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01.
arXiv (quant-ph) 2026-06-11

Fabricating fiber cavity mirror substrates compatible with high coupling efficiency

arXiv:2606.12168v1 Announce Type: cross Abstract: Fiber optical cavities offer small mode volumes and correspondingly strong light-matter interactions in an open Fabry-Perot geometry. However, existing fabrication techniques do not reliably produce substrates with surface profiles amenable to high mode matching between the cavity mode and fiber core, thereby limiting the achievable collection efficiency. Here we present a technique to fabricate fiber mirror substrates while using $in situ$ reflectometry to constrain the achievable mode matching prior to coating. By measuring the back-reflection from freshly cleaved fiber tips, we pre-select 138 fibers compatible with 96.5-99.5% mode matching, and after a single CO$_2$ laser ablation pulse, these fibers remained compatible with 95.3-99.2\%. This simple technique provides rapid feedback during each stage of substrate fabrication, greatly enhancing the yield of viable fiber mirror substrates prior to (expensive) coating runs.

02.
arXiv (quant-ph) 2026-06-15

Quasilinear Equivalence Checking for Detector Error Models

arXiv:2606.14677v1 Announce Type: new Abstract: A Detector Error Model (DEM) is a structured representation of error mechanisms in quantum circuits, which has gained popularity in quantum compilation pipelines for its ability to capture fault-tolerance at a circuit level. It lists error mechanisms as instructions targeting detectors and observables, specifying for each physical fault channel the probability that the fault fires, the detectors it triggers, and the observables it flips. In this paper, we develop an equational theory for DEMs, with its associated categorical semantics. We present a sound, terminating, confluent rewriting system for DEM terms, formulating it as a symmetric monoidal theory (a PROP) over the Giry monad. We prove that every DEM term has a unique normal form, which can be computed efficiently in quasilinear time $O(k|E|\log|E|)$, where $|E|$ is the number of instructions and $k$ bounds the size of a target set. This provides a complete set of invariants (via Tanner graphs) for structural DEM equivalence. We provide the first static decision procedure for DEM equivalence, with rigorous correctness guarantees. It is complete (decides full decoder-equivalence exactly) for non-adaptive quantum error correction (QEC) pipelines, and scales to a sound and applicable decision procedure for partially-adaptive circuits (lattice surgery, distributed QEC, ...) without suffering exponential overhead. We discuss its application to the verification and optimisation of quantum compilers.

03.
bioRxiv (Bioinfo) 2026-06-11

Combinatorial docking and molecular generation to navigate over 100-billion molecules for prospective ligand discovery

Commercially available make-on-demand libraries now exceed 100 billion compounds, requiring over 50 years to screen on 2,000 CPU cores using conventional docking. We present two complementary approaches to address this challenge. CombiDOCK, a combinatorial docking framework, enables exhaustive screening at the 100-billion scale within 40 days. MINT-Dock, a generative framework, accelerates navigation of this space by integrating CombiDOCK with Monte Carlo Tree Search. Benchmarked on 46 diverse targets, CombiDOCK matched full-molecule docking accuracy, and MINT-Dock achieved a 4,800-fold enrichment over random selection. Compared with prior billion-scale brute-force campaigns against {sigma}2, VMAT2, and VAChT, prospective CombiDOCK screens of the 100-billion-molecule library yielded higher hit rates and more potent ligands, while MINT-Dock achieved comparable outcomes across single- and multi-target objectives with >20-fold computational cost reductions. Docking-predicted poses of the best VAChT-binding compounds were confirmed by cryo-EM structures. These methods provide exhaustive and generative paths for navigating the trillion-molecule frontier of drug discovery.

04.
medRxiv (Medicine) 2026-06-16

Development of a symptom-based severity score anchored to health-related quality of life post-COVID-19 within the population-based EPILOC cohorts

Purpose Because simple symptom counts treat all symptoms as equally important and may not adequately capture the HRQoL impact of heterogeneous post-COVID-19 symptoms, we aimed to develop an HRQoL-anchored symptom severity score providing an interpretable measure of post-COVID-19 disease burden. Methods Baseline data from the population-based EPILOC and EPILOC Omicron surveys (adults aged 18-65 years) were used to develop a symptom-based severity score anchored to physical and mental HRQoL assessed with the SF-12. A two-stage modelling approach was applied to identify HRQoL-relevant symptoms and to derive symptom-specific weights for physical and mental component scores, incorporating 30 ordinal symptom severity variables. Symptom-specific weights were extracted to compute physical, mental, and composite severity scores. Score interpretation was examined using external reference measures, including EPILOC case status, self-reported health recovery, and functional consequences. Results A total of 19,004 participants (mean age 44.3 years, 59.6% female) were included. Sixteen symptoms contributed to the physical and eleven to the mental HRQoL score, with a limited subset accounting for most of the HRQoL loss. Severity scores were heavily right-skewed, with 50.6% of participants showing no measurable HRQoL impairment. Higher scores correlated with lower self-reported recovery, and increased probability of rehabilitation use and health-related changes in working time, supporting convergent and criterion-related validity. Conclusions This study introduces a transparent, HRQoL-anchored symptom severity score that measures graded post-COVID-19 burden beyond simple symptom counts. The score may be particularly suited for longitudinal assessment of recovery trajectories.

05.
arXiv (CS.CL) 2026-06-16

G-Loss: Graph-Guided Fine-Tuning of Language Models

Traditional loss functions, including cross-entropy, contrastive, triplet, and su pervised contrastive losses, used for fine-tuning pre-trained language models such as BERT, operate only within local neighborhoods and fail to account for the global semantic structure. We present G-Loss, a graph-guided loss function that incorporates semi-supervised label propagation to use structural relationships within the embedding manifold. G-Loss builds a document-similarity graph that captures global semantic relationships, thereby guiding the model to learn more discriminative and robust embeddings. We evaluate G-Loss on five benchmark datasets covering key downstream classification tasks: MR (sentiment analysis), R8 and R52 (topic categorization), Ohsumed (medical document classification), and 20NG (news categorization). In the majority of experimental setups, G-Loss converges faster and produces semantically coherent embedding spaces, resulting in higher classification accuracy than models fine-tuned with traditional loss functions.

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

The Pragmatic Persona: Discovering LLM Persona through Bridging Inference

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

07.
arXiv (CS.LG) 2026-06-18

Dimension-Free Convergence of Discrete Diffusion Models: Adjoint Equations Induce the Right Space

arXiv:2605.17232v2 Announce Type: replace Abstract: Discrete diffusion has become a leading framework for generative modeling in various applications including language, vision, and biology. Existing convergence theory, however, exhibits fundamental limitations. KL-based analyses diverge under singular priors such as the masked distribution, while bounds in total variation (TV) depend on the state space size $S$ and become vacuous for modern language tasks, where vocabularies contain hundreds of thousands of tokens. We develop a unified adjoint-equation-based framework that establishes dimension-free convergence guarantees in any integral probability metric (IPM). To the best of our knowledge, our bounds are the first to be entirely free of $S$ and applicable to both masked and uniform priors. Importantly, our theory relies only on a single standard rate-matrix regularity assumption and applies to general priors. Five novel techniques drive our improvements: working in the space of observables via adjoint equations rather than directly with probability measures, a regularity analysis that yields bounds on any IPM, a coupling argument that removes $S$-dependence under uniform transitions, and score-marginal cancellation and exit-routing techniques that remove $S$-dependence under masked transitions. Our framework thus sharply departs from prior analyses and avoids the shortcomings of pathspace-KL and existing TV-based approaches. Beyond convergence bounds, our framework provides a versatile toolkit for further theoretical study of discrete diffusion models, including principled choices of loss functions and dimension-free step complexity.

08.
arXiv (CS.CV) 2026-06-16

ActiveSAM: Image-Conditional Class Pruning for Fast and Accurate Open-Vocabulary Segmentation

Segment Anything Model 3 (SAM 3) provides a strong frozen backbone for concept-prompted segmentation, but applying it directly to open-vocabulary semantic segmentation (OVSS) is inefficient: full-resolution decoding is typically run over the entire dataset vocabulary, whereas each image contains only a small active subset of classes. We introduce ActiveSAM, a training-free, zero-shot inference framework that turns SAM 3 into an active-vocabulary segmenter. ActiveSAM first canonicalizes and expands class prompts, then estimates an image-conditioned active set from a low-resolution presence preview. Only the retained classes are decoded at full resolution, using bucketed prompt multiplexing with the frozen SAM 3 decoder. The preview stage uses only class-presence evidence and skips unnecessary segmentation-head computation, while the final stage applies margin-aware background calibration to suppress low-confidence pixels. ActiveSAM requires no target-dataset training, no weight updates, and no oracle class-presence labels. Across eight OVSS benchmarks, ActiveSAM improves the speed-accuracy tradeoff of training-free open-vocabulary semantic segmentation, outperforming the current state-of-the-art SegEarth-OV3 by approximately +1.4 mIoU on average while running up to 5.5x faster on large-vocabulary datasets. ActiveSAM also demonstrates the strongest robustness under image corruption that simulates real-world distribution shift, making it well-suited for deployment in noisy-input domains such as autonomous driving and embodied AI. Code is available at https://github.com/VILA-Lab/ActiveSAM.

09.
arXiv (CS.LG) 2026-06-19

Toward all-optical unsupervised Hebbian learning in deep photonic neuromorphic networks

arXiv:2601.22300v3 Announce Type: replace-cross Abstract: We propose a deep photonic neuromorphic network (PNN) architecture based on phase-change material (PCM) synapses and local optical feedback for online, unsupervised Hebbian learning. The proposed architecture combines optical vector-matrix multiplication, non-volatile PCM synaptic weighting, and local coincidence-driven synaptic adaptation within a multilayer photonic crossbar framework compatible with photonic integrated circuits. Unlike conventional PNNs that rely on externally computed gradients, repeated optical-electrical-optical conversions, or global backpropagation, the proposed framework employs local Hebbian learning governed directly by correlated pre- and post-synaptic optical activity. To investigate the feasibility of the proposed learning mechanism, we implemented the PNN design using fiber-optic components, programmable variable optical attenuators, and real-time software control that incorporates PCM thermal dynamics. Supervised and unsupervised learning behaviors were experimentally evaluated under both offline and online learning conditions using representative image-recognition tasks. The experimental results demonstrate adaptive synaptic evolution, successful optical inference, and autonomous pattern encoding through local Hebbian learning under realistic fiber-optic hardware conditions. These results establish a pathway toward future integrated photonic neuromorphic systems capable of scalable and energy-efficient online Hebbian learning.

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

MOSAIC: Modality-Specific Adaptation for Incremental Continual Learning in Parkinson's Disease Gait Assessment

arXiv:2606.13258v1 Announce Type: new Abstract: Gait-based Parkinson's disease assessment increasingly relies on heterogeneous sensors, but clinical systems rarely collect all modalities simultaneously. New sensors may arrive through device upgrades, protocol changes, or multi-center deployment, while historical patient data are often unavailable because of privacy and storage constraints. This modality-incremental setting faces three challenges: unreliable cross-modal distillation, modality-specific statistical shifts, and reduced plasticity after preservation. We propose MOSAIC, a compact continual learning framework. First, we identify the Toxic Teacher phenomenon and introduce Modality-Specific Warm-Up to stabilize newly learned modality representations before distillation. Second, we propose a statistics-decoupled MSBN architecture that isolates sensor statistics while maintaining a shared semantic backbone. Third, we design a curriculum-guided repulsive objective for Plasticity Recovery, preserving legacy knowledge while recovering modality-specific capacity. Experiments on three multimodal Parkinson's gait datasets show that MOSAIC improves final performance and mitigates forgetting. Project code is available at: https://github.com/minlinzeng/MOSAIC_Modality-Specific-Adaptation-for-Incremental-Continual-Learning-in-PD-Gait-Assessment.git

11.
arXiv (CS.LG) 2026-06-16

Prediction of Runtime Parameters of Parallel Chemistry Applications via Active and Generative Learning

arXiv:2606.16226v1 Announce Type: new Abstract: In this work, we develop two main Machine Learning based approaches to predict the runtime parameters of highly scalable parallel chemistry computations.These approaches employ active and generative learning together with the empirically determined gradient boosted regression tree models chosen among a rich suite of machine learning models. When evaluated on Coupled-Cluster with Singles and Doubles computations, our models achieve a mean absolute error percentage (MAPE) as low as 0.023 and a coefficient of determination as high as 99.9%. Furthermore, when combined with active learning to mitigate the lack of large amounts of training data, our models score a MAPE about 0.2 with 20-25% of the original dataset.

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

Edge Flow: A Tractable and Predictive Continuous-Time Model for Gradient Descent at the Edge of Stability

arXiv:2606.18080v1 Announce Type: new Abstract: Gradient descent in deep learning may operate at the edge of stability (EoS), a regime in which the largest eigenvalue of the loss Hessian hovers near the stability threshold $2/\eta$, where $\eta$ is the learning rate. Classical analysis tools such as gradient flow and the descent lemma do not apply here, motivating the search for a continuous-time model valid at EoS. We propose Edge Flow, a system of three coupled ordinary differential equations that provides a tractable, faithful, and predictive model of gradient descent dynamics at EoS. Edge Flow decomposes the dynamics into a center, an oscillation direction, and an oscillation magnitude. The center follows a modified gradient flow on a symmetrized loss; the direction tracks a top eigenvector of the Hessian via Rayleigh quotient dynamics; and the magnitude grows or decays exponentially depending on whether the sharpness exceeds or falls below the threshold $2/\eta$. Crucially, sharpness stabilization emerges from the coupled dynamics via a self-stabilization feedback loop. Discretizing Edge Flow only requires two gradient evaluations and one Hessian–vector product at each iteration. We demonstrate empirically that Edge Flow tracks the dynamics of gradient descent at least as faithfully as previously proposed continuous-time EoS models, while in addition resolving the oscillation of the sharpness at the onset of EoS, and that it provides a principled framework for understanding and mitigating instabilities in this regime.

13.
arXiv (CS.CV) 2026-06-18

SVHighlights: Towards Extremely Long Sport Video Highlight Detection

While highlight detection for long-form videos is of great practical importance, most existing methods remain limited to short-form content, largely due to the absence of a suitable benchmark. To bridge this gap, we introduce SVHighlights, to the best of our knowledge, the first benchmark for highlight detection in extremely long sports videos, each exceeding one hour in duration, across multiple sports categories. SVHighlights is constructed from pairs of full-length sports videos and their corresponding official highlight videos using a dataset generation pipeline, enabling scalable label generation without conventional per-clip saliency annotation. The benchmark comprises 320 videos with an average duration of 2.00 hours and a total of 640.18 hours, substantially exceeding previous datasets. Existing methods also face fundamental challenges on long videos: models trained on short clips fail to generalize to hour-long content, and their clip-level scoring lacks the broader context needed to identify highlights. To address this and provide a strong baseline, we present TF-SELECTOR, a training-free segment-based approach that divides each video into context-aware segments by merging adjacent shots sharing the same semantic content, and predicts segment-level saliency scores using a large language model with multimodal inputs including visual captions, transcripts, and audio volume. Experiments demonstrate that TF-SELECTOR achieves superior performance across most metrics compared to Video Temporal Grounding (VTG)-tuned baselines, with improvements of +2.50 in HIT@1, +4.04 in HIT@K, and +2.95 in IoU. These results establish SVHighlights as a challenging testbed for long-form highlight detection and demonstrate that a simple segment-based strategy can effectively scale to hour-long videos.

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

Your Agent Has a Genome: Sequence-Level Behavioral Analysis and Runtime Governance of LLM-Powered Autonomous Agents

作者:

arXiv:2606.15579v1 Announce Type: new Abstract: We propose Base Sequence Analysis, a framework that encodes the runtime behavior of LLM-powered autonomous agents into compact symbolic sequences using a four-letter alphabet: X (Explore), E (Execute), P (Plan), and V (Verify). Drawing an analogy to genomic sequence analysis, we apply n-gram pattern mining, Markov transition matrices, and point-biserial correlation to 347 real-world execution traces collected from a production ReAct agent system over 8 days. Our analysis reveals that (1) the trigram P-X-P is the only statistically significant high-risk pattern, lowering success rate by 10.4%; (2) P-ratio is the strongest negative predictor of success (r=-0.256, pV transition probability is only 2.1%, indicating a systemic verification deficit. Based on these findings, we design Governor, a three-layer runtime intervention system comprising a rule engine, a statistical accumulator, and a chi-square-based threshold adaptor. In a natural before/after deployment evaluation (N=101 vs. N=246), Governor achieves a +6.2% absolute increase in task success rate while simultaneously reducing average token consumption by 44%. To validate cross-system generality, we apply the XEPV encoding to 2,000 public SWE-agent trajectories on SWE-bench, confirming that exploration spirals and the E->V verification deficit replicate in an independent system. We outline six research directions including base sequence language models, cross-agent behavioral fingerprinting, and reward shaping, and release an open-source toolkit for reproducibility.

15.
arXiv (CS.CV) 2026-06-17

NTIRE 2024 Challenge on Image Super-Resolution (x4): Methods and Results

This paper reviews the NTIRE 2024 challenge on image super-resolution ($\times$4), highlighting the solutions proposed and the outcomes obtained. The challenge involves generating corresponding high-resolution (HR) images, magnified by a factor of four, from low-resolution (LR) inputs using prior information. The LR images originate from bicubic downsampling degradation. The aim of the challenge is to obtain designs/solutions with the most advanced SR performance, with no constraints on computational resources (e.g., model size and FLOPs) or training data. The track of this challenge assesses performance with the PSNR metric on the DIV2K testing dataset. The competition attracted 199 registrants, with 20 teams submitting valid entries. This collective endeavour not only pushes the boundaries of performance in single-image SR but also offers a comprehensive overview of current trends in this field.

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

SAM-Deep-EIoU: Selective Mask Propagation for Multi-Object Tracking

Multi-object tracking has a heavy-tailed difficulty distribution: most frames are easy for a lightweight base tracker, while a small fraction are intrinsically hard. Video object segmentation (VOS) models can often preserve identity through the hard frames where the base tracker fails, but they are much more expensive in compute and memory. We propose selective mask propagation, a tracking algorithm that dispatches from a base tracker to a VOS model only on windows where an assignment-uncertainty signal fires. The base tracker's output is modified only when the VOS model makes a confident prediction that contradicts the base tracker's identity assignment; weak or inconclusive predictions preserve the base output. The method is training-free, treats both the base tracker and the VOS model as black boxes, and can benefit from replacing the VOS component with a more capable model. On DanceTrack, selective mask propagation improves three different base trackers. On SportsMOT, where identity preservation is central to sports analytics, SAM3-Deep-EIoU with global track association achieves state-of-the-art performance on the benchmark with 86.8 HOTA.

17.
bioRxiv (Bioinfo) 2026-06-17

Correcting spatial transcriptomics data affected by a prevalent transcript leakage problem across platforms, species, and tissues

Spatial transcriptomics has been widely applied to study the spatial distribution of cell types, cell states, and specific gene expression in tissue samples. However, we show that there is a prevalent transcript leakage problem in spatial transcriptomics data, where transcripts expressed by a cell diffuse to its neighborhood and are recurrently detected in the nearby cells. By analyzing published data sets, we show that this problem is general across data produced from different tissues and different species using different imaging-based and sequencing-based spatial transcriptomics platforms. It affects both upstream tasks such as expression quantification as well as downstream tasks such as cell-type annotation and detection of spatially-dependent gene expression. To tackle the transcript leakage problem, we propose a reference-free Bayesian model-based method, DeLeakage, which cleans up the data much more effectively than existing denoising methods. DeLeakage also improves cell-type annotation and avoids false detection of spatially dependent expression.

18.
arXiv (quant-ph) 2026-06-16

Atom–photon Entanglement with a Single Trapped Cesium Atom

arXiv:2605.28968v2 Announce Type: replace Abstract: We demonstrate atom–photon entanglement using a single cesium atom trapped in an optical tweezer. Entanglement is generated by resonant excitation and subsequent spontaneous decay, which entangles the atomic Zeeman state with photon polarization. The photon is collected with a high numerical aperture objective (NA = 0.55) and coupled into a single-mode fiber, enabling atom photon measurements and measurement of the Bell-state fidelity. We obtain raw entanglement fidelity of ${\mathcal F} = 0.942(16)$ and inferred fidelity of ${\mathcal F}_inf = 0.962(26)$ after correcting independently characterized atom measurement errors. Compared with related free-space experiments using $^{87}$Rb, the multilevel structure of the relevant excited state in $^{133}$Cs requires the use of a single short excitation pulse in each entanglement attempt in order to suppress unwanted re-excitation. These results establish a free-space Cs atom–photon interface and provide a step toward dual-species Rb–Cs quantum networking.

19.
arXiv (CS.AI) 2026-06-11

ATLAS: Active Theory Learning for Automated Science

arXiv:2606.12386v1 Announce Type: cross Abstract: Advancing scientific understanding through mechanistic modeling requires posing the right experimental questions to yield maximally informative data. To automate this pursuit within cognitive science, we introduce ATLAS (Active Theory Learning for Automated Science), an active learning framework for the data-driven discovery of interpretable behavioral models. ATLAS iterates between generating mechanistic hypotheses–instantiated as a diverse ensemble of sparse neural networks (Disentangled RNNs)–and designing experiments that optimally distinguish between them. We test this approach on the problem of recovering reinforcement learning agents from their behavior in bandit tasks. ATLAS designs varied sequences of qualitatively novel experiments with temporal structure tailored to underlying agent characteristics. The models trained on these experiments are evaluated against a comprehensive set of metrics for mechanistic modeling that capture behavioral, structural, and computational similarity. ATLAS achieves a 5-10x improvement in sample efficiency across all metrics compared to random experimentation, and its performance is further validated against expert-designed experiments derived from literature. These in silico results showcase ATLAS's potential to accelerate human-interpretable insights in cognitive science and other domains where scientific inquiry relies on discovering mechanistic models.

20.
arXiv (CS.LG) 2026-06-12

How Much Memory Do We Need? Adaptive Memory Gate for Neural Operators

arXiv:2606.13443v1 Announce Type: new Abstract: Neural operators have emerged as a powerful data-driven approach for solving time-dependent PDEs. Among recent advances, memory-augmented neural operators explicitly incorporate past states and have achieved remarkable performance under low-resolution observation settings. However, existing approaches apply a fixed memory weight regardless of observation conditions, such as resolution or physical parameters, limiting their adaptability. Our preliminary experiments reveal that optimal memory weight varies with resolution and viscosity, implying that a fixed memory weight cannot simultaneously optimize performance across diverse settings. We propose AMGFNO, which dynamically modulates memory weight through a learnable gate. On the Kuramoto-Sivashinsky and Burgers' equations, AMGFNO achieves 55-79% nRMSE reduction over at low resolution, with the learned gate value automatically decreasing from $\bar{g} \approx 0.7$ to near-zero as resolution increases.

21.
arXiv (CS.AI) 2026-06-24

BioPIE: A Biomedical Protocol Information Extraction Dataset for Experiment Understanding

arXiv:2601.04524v2 Announce Type: replace Abstract: Understanding biomedical experiments provides a foundation for downstream tasks, e.g., laboratory automation, and facilitates effective cross-disciplinary communication. Two challenges, High Information Density (HID) and Multi-Step Reasoning (MSR), pose unique difficulties for precise experimental understanding. Extracting structured knowledge, e.g., Knowledge Graphs (KGs), is an effective approach to address the HID and MSR. However, existing biomedical datasets for structured knowledge information extraction are limited to a general or coarse-grained level, hindering fine-grained experimental understanding. To address this gap, we introduce Biomedical Protocol Information Extraction Dataset (BioPIE), a dataset providing procedure-centric KGs that capture entities, actions, and relations at a scale sufficient for reasoning across biomedical protocols. We evaluate information extraction methods on BioPIE and implement a question answering system leveraging the dataset for validation, demonstrating improved understanding performance on test sets as well as on the HID and MSR question sets.

22.
arXiv (CS.AI) 2026-06-15

Position: AI Must Become Planet-Centered, Not Just Human-Centered

arXiv:2606.13704v1 Announce Type: cross Abstract: This position paper argues that contemporary AI paradigms are insufficient for supporting complex global goals and introduces Planet-Centered AI (PCAI) as a design philosophy and research agenda that reorients AI toward planetary-scale socio-ecological systems and their long-term trajectories. A planet-centered approach is grounded in systems thinking, treating Earth as an interconnected whole of which humans are part. We diagnose recurring limitations across AI frameworks, many of which remain human-centered, and show why these become especially consequential under current planetary conditions characterized by systemic risk, non-stationarity, and deep uncertainty. We then articulate how PCAI reshapes the AI lifecycle, from problem formulation and model design to evaluation and deployment, by emphasizing alignment with global agendas, developing system-aware AI foundations, trajectory-oriented evaluation, and monitorability. Finally, we advance a falsifiable claim: AI systems optimized without explicit consideration of systemic consequences are more likely to exacerbate systemic instability than to mitigate it.

23.
bioRxiv (Bioinfo) 2026-06-12

The Geometry of Allostery: A Laplacian Minor Hierarchy for Many-Body Protein Communication

Quantifying how cooperative, many-body relationships drive allostery in protein networks remains a major challenge. To address this, we develop the Laplacian minor hierarchy, a mathematical framework that characterizes the geometric invariants of a protein network. Lower-order minors yield standard metrics including the partition function and effective distances, whereas higher-order minors define novel topological measures: cooperation indices, each bounded between zero and one, that characterize pathway correlations at increasing levels of complexity, the third-order minor determines whether allosteric pathways are correlated or uncorrelated, and the fourth-order minor quantifies how distinct pathways communicate through intermediary residues. We apply this framework to analyze the evolutionary adaptation of the PSD95pdz3 domain from Class I to Class II ligand specificity via mutations G330T and H372A. The cooperation index demonstrates a distinct evolutionary hierarchy: the G330T mutation establishes distributed pathway couplings that the H372A mutation subsequently exploits, whereas H372A alone produces minimal global changes. Furthermore, the fourth-order analysis identifies His317 as a critical intermediary node bridging the class-switching (330-372) and class-bridging (330-400) allosteric pathways. These results demonstrate that allosteric dependencies emerge only when mutations accumulate in specific combinations, with a hierarchical organization of pathways structured around position 330 and intermediary nodes His317 and Phe400. Rather than predicting allosteric mechanisms, this framework provides a mechanistic explanation for why and how allostery emerges during protein evolution.

24.
arXiv (CS.CL) 2026-06-11

Fine-tuning Multi-modal LLMs with ART: Art-based Reinforcement Training

There are two main Parameter-Efficient Fine-Tuning (PEFT) techniques for Large Language Models (LLMs). While Low-Rank Adaptation (LoRA) introduces additional weights between the LLM layers, Soft Prompting introduces additional fine-tuning-specific raw tokens to an LLM input. However, both require modification to the computational graphs of precompiled, preoptimized LLMs. As a result, neither is fully supported in high-throughput engines like vLLM. We propose fine-tuning with ART (Art-based Reinforcement Training). The method injects information into a frozen Multimodal Large Language Model (MLLM) by optimizing only its raw visual input, thus enabling the soft-token approach on pre-compiled computational graphs. It relies on backpropagation of gradients back into a plain pixel array and thus supports any fine-tuning objective. Moreover, the optimized visual input can be stylized as task-relevant computational artworks. The approach's effectiveness is confirmed for different sizes of a popular open Qwen architecture and for several textual benchmarks. Specifically, ART reaches accuracy competitive with LoRA across mathematics and structured-tool-use benchmarks.

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

Kairos: A Native World Model Stack for Physical AI

World models are transitioning from passive visual generators to foundational, operational infrastructure for Physical AI: they must natively acquire world knowledge from heterogeneous experience, maintain persistent states over long horizons, and execute efficiently within real deployment constraints. We introduce Kairos, a native world model stack designed around these requirements. (1) Kairos learns the world by pioneering a Native Pre-training Paradigm governed by a Cross-Embodiment Data Curriculum, which organizes open-world videos, human behavioral data, and robot interactions into a progressive developmental pathway. (2) Kairos maintains the world by unified world understanding, generation, and prediction within a Native Unified Architecture equipped with Hybrid Linear Temporal Attention, where sliding-window attention captures local dynamics, dilated sliding windows capture mid-range dependencies, and gated linear attention maintains persistent global memory. We establish formal theoretical bounds demonstrating that this temporal factorization strictly limits error accumulation, mathematically guaranteeing state propagation across extended horizons. (3) Kairos runs the world by incorporating a Deployment-Aware System Co-Design to support low-latency rollout generation on server and consumer-grade hardware for real-world observation-action-feedback loops. Experiments on embodied world-model, long-horizon, and action-policy benchmarks show that Kairos achieves top level performance while offering a strong efficiency-capability trade-off. Together, these results position Kairos as a cohesive operational foundation for future self-evolving physical intelligence.