4 status, polygenic score, family history, and modifiable/lifestyle risk was examined against six plasma biomarkers using linear regression and linear mixed-effects models. Results: APOE e4 was the strongest predictor of plasma biomarker levels. Higher composite risk burden was associated with elevated ptau181, ptau217, ptau217/Ab42, and GFAP levels, and lower Ab42/40 levels. A higher risk burden was predictive of accelerated ptau181 accumulation. Discussion: Cumulative AD risk burden is broadly associated with plasma biomarker levels and specifically predicts accelerated ptau181 accumulation in cognitively unimpaired older adults, supporting structured composite risk profiling as a framework for AD risk stratification.

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02.
arXiv (CS.AI) 2026-06-17

The Discrete-Log Clock: How a Transformer Learns Modular Multiplication

Authors:
Huu Danh Nguyen↗

arXiv:2606.17399v1 Announce Type: cross Abstract: When small transformers grok modular multiplication, prior work reports that the learned embedding has a "dense" Fourier spectrum requiring all frequencies. This contrasts with modular addition, where only a sparse set of key frequencies suffices. We show this density is an artifact of analyzing in the wrong basis. The natural Fourier transform for multiplication is not the standard additive DFT but the multiplicative character transform, which decomposes functions on the multiplicative group $(\mathbb{Z}/p\mathbb{Z})^*$ into its irreducible representations. Applying this transform to a grokked transformer trained on $a \cdot b \bmod 113$, we find the embedding spectrum becomes highly sparse (Gini coefficient 0.58 vs. 0.07 in the additive basis) with only 4 key frequencies carrying significant energy. Furthermore, 96.9% of MLP neurons are cleanly tuned to a single multiplicative frequency, and neuron activation heatmaps reveal 2D-periodic structure when reordered by the discrete logarithm. These results demonstrate the transformer reduces multiplication to addition in discrete-log space, implementing a "Discrete-Log Clock" algorithm analogous to Nanda et al.'s Clock algorithm for addition. The methodology generalizes: matching the analysis basis to the algebraic structure of the task reveals interpretable structure where standard tools see noise.

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03.
arXiv (CS.LG) 2026-06-15

Structured Noise Adaptation for Sequential Bayesian Filtering with Embedded Latent Transfer Operators

Authors:
Naichang Ke↗Pongpisit Thanasutives↗Yoshinobu Kawahara↗

arXiv:2606.14195v1 Announce Type: new Abstract: Kalman filters based on the Embedded Latent Transfer Operators (ELTO) emerge as novel statistical tools for sequential state estimation. However, a critical limitation stems from their use of simplified noise models, which fail to dynamically adapt to non-stationary processes. To address this limitation, we introduce an ELTO-based Bayesian filtering approach with a new structured parameterization for the filter's noise model. This parameterization enables structured noise adaptation, which couples the data-driven learning of an optimal time-invariant noise model with dynamic parameter adaptation that responds to changes in dynamics within non-stationary processes. Empirical results show that our structured noise adaptation improves the filter's dynamic state estimation performance in noisy, time-varying environments.

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04.
arXiv (CS.CV) 2026-06-16

Structure-aware Knowledge-guided Heterogeneous Mamba for Zygomaticomaxillary Suture Assessment

Authors:
Xiaoqi Guo↗Birui Chen↗Xinquan Yang↗Chaoyun Zhang↗Xuefen Liu↗Mianjie Zheng↗Kun Tang↗Xuguang Li↗Wen Ma↗Yanhua Xu↗Linlin Shen↗

The Zygomaticomaxillary Suture is a key circummaxillary structure that connects the zygomatic bone and the maxilla, which serves as a primary site of resistance during maxillary advancement, and its maturation status directly influences the timing and efficacy of orthopedic interventions. However, accurate staging of ZMS maturation remains challenging due to subtle high-frequency transitions in suture lines and the global semantic ambiguity between adjacent stages. To address this, we present the first public ZMS dataset, comprising 3,790 ZMS images covering the entire age range from 4 to 24 years. Based on this dataset, we propose SKMamba, a Structure-aware and Knowledge-guided Mamba-based multi-modal framework for automated ZMS maturation assessment. SKMamba adopts a decoupled dual-path architecture that mimics the hierarchical diagnostic process used by experienced orthodontists. We first introduce an Implicit Edge Extractor (IEE), which leverages structural pre-training to reduce trabecular noise and accentuate sutural boundaries. Complementarily, a Cross-Modal Semantic Alignment (CSA) module is designed to incorporate anatomical descriptions from a large language model (LLM). This module helps align local morphological cues with global semantic descriptions while ensuring that objective morphological evidence remains the primary basis for decisions. Extensive experiments on our ZMS dataset demonstrate that SKMamba achieves state-of-the-art performance compared to existing methods. Code is available at https://github.com/galaxygxq1116/SKMamba.

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05.
arXiv (CS.CV) 2026-06-17

Beyond Benchmarks: Continuous Edge Inference for Fine-Grained Roadside Perception

Authors:
Aditya Mishra↗Haroon Lone↗

Continuous AI inference on resource-constrained edge hardware introduces deployment effects that are largely invisible to conventional benchmark evaluation, including temporal instability in streaming video, thermal throttling under sustained load, and workload-dependent performance variability. We present Edge-TSR, a deployment-oriented continuous edge inference system for sustained roadside perception on the NVIDIA Jetson Orin Nano. Edge-TSR integrates detection, tracking, fine-grained classification, and a lightweight track-aware temporal stabilization mechanism that improves streaming inference consistency with negligible computational overhead. Our central finding is that benchmark-centric evaluation systematically overstates deployed edge inference performance. Across three state-of-the-art baselines, we observe consistent 20-30% relative degradation when transitioning from static-image evaluation to real-world streaming deployment. Edge-TSR addresses this gap through temporal inference stabilization, recovering up to 10.16% classification accuracy over per-frame inference baselines while maintaining sustained real-time performance under continuous operation. We evaluate the complete system under diverse real-world deployment conditions, jointly characterizing inference quality, latency, throughput, and thermal behavior during long-duration operation. A 55-minute vehicular deployment over a 26 km route demonstrates sustained operation at 16.18 FPS within safe thermal limits on a single embedded device without cloud offload. Our findings show that deployment-aware evaluation and temporal inference stabilization are necessary components of continuously operating edge AI systems intended for real-world sensing deployments. We release a sample annotated streaming video evaluation dataset and full system implementation to support reproducible deployment-centric evaluation.

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07.
medRxiv (Medicine) 2026-06-15

Population-scale genomics reveals divergent pathogenicity of variant classes across paralogous collagen IV genes

Authors:
Tzoumkas↗Doctor↗G. T↗Sadeghi-Alavijeh↗Gale↗D. P↗

Monoallelic pathogenic or likely pathogenic variants in COL4A3 and COL4A4 occur in approximately 1 in 106 individuals, yet whether these paralogous genes confer equivalent pathogenicity for the same variant classes has not been tested at population scale. Using whole-genome sequencing data from the UK Biobank (UKB; n = 500,000), with replication in the All of Us Research Program (n = 414,000), we performed per-variant association testing, gene-based collapsing analyses and phenome-wide association studies (PheWAS) across haematuria, proteinuria and chronic kidney disease. We identified 64 COL4A3 and 92 COL4A4 rare variants significantly associated with haematuria or proteinuria, generating a quantitative allelic series for clinical variant interpretation. Glycine substitutions within collagenous domains conferred similar risks in both genes. In contrast, truncating and non-collagenous domain (NC1) missense variants were strongly associated with haematuria and proteinuria in COL4A4 carriers but showed substantially attenuated or absent associations in COL4A3 carriers despite comparable carrier frequencies and predicted pathogenicity scores. These findings were independently replicated in All of Us. Genome-wide association analysis identified the COL4A3/COL4A4 locus as the dominant genetic determinant of haematuria, with the signal attributable to the aggregate effects of rare coding variants and no evidence of independent common variant or trans-acting modifier effects. These findings demonstrate substantial gene-specific differences in tolerance to truncating and NC1 variants between COL4A3 and COL4A4, challenging assumptions of equivalent pathogenicity across paralogous collagen IV genes. Gene identity and not variant class alone, should inform risk stratification, variant interpretation and genetic counselling in individuals carrying collagen IV risk genotypes.

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

PreAct: Computer-Using Agents that Get Faster on Repeated Tasks

Authors:
Bojie Li↗

arXiv:2606.17929v1 Announce Type: new Abstract: Computer-using agents drive real software through the screen – clicking and typing – but they solve every task from scratch: asked to repeat a task, an agent re-reads the screen, re-reasons every tap, and pays the full cost again. We present PreAct, which lets such an agent get faster on tasks it has done before. The first time it succeeds, PreAct compiles the run into a small state-machine program-states that check the screen, transitions that act-and on later runs replays it directly instead of invoking the agent 8.5-13x faster, with no per-step language-model calls. Replay is not blind: at each step PreAct checks that the screen matches what the program expects before acting, and hands control back to the agent the moment something is off. PreAct applies the same discipline when deciding what to keep: a freshly compiled program enters the store only if, re-run from a clean state, an independent evaluator confirms it solved the task-catching programs that replay to their last step yet leave the task undone. Across a mobile, a desktop, and a web benchmark, this store-time check separates repeated runs that improve from ones that degrade as faulty programs accumulate, worth 1.75-2.6 tasks per benchmark, the same direction on all three; a fallback that explores afresh when no program fits brings PreAct level with a strong record-and-replay baseline. We also report what did not matter: prompt wording, runtime guardrails, and whether a language model or a plain embedding retriever selects which program to reuse.

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09.
arXiv (CS.CL) 2026-06-16

KVEraser: Learning to Steer KV Cache for Efficient Localized Context Erasing

Authors:
Mufei Li↗Shikun Liu↗Dongqi Fu↗Haoyu Wang↗Yinglong Xia↗Hong Li↗Hong Yan↗Pan Li↗

Post-hoc context erasing over the KV cache is challenging because a local edit has a global consequence: once a span has been processed, its influence propagates into the cached states of all subsequent tokens. This issue arises naturally in long-context LLM applications, where stale retrieved facts, incorrect tool observations, retracted user preferences, or harmful prompt injections may be identified only after prefill. Exact erasing must then recompute all tokens after the deleted span, making its computational cost depend on suffix length rather than erased-span length. We introduce KVEraser, a learned KV-cache editing method for efficient localized context erasing. Given a processed context and a span to remove, KVEraser replaces only the KV states of the erased interval with learned steering states while reusing the remaining cache unchanged. To learn a transferable erasing mechanism, we build a two-stage training pipeline: generic span-neighbor pre-training teaches the eraser to suppress the influence of the erased span, while task-specific fine-tuning adapts this capability to downstream scenarios. Experiments show that KVEraser nearly matches full recomputation in post-erasure performance on in-domain tasks across 1K–32K context lengths, while its latency increases by only 24% compared with a 17.6x increase for full recomputation. KVEraser also generalizes to unseen long-document QA tasks with harmful factual distractors, achieving the best performance among approximate baselines with a 3–4x speedup over full recomputation.

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10.
arXiv (CS.LG) 2026-06-18

RNN(p) for Power Consumption Forecasting

Authors:
Roberto Baviera↗Pietro Manzoni↗

arXiv:2209.01378v3 Announce Type: replace Abstract: An elementary Recurrent Neural Network that operates on p time lags, called an RNN(p), is the natural generalisation of a linear autoregressive model ARX(p). It is a powerful forecasting tool for variables displaying inherent seasonal patterns across multiple time scales, as is often observed in energy, economic, and financial time series. The architecture of RNN(p) models, characterised by structured feedbacks across time lags, enables the design of efficient training strategies. We conduct a comparative study of learning algorithms for these models, providing a rigorous analysis of their computational complexity and training performance. We present two applications of RNN(p) models in power consumption forecasting, a key domain within the energy sector where accurate forecasts inform both operational and financial decisions. Experimental results show that RNN(p) models achieve excellent forecasting accuracy while maintaining a high degree of interpretability. These features make them well-suited for decision-making in energy markets and other fintech applications where reliable predictions play a significant economic role.

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11.
PLOS Computational Biology 2026-06-17

Combining machine learning and iterative experiments to keep pace with emerging viral variants of concern

Authors:
Thomas Sheffield↗

by Thomas Sheffield, Ryan C. Bruneau, Stephen Won, Kenneth L. Sale, Brooke Harmon, Le Thanh Mai Pham Modeling and predicting viral mutations before they emerge plays a crucial role in pandemic preparedness, enabling the early identification of emerging variants of concern (VOCs) and guiding timely updates to vaccines, diagnostic tests, and therapeutic strategies. However, existing machine learning models and large-scale experiments lose their predictive power as viral variants evolve further from the original strains in sequence space. Here, we present a scalable framework that integrates random forest and neural network machine learning models with targeted high-throughput experimentation to anticipate and evaluate emerging SARS-CoV-2 receptor-binding domain (RBD) variants. Using public datasets, we trained predictive models for binding to human Angiotensin-converting enzyme 2 (ACE2), RBD expression, and antibody escape, and refined these models through iterative integration of experimental data focused on over 200 variants derived from wild-type (WT) and Omicron strains. Through an indirect transfer learning approach, our machine learning models achieved high accuracy having correlation coefficients of up to 0.79 for antibody binding. The models were also generalizable across diverse antibody types including heavy-chain-only antibodies (HCAbs) by encoding complementarity-determining regions (CDRs) as input features. This dynamic approach enables rapid assessment of emerging variants, facilities prioritization of the therapeutic strategies, and supports a proactive, data-driven response to evolving viral threats.

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13.
arXiv (quant-ph) 2026-06-12

Influence-solvability: a systematic theory of $(1+1)D$ solvability and its application to brickwork circuits

Authors:
Friedrich H\"ubner↗Sun Woo P. Kim↗

arXiv:2606.12538v1 Announce Type: cross Abstract: `Solvable' circuits, such as dual unitaries and its generalisations, have arisen as paradigmatic examples of tractable chaotic non-equilibrium dynamics, both in classical and quantum systems. However, while increasingly more complicated sufficient conditions have been proposed, a systematic theory classifying and understanding general features of solvable circuits is missing. We develop such a theory by introducing influence-solvable circuits, a class of $(1+1)D$ circuits whose influence matrix, which represents the `bath' generated by its own evolution, is given by a uniform MPS with finite bond-dimension $\chi$. This property allows for efficient computation of subsystem dynamics and essentially contains all known examples of solvable circuits. We derive a set of necessary and sufficient local conditions by using a version of the fundamental theorem of MPS for open boundary conditions. Next we apply our theory to brickwork circuits with $\chi=1$ influence-solvability and perform a systematic classification of classical brickwork circuits with local dimension up to $d=3$ and quantum brickwork circuits with $d=2$. Our search reveals new solvable circuits that are not captured by known solvability conditions.

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14.
arXiv (CS.CL) 2026-06-11

StanceNakba Shared Task: Actor and Topic-Aware Stance Detection in Public Discourse

Authors:
Kholoud K. Aldous↗Md Rafiul Biswas↗Mabrouka Bessghaier↗Shimaa Ibrahim↗Kais Attia↗Wajdi Zaghouani↗

We present StanceNakba 2026, a shared task on stance detection in polarized social media discourse related to the Palestinian-Israeli conflict, organized as part of Nakba-NLP 2026 at LREC-COLING 2026. The task introduces two subtasks: Subtask A (Actor-Level Stance Detection), which classifies English social media posts as Pro-Palestine, Pro-Israel, or Neutral; and Subtask B (Cross-Topic Stance Detection), which identifies Favor, Against, or Neither stances in Arabic posts toward two conflict-related topics, normalization with Israel and refugee presence in Jordan. The task is grounded in an annotated dataset of 2,606 social media posts. A total of 7 teams participated in Subtask A and 6 teams in Subtask B. Participating systems primarily fine-tuned Arabic and multilingual transformer-based models, including MARBERT, AraBERT, and DeBERTa-v3 variants, with several teams employing cross-validation, ensemble methods, and topic-conditioned architectures. The best-performing systems achieved a Macro F1 of 0.9620 on Subtask A and 0.8724 on Subtask B, demonstrating that transformer-based approaches are highly effective for conflict-domain stance detection while highlighting persistent challenges in cross-topic generalization and neutral class prediction.

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15.
arXiv (CS.LG) 2026-06-12

The Range Shrinks, the Threat Remains: Re-evaluating LLM Package Hallucinations on the 2026 Frontier-Model Cohort

Authors:
Aleksandr Churilov↗

arXiv:2605.17062v2 Announce Type: replace-cross Abstract: Spracklen et al. (USENIX Security '25) showed that code-generating large language models hallucinate package names that do not exist on PyPI or npm at rates ranging from 5.2% on commercial models to 21.7% on open-source models, creating an attack surface for slopsquatting – the registration of malicious packages under hallucinated names. We replicate their methodology on five frontier code-capable LLMs released between October 2025 and March 2026: Claude Sonnet 4.6, Claude Haiku 4.5, GPT-5.4-mini, Gemini 2.5 Pro, and DeepSeek V3.2. Across 199,845 paired Python and JavaScript prompts validated against PyPI and npm master lists, we measure overall hallucination rates between 4.62% (Claude Haiku 4.5) and 6.10% (GPT-5.4-mini) – an order-of-magnitude compression of the inter-model spread observed by Spracklen, but not a retirement of the threat. Beyond replication, we identify a set of 127 package names (109 on PyPI, 18 on npm) that all five evaluated models invent identically; following coordinated disclosure with PyPI Security and Socket.dev, 53 of these (41 on PyPI, 12 on npm) remain registrable by an attacker after each registry's existing defenses, constituting a model-agnostic supply-chain attack surface that no single-model study can reveal. We further document a Python-over-JavaScript hallucination asymmetry that inverts Spracklen's 2024 finding, identify a Haiku-below-Sonnet inversion within the Anthropic family, and observe a Jaccard-similarity peak between DeepSeek V3.2 and GPT-5.4-mini (J = 0.343) suggestive of shared training-data origins.

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

SketchXplain: Intuitive Visual Explanations of Image Classifiers with Sketches

Authors:
Wencan Zhang↗Mario Michelessa↗Xuejun Zhao↗Brian Y. Lim↗

arXiv:2606.17646v1 Announce Type: cross Abstract: Saliency map visualizations explain image-based AI predictions by pointing to regions, but these are often unintuitive and semantically unclear, leaving an interpretability gap. We argue that AI explanations should be intuitive – coherent to user knowledge, yet simple and selective to accelerate interpretation. Inspired by artistic drawings, we propose SketchXplain to generate sketch-based visual explanations for intuitive image-based explainable AI (XAI). Combining techniques in saliency maps, concept-bottleneck models, and sketch optimization, SketchXplain integrates saliency to select coherent observation artifacts, concepts for knowledge coherence, cues to represent them, and abstraction for simplicity. Evaluating on face expression recognition, modeling and user studies showed that SketchXplain supported quicker interpretation with more aligned visualizations than saliency maps or simple drawings. Further evaluation on skin lesion diagnosis found that SketchXplain more coherently visualized disease symptoms, better supporting lay diagnosis. Thus, this work illustrates the value of sketches for intuitive, simple, coherent, and quick image-based XAI visualizations.

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

Enhancing Pathological VLMs with Cross-scale Reasoning

Authors:
Chi Phan↗Tianyi Zhang↗Qiaochu Xue↗Yufeng Wu↗Dan Hu↗Zeyu Liu↗Sudong Wang↗Yueming Jin↗

Pathological images are inherently multi-scale, requiring pathologists to integrate evidence from global tissue architecture at low magnification to cellular morphology at higher magnification for accurate diagnosis. While existing pathological datasets for vision-language model (VLM) include various scales, they often lack an explicit cross-scale reasoning objective. This limitation prevents VLMs from capturing essential cross-scale representations and learning evidence-based reasoning. To bridge this gap, we introduce the first cross-scale training and evaluation paradigm that formulates pathology interpretation as multi-magnification reasoning. However, creating such a task reveals a critical challenge: multi-image visual question answering (VQA) is prone to text-only shortcuts, which allow models to guess answers using magnification-dependent artifacts rather than visual evidence. To address this, we propose a leakage-aware curation pipeline that combines adversarial text-only screening with constraint-guided question design. Using this pipeline, we construct Scale-VQA, a high-quality benchmark with 4,685 multiple-choice questions grounded in 2,537 pathology images across multiple magnification levels. Finally, we present ScaleReasoner-R1, a model trained via reinforcement learning to optimize performance on the cross-scale VQA task. ScaleReasoner-R1 achieves state-of-the-art performance on our cross-scale reasoning benchmark and generalizes to SOTA performance on established single-scale benchmarks. Findings suggest that even the limited cross-scale supervision can significantly improve pathological understanding. The code and demos will be open-sourced.

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18.
medRxiv (Medicine) 2026-06-18

Human Intuition vs. Computational Precision: Neurologists, Feature-based Models, and Deep Learning for Stroke Prognosis

Authors:
Herzog↗Blindenbacher↗Globas↗Haeberlin↗M. I↗Baumgartner↗Capecchi↗Inauen↗Sick↗Majoie↗C. B↗van Zwam↗…

Background: Prognostication in large vessel occlusion (LVO) stroke remains challenging. Although several prognostic models exist, their comparison to clinician performance, human-model interaction, and specific sources of human bias remain poorly understood. Methods: Using pre-treatment clinical and CT data from the MR CLEAN trial (n=500), six neurologists predicted three-month modified Rankin Scale (mRS) scores for 40 patients, both unaided and assisted by a validated feature-based model (MR PREDICTS). Human performance was benchmarked against MR PREDICTS and a multimodal, interpretable deep learning (DL) approach using raw imaging data. We explicitly assessed neurologists? ability to estimate model-required imaging features and identified systematic human biases. Models were additionally validated in a larger MR CLEAN trial cohort (n=404). Results: For predicting the full mRS distribution, standalone models achieved good ordinal agreement (MR PREDICTS quadratic weighted kappa (QWK) 0.51 [0.24 to 0.70]; DL model 0.49 [0.25 to 0.67]), significantly outperforming unaided neurologists (QWK 0.27 [0.10, 0.42]). Neurologists showed systematic overoptimism, predicting lower mRS scores than observed. Furthermore, there was poor accuracy in extracting imaging features. Raters? ASPECTS predictions deviated by 3.4 points from the confirmed scores, and collateral score accuracy was 44.6%. However, for predicting binary mRS (0-2 vs. 3-6), accuracy was comparable between unaided neurologists (64.17% [55.42% to 72.92%]) and models (MR PREDICTS 67.50% [52.50% to 82.50%]; DL model 63.16% [47.37% to 78.95%]). Model-assistance modestly improved and harmonized neurologists? predictions (QWK 0.41 [0.22 to 0.55]; binary accuracy 68.75% [58.33% to 78.34%]. Model performance remained robust in the larger cohort. Conclusions: Multimodal prognostic models outperform clinicians in predicting the full range of mRS outcomes, while human error in imaging assessment and systematic optimism bias are primary drivers of prognostic inaccuracy. End-to-end DL models eliminate human-input variability and hold strong potential as an automated second opinion to support prognostication and decision-making in acute LVO stroke.

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19.
arXiv (CS.LG) 2026-06-17

Discovering Functionally Selective Brain Regions with a Deep Topographic Multimodal Model

Authors:
Badr AlKhamissi↗Johannes Mehrer↗Lara Marinov↗Ahmed Abdelaal↗Abdulkadir Gokce↗Martin Schrimpf↗

arXiv:2606.09770v2 Announce Type: replace-cross Abstract: Nearby neurons in cortex share similar response profiles, producing systematic spatial organization across sensory and cognitive systems. Recent topographic models reproduce aspects of this structure but remain unimodal and spatially constrain each layer separately, yielding fragmented maps that capture neither the contiguity of cortical processing streams nor their integration across modalities. We introduce Topo-Omni, a topographic multimodal model in which visual, auditory, and language/cognitive processing share a single contiguous in-silico sheet. Built by fine-tuning a pretrained foundation model with a spatial smoothness objective, this architecture develops clusters across modalities that are consistent with human neuroimaging, from sensory to cognitive systems. Driving or suppressing a cluster selectively biases or impairs perception, paralleling human intervention studies. Finally, we use our model to screen for novel clusters in-silico and discover new natural landscape and animal networks which we validate in human data. A single spatial principle thus organizes representations across modalities and processing stages, yielding testable hypotheses about cortical organization.

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

DeepRoot: A KG-Coordinated Multi-Agent System for Therapeutic Reasoning over Historical Medical Texts

Authors:
Zijian Carl Ma↗Sean J. Wang↗Sijbren Kramer↗Li Erran Li↗

arXiv:2606.15931v1 Announce Type: cross Abstract: Historical medical archives and traditional medicines hold immense potential for drug discovery and remain a primary source for current drug development. However, pre-ontological prose and idiosyncratic taxonomies prevent the standardization and medical modernization of the data for use in current biomedical pipelines. Furthermore, no existing LLM agent system, whether tool-calling, retrieval-augmented, or agentic deep-research, can convert such text into verifiable drug-discovery leads at scale. We close this gap with DeepRoot, a multi-agent LLM system that jointly builds and utilizes a verified knowledge graph, showing that grounding and reasoning – often conflated – are separable axes the system can compose for therapeutic reasoning. Applied to the Shen Nong Ben Cao Jing, DeepRoot recovers $10$ of $21$ held-out compound-disease treatment pairs at R@$20$ ($47.6\%$ vs $4.8\%$ for a raw corpus LLM and $\sim\!2.4\%$ random) and dominates an LLM-as-judge audit for reasoning quality over baseline LLMs and LLMs with direct tool-call access to the same APIs DeepRoot itself queries. Tool-using LLMs hallucinate evidence on $87\%$ of claims, versus 7-10% for DeepRoot. Graph-only inference hallucinates $0\%$ but ranks lowest on reasoning coherence; DeepRoot KG+LLM is the only condition to win on both axes, pointing toward a route for systematic mining and repurposing of historical medical knowledge.

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

MPMWorlds: Material-Point-Method Simulations for Inferring and Extrapolating Physical Dynamics

Authors:
\v{Z}iga Kova\v{c}i\v{c}↗Kevin Ellis↗

To study the ability to infer physical dynamics from videos and extrapolate them forward in time, we assemble a dataset of 2D Material Point Method (MPM) physical simulations covering rich physical phenomena such as deformable objects, fluids, kinetic objects, and emitters. We study code generation and video diffusion approaches on this dataset, identifying their strengths and weaknesses by varying the amount of physically relevant side information. The code generation model, beyond giving a working demonstration of automatic synthesis of MPM simulations, reveals that such an approach struggles with inferring physical parameters from visual input, but relative to video diffusion, produces physically and temporally stable extrapolations forward in time, while the video diffusion model more strongly identifies geometric properties from visual input but produces physically implausible extrapolations.

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

The Pragmatic Persona: Discovering LLM Persona through Bridging Inference

Authors:
Jisoo Yang↗Jongwon Ryu↗Minuk Ma↗Trung X. Pham↗Junyeong Kim↗

Large Language Models (LLMs) reveal inherent and distinctive personas through dialogue. However, most existing persona discovery approaches rely on surface-level lexical or stylistic cues, treating dialogue as a flat sequence of tokens and failing to capture the deeper discourse-level structures that sustain persona consistency. To address this limitation, we propose a novel analytical framework that interprets LLM dialogue through bridging inference – implicit conceptual relations that connect utterances via shared world knowledge and discourse coherence. By modeling these relations as structured knowledge graphs, our approach captures latent semantic links that govern how LLMs organize meaning across turns, enabling persona discovery at the level of discourse coherence rather than surface realizations. Experimental results across multiple reasoning backbones and target LLMs, ranging from small-scale models to 80B-parameter systems, demonstrate that bridging-inference graphs yield significantly stronger semantic coherence and more stable persona identification than frequency or style-based baselines. These results show that persona traits are consistently encoded in the structural organization of discourse rather than isolated lexical patterns. This work presents a systematic framework for probing, extracting, and visualizing latent LLM personas through the lens of Cognitive Discourse Theory, bridging computational linguistics, cognitive semantics, and persona reasoning in large language models. Codes are available at https://github.com/JiSoo-Yang/Persona_Bridging.git

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23.
arXiv (CS.AI) 2026-06-19

KG-SoftMAP: Soft Knowledge-Graph Priors for Bayesian Network Structure Learning from Sparse Discrete Data

Authors:
Guoliang Xu↗James E. Corter↗

arXiv:2606.10358v2 Announce Type: replace-cross Abstract: Learning Bayesian network (BN) structure from sparse discrete data is hard: when each instance records only a few variables, most variable pairs lack the joint observations needed for reliable scoring, and data-only methods recover little structure. However, imperfect domain knowledge, expressible as a weighted directed knowledge graph (KG), is often available. We propose KG-SoftMAP, which encodes such a KG as a finite-strength, confidence-weighted edge prior and maximizes a MAP objective combining the BDeu score with a logit-form prior; the KG may be expert-curated or LLM-extracted. On synthetic benchmarks with known DAGs, KG-SoftMAP reaches Directed-F1 (DF1) $0.19$–$0.32$ at observation rate $\rho=0.05$ and DF1 $0.44$–$0.97$ at $\rho\geq0.2$, while every data-only learner tested stays near zero under the same sparse masks. Recovery tracks KG quality: controlled corruption degrades it smoothly, a zero-signal KG yields DF1 $0.00$, and a blindly LLM-extracted KG with imperfect precision and recall still drives substantial recovery. On three real sparse educational datasets, the learned BN acts as a concept-level posterior model: on SAF it matches logistic regression (LR) within $0.03$ F1_FAIL while providing an inspectable concept graph, calibrated Fail probabilities, and tractable posterior queries from partial observations.

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24.
arXiv (CS.AI) 2026-06-16

Metric Match: A Subset Selection Approach to Evaluating LLM Judge Reliability

Authors:
Alyssa Unell↗Natalie Dullerud↗Naomi Boneh↗Meena Jagadeesan↗Tatsu Hashimoto↗Nigam Shah↗Sanmi Koyejo↗

arXiv:2606.15029v1 Announce Type: new Abstract: LLM judges are used to reduce the need for costly human labor in evaluating open-ended text generation. However, the reliability of these judges depends critically on their alignment with human raters – a property that itself depends on costly human annotations. In this work, we develop a method (Metric Match) for estimating correlation-based reliability metrics of LLM judges from limited annotations. Metric Match selects a subset of samples for human annotation such that the subset matches the population reliability metric with respect to acquired synthetic labels. We empirically show that Metric Match achieves a win-rate of 0.838 against random subset selection across four different correlation metrics and 15 datasets, with an 18.7% decrease in average estimation error and reduces annotation needs by 32.5%. We provide a cost model and highlight a medical case study where our method saves $1,041.67 compared to random selection for expert annotation. Further, we shift our task from reliability estimation to reliability classification of whether a given judge is above a deployment threshold, outperforming random selection with Metric Match. All project code is publicly available, and we additionally provide an installable package for ease of use.

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25.
arXiv (CS.CV) 2026-06-12

PROBE: Probabilistic Occupancy BEV Encoding with Analytical Translation Robustness for 3D Place Recognition

Authors:
Jinseop Lee↗Byoungho Lee↗Gichul Yoo↗

We present PROBE (PRobabilistic Occupancy BEV Encoding), a learning-free LiDAR place recognition descriptor that models each BEV cell's occupancy as a Bernoulli random variable. Rather than relying on discrete point-cloud perturbations, PROBE analytically marginalizes over continuous Cartesian translations via the polar Jacobian, yielding a distance-adaptive angular uncertainty $\sigma_\theta = \sigma_t / r$ in $\mathcal{O}(R{\cdot}S)$ time. The primary parameter $\sigma_t$ represents the expected translational uncertainty in meters, a sensor-independent physical quantity that enhances cross-sensor generalization while reducing the need for extensive per-dataset tuning. Pairwise similarity combines a Bernoulli-KL Jaccard with exponential uncertainty gating and FFT-based height cosine similarity for rotation alignment. Evaluated on four datasets spanning four diverse LiDAR types, PROBE achieves the highest accuracy among handcrafted descriptors in multi-session evaluation and competitive single-session performance relative to both handcrafted and supervised baselines. The source code and supplementary materials are available at https://sites.google.com/view/probe-pr.

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