Academic Intelligence · Curated Daily

探索全球前沿学术脉络

AcademicHub 汇聚顶级期刊与预印本平台的实时文献。定制您的专属科研雷达,利用大语言模型自动生成交叉领域文献分析简报。

01.
arXiv (CS.AI) 2026-06-15

COGNITION: From Evaluation to Defense against Multimodal LLM CAPTCHA Solvers

arXiv:2512.02318v4 Announce Type: replace-cross Abstract: This paper studies how multimodal large language models (MLLMs) undermine the security guarantees of visual CAPTCHA. We identify the attack surface where an adversary can cheaply automate CAPTCHA solving using off-the-shelf models. We evaluate 7 representative MLLMs on 18 real-world CAPTCHA task types, measuring single-shot accuracy, success under limited retries, end-to-end latency, and per-solve cost. We further validate our findings through a supplemental external dataset and an adaptive-attacker setting with session memory, while also analyzing the impact of task-specific prompt engineering and few-shot demonstrations on solver effectiveness. We reveal that MLLMs can reliably solve recognition-oriented and low-interaction CAPTCHA tasks at human-like cost and latency, whereas tasks requiring fine-grained localization, multi-step spatial reasoning, or cross-frame consistency remain significantly harder for current models. By examining the reasoning traces of such MLLMs, we investigate the underlying mechanisms of why models succeed/fail on specific CAPTCHA puzzles and use these insights to derive defense-oriented guidelines for selecting and strengthening CAPTCHA tasks. To validate these principles, we present a proof-of-concept by hardening a vulnerable CAPTCHA type using our guidelines. We demonstrate that incorporating fine-grained localization and implicit counting reduces the success rate of state-of-the-art MLLMs from over 95\% to 0\%, confirming that structural changes can effectively mitigate the threat. We conclude by emphasizing the urgent need for CAPTCHA redesign as MLLM capabilities increasingly threaten existing defenses. Code Availability (https://doi.org/10.5281/zenodo.20406852).

02.
arXiv (quant-ph) 2026-06-16

What does measuring one qubit reveal about another? $K$-networks as a directed diagnostic for quantum circuits

arXiv:2606.16549v1 Announce Type: new Abstract: Many-qubit circuit states are hard to inspect directly, so they are often summarized by pairwise graph weights. Common pairwise weights report symmetric correlations, while many circuit questions are directed and basis-specific: if qubit $i$ is measured in a given basis, how strongly does the outcome reshape the conditional state of qubit $j$? We define $K_{i\to j}$, a directed, basis-conditioned edge weight for this question. It is large when the two measurement outcomes occur with comparable probability and leave qubit $j$ in clearly different conditional states; it is zero when the source outcome is deterministic or the target states are indistinguishable. The scalar uses standard binary-ensemble distinguishability; the paper's contribution is to turn this conditional comparison into a directed network layer for circuit states. The resulting networks are computable from two-qubit reduced density matrices. They are diagnostic (not entanglement measures): for pure two-qubit states $K$ reduces to the tangle $C^2$ (squared concurrence)[WoottersConcurrence,CKWTangle], while separable mixed states can reach $K=1$. Examples on teleportation, Grover, QAOA, and random circuit families show the intended use: $K$-networks map feed-forward, phase, and interaction-graph structure that symmetric or computational-basis summaries can leave weak or absent.

03.
arXiv (CS.AI) 2026-06-18

RippleBench: Capturing Ripple Effects Using Existing Knowledge Repositories

arXiv:2512.04144v2 Announce Type: replace Abstract: Targeted interventions on language models, such as unlearning or model editing, aim to modify specific information, but their effects often propagate to related, unintended areas (e.g., removing virology content may degrade performance on allergies); these side-effects are commonly referred to as the ripple effect. We introduce RippleBench-Maker, an automatic pipeline that retrieves semantic neighbors of any source concept from a knowledge repository and generates multiple-choice questions at varying semantic distances. We instantiate this framework using WikiRAG, an open-source RAG system over English Wikipedia, to construct RippleBench-WMDP-Bio (584 seed topics, 352,961 questions), and evaluate eight unlearning methods on Llama3-8B-Instruct. All eight exhibit accuracy drops that are largest near the unlearned target and decay with semantic distance, each with a distinct propagation profile. We replicate these findings across Mistral-7B, Zephyr-7B, and Yi-34B; cross-model delta curves are nearly identical, suggesting ripple effects are a property of the unlearning method rather than the base model. We validate all major pipeline stages using a four-experiment Mechanical Turk study (5,200+ responses, 61 workers). We release all code, data, and infrastructure.

04.
arXiv (CS.CL) 2026-06-15

OLaPh: Optimal Language Phonemizer

Phonemization is a critical component in text-to-speech synthesis. Traditional approaches rely on deterministic transformations and lexica, while neural methods offer potential for higher generalization on out-of-vocabulary (OOV) terms. We introduce OLaPh (Optimal Language Phonemizer), a hybrid framework that integrates extensive multilingual lexica with advanced NLP techniques and a statistical subword segmentation function. Evaluations on the WikiPron benchmark show OLaPh significantly outperforms established baselines in overall accuracy and maintains robustness on OOV data through advanced fallback mechanisms. To further explore neural generalization, we utilize the framework to synthesize a high-consistency training corpus for an instruction-tuned Large Language Model (LLM). While the deterministic framework remains more accurate overall, the LLM demonstrates strong generalization, matching or partly exceeding the framework's performance. This suggests that the LLM successfully internalized phonetic intuitions from the synthetic data that transcend the framework's capabilities. Together, these tools provide a comprehensive, open-source resource for multilingual grapheme-to-phoneme conversion (G2P) research.

05.
arXiv (CS.CL) 2026-06-15

LLMs Contain Multitudes: How Deployment Context Reshapes Model-Level Preferences and Values

Large language models (LLMs) are increasingly characterised in recent evaluation work as having stable, model-level preference and value systems. However, accompanying robustness checks are limited to incidental prompt perturbations such as syntax variation and option reordering. This leaves open whether the measured properties survive when the surrounding task context changes, as it does in most real deployments. We test this directly across two established pairwise paradigms: ranking country preferences and eliciting utility judgements. In both, we make the deployment context – the high-level task the model is performing while making concrete value-dependent choices – our controlled variable, varied across framings such as writing a Reddit post or a news article. Across five LLMs and over 1.2M pairwise decisions, deployment context produces variation far larger than prompt paraphrasing and temperature controls. In country preference rankings over 15 countries, context induces widespread, statistically significant rank shifts; the aggregate Global North favouritism reported in prior work is itself context-dependent, with each model's bias shifting systematically across contexts. In utility elicitation over 50 outcomes, broad cross-category ordering is preserved, but fine-grained rankings within domains vary substantially, and cardinal exchange rates between outcomes (e.g. how many lives in one region equal one in another) shift by a factor of 2.47 at the median. Reported model-level preferences and utilities are therefore better understood as context-conditioned measurements than fixed model-level properties: safety guarantees obtained under one framing provide limited assurance in another.

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

FBSDiff++: Improved Frequency Band Substitution of Diffusion Features for Efficient and Highly Controllable Text-Driven Image-to-Image Translation

With large-scale text-to-image (T2I) diffusion models achieving significant advancements in open-domain image creation, increasing attention has been focused on their natural extension to the realm of text-driven image-to-image (I2I) translation, where a source image acts as visual guidance to the generated image in addition to the textual guidance provided by the text prompt. We propose FBSDiff, a novel framework adapting off-the-shelf T2I diffusion model into the I2I paradigm from a fresh frequency-domain perspective. Through dynamic frequency band substitution of diffusion features, FBSDiff realizes versatile and highly controllable text-driven I2I in a plug-and-play manner (without need for model training, fine-tuning, or online optimization), allowing appearance-guided, layout-guided, and contour-guided I2I translation by progressively substituting low-frequency band, mid-frequency band, and high-frequency band of latent diffusion features, respectively. In addition, FBSDiff flexibly enables continuous control over I2I correlation intensity simply by tuning the bandwidth of the substituted frequency band. To further promote image translation efficiency, flexibility, and functionality, we propose FBSDiff++ which improves upon FBSDiff mainly in three aspects: (1) accelerate inference speed by a large margin (8.9$\times$ speedup in inference) with refined model architecture; (2) improve the Frequency Band Substitution module to allow for input source images of arbitrary resolution and aspect ratio; (3) extend model functionality to enable localized image manipulation and style-specific content creation with only subtle adjustments to the core method. Extensive qualitative and quantitative experiments verify superiority of FBSDiff++ in I2I translation visual quality, efficiency, versatility, and controllability compared to related advanced approaches.

07.
arXiv (CS.LG) 2026-06-19

Marginal Advantage Accumulation for Memory-Driven Agent Self-Evolution

arXiv:2606.20475v1 Announce Type: new Abstract: In batch-style trace distillation, the same memory operation may receive contradictory feedback across different batches. Existing methods lack a cross-batch, operation-level evidence accumulation mechanism, making it impossible to distinguish stably effective operations from accidental hits. This paper formalizes the requirement as two structural conditions, alignability and comparability, and proposes Marginal Advantage Accumulation (MAA). MAA constructs differential signals to make them comparable across batches, accumulates signed evidence per operation via EMA, and ensures cross-batch traceability through semantic identity merging. As a post-processing architecture, MAA achieves the best results in 14 out of 16 settings across 4 benchmarks and 4 target models, consistently outperforming existing batch-level distillation baselines and matching or surpassing online alternatives in most settings, while reducing optimization-phase token consumption by approximately 75%.

08.
arXiv (CS.AI) 2026-06-11

TileFuse: A Fused Mixed-Precision Kernel Library for Efficient Quantized LLM Inference on AMD NPUs

arXiv:2606.11357v1 Announce Type: cross Abstract: With the growing demand for on-device LLM inference, edge SoCs increasingly integrate NPUs to improve performance and energy efficiency under tight power and thermal budgets. However, practical LLM deployment on current client NPUs remains difficult: widely used quantization formats such as AWQ do not map cleanly onto many existing NPU software stacks, which are often proprietary and expose limited low-level control. In this work, we present TileFuse, a close-to-metal mixed-precision kernel library for AMD XDNA2 NPUs that targets transformer linear layers in quantized LLM inference. TileFuse brings practical low-bit formats such as AWQ-style W4A16 and W8A16 directly onto XDNA2, rather than forcing the model to be reshaped around an NPU-specific quantization scheme. TileFuse co-designs weight layout, metadata placement, mixed-precision microkernels, and array-level dataflow. Specifically, it fuses unpacking, dequantization, and GEMM/GEMV execution into a single kernel flow, introduces an interleaved pre-tiling layout that supports GEMM dimensions up to 32K, and redesigns GEMV dataflow to utilize the full 4x8 AIE array. Across kernel-level evaluations, TileFuse improves performance by up to 121.6% for GEMM and 281% for GEMV over full-precision baselines, while delivering more than 2x performance and energy-efficiency gains over strong iGPU baselines on GEMM. In end-to-end LLM experiments on Ryzen AI laptops, TileFuse achieves up to 2.0x lower prefilling latency with more than 64.6% lower energy consumption. Together, these results show that XDNA2 is a practical target for AWQ-style edge LLM inference and that native NPU support for off-the-shelf quantization can make NPUs substantially more usable in real client deployments.

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

Dual-Uncertainty Guided Policy Learning for Multimodal Reasoning

Reinforcement learning with verifiable rewards (RLVR) has advanced reasoning capabilities in multimodal large language models. However, existing methods typically treat visual inputs as deterministic, overlooking the perceptual ambiguity inherent to the visual modality. Consequently, they fail to distinguish whether a model's uncertainty stems from complex reasoning or ambiguous perception, preventing the targeted allocation of exploration or learning signals. To address this gap, we introduce DUPL, a dual-uncertainty guided policy learning approach for multimodal RLVR that quantifies and leverages both perceptual uncertainty (via symmetric KL divergence) and output uncertainty (via policy entropy) to guide policy updates. By establishing an uncertainty-driven feedback loop and employing a dynamic branch prioritization mechanism, DUPL recalibrates the policy advantage to focus learning on states with high perceptual or decisional ambiguity, enabling effective targeted exploration beyond passive data augmentation. Evaluated on diverse multimodal reasoning benchmarks spanning mathematical and general domains, DUPL achieves solid gains. It improves Qwen2.5-VL accuracy by up to $12.3%$ (3B) and $7.9%$ (7B), and Qwen3-VL-Instruct by up to $10.7%$ (4B) and $12.4%$ (8B), consistently outperforming GRPO, while seamlessly generalizing to alternative algorithms (DAPO, $+6.5%$ avg) and architectures (LLaVA-OneVision-1.5, $+4.7%$ avg). These results demonstrate that DUPL is an effective and generalizable approach for multimodal RLVR.

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

Beyond the Commitment Boundary: Probing Epiphenomenal Chain-of-Thought in Large Reasoning Models

Chain-of-thought (CoT) reasoning is the dominant paradigm for inference-time scaling in language models, yet the causal influence of individual steps on the final answer poorly understood. We estimate each step's causal importance via early exit and use this measure to study how answers form across the reasoning traces of several model families. Across diverse tasks, we find that reasoning typically crosses a commitment boundary – a sharp transition from transient intermediate guesses to a stable, high-confidence answer. This transition often happens in a single step, well before the model's reasoning block ends, and is followed by epiphenomenal CoT steps that leave the final answer probability unaltered. Using attention probes, we show that answer-formation stages can be linearly decoded from intermediate reasoning steps with high accuracy and generalize robustly to unseen reasoning tasks. We exploit this signal to early-exit reasoning blocks at the commitment boundary, reducing the length of CoTs up to 55\% on average with negligible impact on model performance.

11.
arXiv (CS.AI) 2026-06-17

Surveying GenAI-based Automation in Printed Circuit Board Design and Test

arXiv:2606.17074v1 Announce Type: cross Abstract: Generative artificial intelligence (GenAI) is increasingly used for applications in the hardware and software domains. It purports to reduce the manual effort involved in the development and testing of complex systems before release. Within the hardware space, most tasks have focused on design automation of integrated circuits, particularly with hardware description languages. However, other types of hardware also exist! In this survey, we instead examine how GenAI has been and is being across the printed circuit board (PCB) design life cycle. This includes everything from supply chains, system specification, circuit design, layout and optimisation, validation and test, and PCB assembly and distribution. Through this lens we present a taxonomy of discovered works, categorising them according to their intent and contributions. This survey also identifies key technical challenges that GenAI faces in this space, such as domain-specific data scarcity and limited support for integration with existing PCB tools. Finally, future research directions are discussed: our survey shows that there are many opportunities remaining when considering how GenAI may be integrated into various tasks in PCB design and test.

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

Deep Unfolded Latent Optimally Partitioned-l2/l1 Networks for Data-driven Block-Sparse Recovery

arXiv:2606.12740v1 Announce Type: new Abstract: The convex Latent Optimal Partition (LOP)-l2/l1 approach enables block-sparse signal recovery with unknown partitions but relies on manual hyperparameter tuning. Additionally, numerical instability in differentiating its proximal operator prevents its automatic parameter tuning via Deep Unfolding (DU). To address these limitations, we propose two architectures: a stable framework utilizing implicit differentiation and a flexible variant leveraging Deep Weight Factorization (DWF). The DWF-based approach also supports nonconvex smooth data fidelity terms. Numerical experiments demonstrate that DU-LOP-l2/l1 yields competitive performance and high resilience against impulsive noise.

13.
arXiv (CS.CV) 2026-06-19

SpatialSV: Internalizing Interpretable 3D Spatial Awareness in MLLMs via Task-Oriented Visual Supervision

Unlocking the spatial intelligence of multimodal large language model (MLLMs) is crucial for understanding and interacting with the 3D world. Prevailing approaches typically inject spatial priors via external tools, which impose significant inference overhead, or rely on latent feature distillation, which remains uninterpretable and lacks fine-grained geometric constraints. To address these issues, we propose SpatialSV, a framework designed to internalize robust 3D spatial awareness within MLLMs while simultaneously offering inherent interpretability. Deviating from passive feature imitation, SpatialSV employs task-oriented visual supervision, compelling the model to actively lift its 2D visual features into explicit 3D representations, including depth maps, camera poses, and point clouds. Crucially, this 2D-to-3D lifting process provides a transparent window into the model's representations: the resulting 3D reconstructions serve as an intuitive proxy for visualizing and diagnosing the quality of the model's intrinsic spatial knowledge. Extensive experiments across multiple models and benchmarks demonstrate the effectiveness of SpatialSV in enhancing and interpreting MLLMs' spatial intelligence. Furthermore, the framework exhibits strong generalization in semi-supervised settings, validating its potential to leverage unlabeled visual data for scalable, interpretable spatial representation learning.

14.
arXiv (CS.CL) 2026-06-12

GENEB: Why Genomic Models Are Hard to Compare

Progress in genomic foundation models is difficult to assess due to fragmented benchmarks, incompatible evaluation protocols, and task-specific reporting. As a result, claims of superiority or generality across models are often not directly comparable. We introduce GENEB, a large-scale diagnostic benchmark that evaluates frozen representations from 40 genomic foundation models across 100 tasks spanning 13 functional categories under a unified probing-based protocol, including few-shot regimes. GENEB enables controlled comparison across model scale, architecture, tokenization, and pretraining data while explicitly exposing task-level trade-offs. Our analysis shows that aggregate leaderboards are unstable: model rankings vary sharply across task categories, scale provides only modest and inconsistent gains, and architectural and pretraining alignment frequently outweigh parameter count. These results highlight limitations of current evaluation practices and position GENEB as a reference framework for principled comparison and category-aware model selection in genomic machine learning.

15.
arXiv (quant-ph) 2026-06-17

Frequency-Division Multiplexed CV-QKD System

arXiv:2603.20718v2 Announce Type: replace Abstract: We propose a frequency-division multiplexed (FDM) continuous-variable quantum key distribution (CV-QKD) system with enhanced spectral efficiency through optimized channel spacing of low-symbol-rate signals. A four-channel 10-Mbaud FDM-CV-QKD system was experimentally demonstrated using Gaussian modulation, a transmitted local oscillator, and homodyne detection. Despite the inter-channel interference, under a finite-size scenario (m=1.25x10^6), the system achieved a 3.6-fold back-to-back secret key rate gain and outperformed the single-channel frequency-upconverted signal up to 26.8 km.

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

V2P-Manip: Learning Dexterous Manipulation from Monocular Human Videos

Achieving autonomous robotic dexterous manipulation requires precise, human-like action sequences at scale. As a scalable supplement to costly teleoperation data, extracting trajectories with both visual fidelity and physical plausibility from monocular videos represents a promising frontier in embodied AI. To this end, we introduce V2P-Manip, an efficient framework designed to learn dexterous manipulation policies directly from human demonstration videos. We establish an efficient, integrated pipeline encompassing 3D asset acquisition, trajectory estimation, and dexterous policy learning. To bridge the gap between visual perception and physical constraints, we introduce a two-stage refinement process to enforce spatial alignment and physical consistency. Evaluations on the TACO and OakInk benchmarks demonstrate that our approach significantly outperforms previous methods in pose accuracy, adaptability to unstructured environments, and training efficiency. Ultimately, experimental results confirm an average success rate of over 75% across multiple synthetic manipulation tasks and validate the adaptability of the extracted manipulation priors across diverse dexterous hand embodiments.

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

Given, When, Then, Again: Mining Subscenario Refactoring Candidates in Behaviour-Driven Test Suites with ML Classifiers and LLM-Judge Baselines

Context. Behaviour-Driven Development (BDD) test suites accumulate duplicated step subsequences. Three published refactoring patterns are available (within-file Background, within-repo reusable-scenario invocation, cross-organisational shared higher-level step), but no prior work automates which recurring subsequences are worth extracting or which mechanism applies. Objective. Rank recurring step subsequences ("slices") by refactoring suitability (extraction-worthy), pre-map each to one of the three patterns, and quantify prevalence across the public BDD ecosystem. Method. Every contiguous L-step window (L in [2, 18]) in a 339-repository / 276-upstream-owner Gherkin corpus is keyed by paraphrase-robust cluster identifiers and counted under three scopes. SBERT / UMAP / HDBSCAN clustering recovers paraphrase-equivalent slices. Three authors label a stratified 200-slice pool against a written rubric. An XGBoost extraction-worthy classifier trained under 5-fold cross-validation is compared with a tuned rule baseline and two open-weight Large Language Model (LLM) judges. Results. The miner produces 5,382,249 slices collapsing to 692,020 recurring patterns. Three-author Fleiss' kappa = 0.56 (extraction-worthy) and 0.79 (mechanism). The classifier reaches out-of-fold F1 = 0.891 (95% CI [0.852, 0.927]), outperforming both the rule baseline (F1 = 0.836, p = 0.017) and the better LLM judge (F1 = 0.728, p = 1.5e-4). 75.0%, 59.5%, and 11.7% of scenarios carry a within-file Background, within-repo reusable-scenario, and cross-organisational shared-step candidate, respectively; the figures are stable under a sweep of the classifier decision threshold. Conclusion. Paraphrase-robust subscenario discovery yields a corpus-wide census of BDD refactoring candidates; pipeline, classifier predictions, labelled pool, and rubric are released under Apache-2.0.

18.
arXiv (CS.AI) 2026-06-19

AI-enhanced tuning of quantum dot Hamiltonians toward Majorana modes

arXiv:2601.02149v4 Announce Type: replace-cross Abstract: We propose a neural network-based model capable of learning the broad landscape of working regimes in quantum dot simulators, and using this knowledge to autotune these devices - based on transport measurements - toward obtaining Majorana modes in the structure. The model is trained in an unsupervised manner on synthetic data in the form of conductance maps, using a physics-informed loss that incorporates key properties of Majorana zero modes. We show that, with appropriate training, a deep vision-transformer network can efficiently memorize relation between Hamiltonian parameters and structures on conductance maps and use it to propose parameters update for a quantum dot chain that drive the system toward topological phase. Starting from a broad range of initial detunings in parameter space, a single update step is sufficient to generate nontrivial zero modes. Moreover, by enabling an iterative tuning procedure - where the system acquires updated conductance maps at each step - we demonstrate that the method can address a much larger region of the parameter space.

19.
arXiv (CS.AI) 2026-06-12

Representing Time Series as Structured Programs for LLM Reasoning

arXiv:2606.12481v1 Announce Type: cross Abstract: Large language models (LLMs) have demonstrated strong reasoning and instruction-following capabilities, making them potentially powerful tools for time-series analysis. However, time series lie outside their native textual modality, raising a fundamental question: how should time series be represented so that LLMs can reason about them effectively? Existing work typically serializes raw numerical sequences or fine-tunes pre-trained LLMs on time-series data. These approaches place the burden of extracting temporal structure directly on the LLM, creating a modality mismatch that often degrades performance on long sequences and introduces substantial computational overhead. In this work, we introduce Time-Series-to-Structured-Program representation (T2SP), a deterministic, training-free method that represents a time series as a structured symbolic program. T2SP decomposes time series into trends, periods, and salient events, expressing them in a program-friendly format aligned with the textual and code-like modalities on which LLMs are natively trained. By shifting temporal-structure extraction from the model to the representation itself, T2SP enables off-the-shelf LLMs to leverage their existing reasoning capabilities for time-series understanding. We evaluate T2SP on three reasoning tasks – editing, captioning, and question answering – where it consistently improves performance, reduces reasoning time, and lowers failure rates compared with raw-string representations. Our results demonstrate that T2SP provides an effective interface between time series and LLMs.

20.
bioRxiv (Bioinfo) 2026-06-17

MetaHarmonizer: robust biomedical metadata harmonization and a contamination control for inflated LLM performance on public benchmarks

Public biomedical repositories hold substantial reuse potential, but inconsistent metadata routinely blocks integration across studies. Recent LLM-based harmonization approaches address scale but suffer from non-determinism, hallucinated ontology terms, and, in their highest-accuracy configurations, dependence on proprietary APIs or labeled fine-tuning data. A more fundamental concern is that LLM accuracies on widely-used public benchmarks may substantially inflate transferable capability: under a contamination-controlled evaluation protocol we developed, the apparent LLM-only advantage on the GDC schema-mapping benchmark is inverted, and three out of five LLMs recover 80 -100% of GDC identifiers from zero-schema context, suggesting direct memorization. Building on this insight, we present MetaHarmonizer, an automated metadata harmonization system designed to be robust by construction: SchemaMapper aligns attribute names across schemas, and OntologyMapper standardizes values to controlled vocabularies. Both modules implement a multi-stage cascade that escalates to more resource-intensive methods only when earlier stages fall short, with all candidates grounded in pre-defined controlled vocabularies to preclude hallucinated outputs and LLMs used only as bounded preprocessing components rather than inference-time dependencies. On the GDC schema-matching benchmark, SchemaMapper with the deployment-optimized LLM-generated alias dictionary achieved 71.6% Top-1 accuracy and the higher Recall@GT than Magneto bipartite variants, recovering significantly more ground-truth mappings; with the best performing alias dictionary, it reached the highest Top-1/Top-5/Recall@GT, and also matched the best Magneto reranker (fine-tuned LLM-reranker) on MRR; and it also outperforms LLM-only performance under contamination-controlled conditions. On four EFO benchmarks, OntologyMapper achieved 77.9 - 95.5% Top-1 accuracy, outperforming text2term by up to 16.4 pp and direct LLM inference (against the smaller corpus) by 19.2 pp because memorization is not a viable shortcut for this task. Across both modules, calibrated confidence scores separate correct from incorrect predictions (AUC 0.73 - 0.94), enabling principled human-in-the-loop triage. Inference is fully local, deterministic, and computationally efficient - seconds on schema mapping and under a minute for ontology mapping of up to ~7,000 terms against the pre-indexed 33,230-term corpus. Released as a Python package with a domain-agnostic architecture, MetaHarmonizer provides a scalable foundation for improving the FAIRness of biomedical data and enabling cross-study integration, alongside an evaluation methodology applicable to any LLM-augmented bioinformatics benchmark built on public benchmarks.

21.
arXiv (CS.CV) 2026-06-17

Predicting Immune Biomarkers with MultiModal Mixture-of-Expert Pathology Foundation Models Empowers Precision Oncology

Predicting immune biomarkers associated with the tumor immune microenvironment (TIME) is critical for advancing precision oncology, yet existing approaches are largely limited to single image modalities and suffer from insufficient resolution and incomplete utilization of complementary clinical and biological information. Here we introduce MixTIME, a multimodal foundation model that leverages a mixture-of-experts (MoE) architecture to integrate pathology foundation models trained across distinct modalities: image only (UNIv2), image text (CONCHv1.5), and image transcriptomic (STPath) representations for pixel-level and slide-level prediction of multiplex immunofluorescence (mIF) protein expression from hematoxylin and eosin (HE) whole-slide images. MixTIME employs a learnable router to dynamically weight expert contributions and is trained with a distribution- and tendency-aware loss function. Benchmarked on two datasets of different scales, MixTIME achieves state-of-the-art performance across 17 protein markers as measured by correlation metrics. The predicted mIF profiles substantially enhance downstream tasks, including spatial domain identification, survival prediction, and AI-assisted pathology report generation validated by expert pathologists from multiple institutes across the world. Furthermore, MixTIME enables longitudinal tracking of protein expression dynamics across clinical time points and reveals protein gene interaction patterns linked to drug resistance and immune suppression in tumor microenvironments. Collectively, MixTIME provides a scalable framework for multimodal biomarker discovery and clinical translation in computational pathology.

22.
arXiv (CS.CV) 2026-06-17

Revisiting LLM Adaptation for 3D CT Report Generation: A Study of Scaling and Diagnostic Priors

Recent advances in multimodal learning, including large language models (LLMs) and vision-language models (VLMs), have demonstrated strong adaptability to natural images. However, extending their use to the medical domain, particularly for volumetric (3D) images, is challenging due to high computational complexity, volumetric dependencies and the semantic gap between visual features and clinical terminology. Naively fine-tuning LLMs on limited medical data often leads to overfitting and clinical hallucination, where linguistic fluency is prioritized over clinical factuality. In this study, we investigate parameter-efficient adaptation strategies for volumetric CT report generation and introduce RAD3D-Prefix, a lightweight diagnostic-prior conditioning framework that minimizes the need for extensive parameter training. This module integrates image embeddings with multi-label diagnostic classification logits, preserving critical clinical details while bridging the semantic gap. By keeping the LLM frozen, our method requires minimal trainable parameters and mitigates the risk of overfitting on small, domain-specific datasets. Through a systematic study spanning LLMs from 96.1M to 1.6B parameters, we find that fine-tuning is most beneficial for smaller LLMs, whereas freezing larger (~1B+ LLMs and training only lightweight projection layers provides a superior trade-off between performance, generalization, and computational efficiency. Across multiple automatic metrics and a clinical reader study, RAD3D-Prefix outperforms comparable parameter-efficient baselines and demonstrates strong out-of-domain generalization while using substantially fewer trainable parameters than fully fine-tuned alternatives.

23.
arXiv (quant-ph) 2026-06-16

Quantum-classical hybrid models based on error correction for time series forecasting

arXiv:2606.15213v1 Announce Type: new Abstract: Time series forecasting largely benefits from combining the strengths of different models, especially using a scheme where a model corrects another model by capturing supplementary patterns from forecasting errors. Concurrently, quantum models are providing a means to augment the classical capacity, including in time series forecasting, by acting alongside classical models in hybrid architectures. In this work, we propose the first forecasting system based on error correction that jointly uses quantum and classical models. Here, quantum models first extract patterns by exploring quantum phenomena, and classical models capture the remaining patterns from the quantum errors. Compared to classical single models and classical-classical hybrid models based on error correction, the complementary capacity that emerges from this quantum-classical system provided the best results in most of the addressed problems. Therefore, this work paves the way to introduce quantum models in established hybridization schemes for time series forecasting.

24.
arXiv (quant-ph) 2026-06-15

Certifying Macroscopic Quantum Mechanics via Hypothesis Testing with Finite Data

arXiv:2506.22092v2 Announce Type: replace Abstract: We address the challenge of certifying quantum behavior with single macroscopic massive particles, subject to decoherence and finite data. We propose a hypothesis testing framework that distinguishes between classical and quantum mechanics based on position measurements. While interference pattern visibility in single-particle quantum superposition experiments has been commonly used as a sufficient criterion to falsify classical mechanics, we show that, from a hypothesis testing perspective, it is neither necessary nor efficient. Focusing on recent proposals to prepare macroscopic superposition states of levitated nanoparticles, we show that the likelihood ratio test – which leverages differences across the entire probability distribution – provides an exponential reduction in measurements needed to reach a given confidence level. These results generalize to a broad class of quantum states, and offer a principled, efficient method to falsify classical mechanics in interference experiments, relaxing the experimental constraints faced by current efforts to test quantum mechanics at the macroscopic scale.

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

Harnessing cortical geometry, wiring, and function as inductive biases for recurrent neural networks

arXiv:2606.14975v1 Announce Type: cross Abstract: How the wiring and functional organization of cortex shape recurrent computation remains a central question in both neuroscience and machine learning. Here, we leverage data released through the Machine Intelligence from Cortical Networks (MICrONS) program–a functional connectomics resource spanning multiple areas of mouse visual cortex, in which dense calcium imaging is co-registered with high-resolution electron microscopy reconstruction from the same animal–to build biologically grounded recurrent neural networks. Using neuronal spatial coordinates, anatomical connectivity, and function-derived relationships from nearly 12,000 coregistered excitatory neurons, we initialize recurrent weights and impose communication-aware spatial constraints during learning. Across three cognitive decision-making tasks, networks constrained by cortical structure and function consistently outperform baseline and partially constrained models. Functional weight initialization provides the largest gain, while real spatial embedding yields robust additional improvements across conditions. These biologically grounded networks also develop low-entropy, modular, and small-world organization, and retain strong performance even when recurrence is restricted to positive weights. Together, our results show that the machinery of cortex–its geometry, wiring, and functional structure–can be harnessed as a powerful inductive basis for building recurrent networks that learn more effectively while converging toward key organizational principles of biological computation.