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01.
arXiv (CS.LG) 2026-06-11

Phase Transitions in Attention: A Bayesian Theory of Copy Head Emergence

arXiv:2606.12058v1 Announce Type: cross Abstract: Attention is the key mechanism underlying in-context learning in transformers, and attention patterns have been observed empirically to emerge abruptly during training. We present a Bayesian theory of feature learning in attention; we then focus on how the copy subcircuit in the first layer of an induction head is learned by analyzing a single-layer softmax attention network trained on a copy task. We derive a closed-form posterior over the attention matrix and reduce it to a low-dimensional order parameter space. This reduction reveals a phase transition in the amount of training data, which we verify using both Bayesian sampling and standard training with Adam. We contrast our results with linear attention and find that softmax attention exhibits a first-order phase transition while in linear attention an initial second-order phase transition is followed by a smooth, continuous evolution toward the structured attention pattern (crossover). Our work provides a first-principles theoretical account of the abrupt emergence of the copy subcircuit, reminiscent of the one observed in training large language models.

02.
bioRxiv (Bioinfo) 2026-06-19

Children's DNA Methylation and Family Dynamics in a Congo Basin Subsistence Community: Links with Parental Conflict and Fathers' Caregiving

Family environments may contribute to children's long-term health through biological processes, including epigenetic regulation such as DNA methylation (DNAm). However, most studies in this area focus on Euro-American populations while also rarely including fathering data. The current study investigated children's blood DNAm associations with positive (father caregiving) and negative (parental conflict) family dynamics in a smaller-scale subsistence society living in the Congo Basin rainforest. We measured DNAm from dried blood spots of 54 children (mean age=8.48 years) and conducted three epigenome-wide association studies aimed at discovering differential co-methylated regions (CMRs) associated with family dynamics. Via path models, we investigated the health implications and shared contribution of family factors of the identified CMRs. Differential DNAm associated with family dynamics was localized to genes related to stress, immunology, development, and aging, thus possibly linking to children's physical health and were simultaneously connected to other family factors such as number of siblings. Our findings suggested similarities in biological embedding of family factors across socio-ecologically diverse contexts.

03.
arXiv (CS.LG) 2026-06-12

A solvable model for unsupervised federated learning

arXiv:2606.13045v1 Announce Type: cross Abstract: We introduce a theoretical framework for analyzing federated learning in a generative setting through a teacher-multiple interacting students scenario, in which each student receives a distinct realization of the data, either through a different noise corruption or by accessing a different subset, possibly of varying size. Using theoretical tools in equilibrium disordered system, we analytically show that interactions among students systematically enhance learning performance: highly noisy students require fewer samples to recover the underlying pattern, while low-noise students achieve a larger overlap with the ground-truth signal. We derive the optimal Bayesian conditions for teacher recovery as functions of the sample complexity, noise level, and interaction strength, and validate these predictions through numerical simulations. The resulting dynamics can be mapped onto equilibrium sampling in a Restricted Boltzmann Machine with a structured hidden layer, providing a principled theoretical understanding of how interactions improve distributed generative modeling.

04.
arXiv (CS.AI) 2026-06-12

An LLM System for Autonomous Variational Quantum Circuit Design

arXiv:2606.13380v1 Announce Type: cross Abstract: The design of high performing quantum circuits remains largely dependent on human expertise. We introduce an autonomous agentic framework that employs large language models (LLMs) to conduct iterative quantum circuit designs under explicit design constraints. Our system integrates seven components: Exploration, Generation, Discussion, Validation, Storage, Evaluation, and Review. These components form a closed-loop workflow that combines web-based knowledge acquisition, literature-grounded critique, executable code generation, and experimental feedback. We evaluate the framework on two tasks: quantum feature map construction for quantum machine learning and ansatz generation for variational quantum eigensolver applications in quantum chemistry. In image classification benchmarks, the best generated feature map outperforms representative quantum feature maps and, when scaled to larger qubit counts, surpasses the classical radial basis function kernel. In molecular ground state estimation across seven molecules, the generated ansatz attains competitive accuracy with widely used chemically inspired and hardware-efficient constructions while satisfying the imposed scaling constraints. These results establish LLM driven agentic system as a viable paradigm for automated quantum circuit design and illustrate how AI systems can participate in iterative scientific optimization workflows across scientific domains.

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

Minim: Privacy-Aware Minimal View for Agents via Trusted Local Sanitization

arXiv:2606.13949v1 Announce Type: new Abstract: Modern LLM-powered autonomous agents increasingly rely on rich user interface (UI) state observations to achieve reliable action grounding in complex digital environments. However, many deployments transmit the full UI state to remote inference servers even when most elements are irrelevant to the current task, which can leak sensitive but unnecessary context such as authentication codes, private notifications, and background application states. We propose MINIM, a trusted local broker that performs privacy-aware minimization on the client side before any observation leaves the device. Grounded in Contextual Integrity (CI), MINIM learns a dual-score representation for each UI element by predicting an inherent sensitivity score (s) and a task-conditioned necessity score (n). These scores drive a ternary disclosure policy that keeps essential elements, abstracts sensitive attributes when needed, and removes task-irrelevant content. We optimize a CI-aware objective that penalizes necessity errors more strongly on high-risk content, enabling aggressive pruning while preserving task-critical information. Experiments on real-world UI observations derived from WebArena show that MINIM substantially reduces task-irrelevant sensitive leakage while preserving task-critical semantic context and the interactive affordances required for reliable agent actions.

06.
Nature Biotechnology 2026-06-19

Efficient site-specific gene addition using R2 retrotransposons in tobacco and rice

作者:

Precise integration of multikilobase DNA fragments remains a major technical barrier in plants. Here we introduce non-long terminal repeat (non-LTR) R2 retrotransposons as a versatile system for targeted gene integration in plants. We reconstituted R2 activity in Nicotiana benthamiana and benchmarked insertion efficiency and fidelity using a TMV-based episomal reporter system. We demonstrate site-specific integration of GFP (2.2 kb) and recombinase-compatible landing pads (0.6 kb) into 28S rDNA arrays, with intact cassette insertion frequencies up to 75% and 53%, respectively. To temporally constrain donor availability and avoid DNA intermediates, we combined in planta effector expression with recombinant RNA virus-mediated donor delivery. We apply R2 retrotransposons for targeted insertion of resistance cassettes within the rDNA of rice callus, achieving integration efficiencies up to 17%. These results position R2 retrotransposons as a double-strand break-free system for RNA-templated insertion of multikilobase gene cassettes at rDNA loci, for safe-harbor trait stacking in plants with potential applications in crop improvement and synthetic biology. Retrotransposons are applied in plants for safe-harbor transgene integration.

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

Whose hotel does the AI recommend? An algorithm audit of reputation signals in LLM-assisted hotel selection

Travelers increasingly ask large language model (LLM) assistants which hotel to book, making these systems gatekeepers of property visibility – yet what moves their recommendations is undocumented. We conduct a pre-specified algorithm audit using a randomized choice-based conjoint: across personas, prompt templates, and twelve open-weight and proprietary models, assistants choose among five hotels whose guest rating, review volume and recency, management response, chain affiliation, price, eco-certification, and list position are independently randomized. We estimate the average marginal component effect of each signal on the probability of recommendation. Guest rating and price dominate (a top rating raises selection by 31.6 percentage points; a high price lowers it by 30.0), reproducing human valence-and-price primacy but over-weighting eco-certification and ignoring management response. List position – a content-free artifact – shifts recommendations causally, worth about \$12 per night. Stated reasons track revealed weights imperfectly. The findings ground generative engine optimization and the accountability of AI infomediaries in causal evidence.

08.
arXiv (quant-ph) 2026-06-16

High-Order Hermite Optimization: Fast and Exact Gradient Computation in Open-Loop Quantum Optimal Control using a Discrete Adjoint Approach

arXiv:2505.09857v5 Announce Type: replace-cross Abstract: This work introduces the High-Order Hermite Optimization (HOHO) method, an open-loop discrete adjoint method for quantum optimal control. Our method is the first of its kind to efficiently compute exact (discrete) gradients when using continuous, parameterized control pulses while solving the forward equations (e.g. Schrodinger's equation or the Linblad master equation) with an arbitrarily high-order Hermite Runge-Kutta method. The HOHO method is implemented in QuantumGateDesign$.$jl (https://github.com/leespen1/QuantumGateDesign.jl), an open-source software package for the Julia programming language, which we use to perform numerical experiments comparing the method to Juqbox$.$jl (https://github.com/LLNL/Juqbox.jl). For realistic model problems we observe speedups up to 775x.

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

WeGenBench: A Multidimensional Diagnostic Benchmark towards Text-to-Image Model Optimization

Recent text-to-image generation models have demonstrated remarkable capabilities in synthesizing highly realistic images from text inputs alone. Although existing benchmarks can evaluate the generation capabilities of various models to some extent, they struggle to comprehensively and accurately measure performance across multiple dimensions, often failing to reveal the inherent deficiencies of models in specific categories. To address these limitations, we propose WeGenBench, a novel benchmark designed for the comprehensive, multi-perspective evaluation of text-to-image generation capabilities. Our benchmark comprises a total of 4,000 test prompts across two primary categories, meticulously balanced between Chinese and English to evaluate bilingual and cross-cultural generation capabilities. Beyond macroscopic scene classification, we annotate each prompt with multi-dimensional tags tailored to the distinct content and challenges of each language, thereby refining the generation tasks into more specific sub-categories. Through a cross-dimensional evaluation mechanism leveraging both scene classifications and multi-dimensional tags, WeGenBench can precisely pinpoint model shortcomings in specific generation categories. Furthermore, to measure generation quality more accurately, we design and validate several novel evaluation metrics by integrating Vision-Language Models (VLMs), which assess model performance on domain-specific tasks from three core aspects. Crucially, our approach yields both the assessment outcomes and the detailed reasoning trajectories, facilitating a rigorous verification of the accuracy and soundness of the evaluation results. Finally, we conduct systematic benchmarking on current state-of-the-art methods and provide an in-depth analysis of the limitations present in existing models.

10.
arXiv (quant-ph) 2026-06-15

Stab-QRAM: A Clifford-Only Quantum Oracle for Affine Boolean Data

arXiv:2509.26494v3 Announce Type: replace Abstract: Oracle-based quantum algorithms require coherent evaluation of classical functions on superposed inputs, and in fault-tolerant architectures this cost is dominated by non-Clifford gates: generic lookup constructions incur $T$-counts that grow with the data size. Here we show that affine Boolean functions $f(\mathbf{x})=A\mathbf{x}+\mathbf{b}$ over $\mathbb{F}_2$ – the algebraic core of parity checks, linear feedback shift registers, and cipher linear layers – are exactly the functions admitting computational-basis-preserving Clifford oracles, and we develop this correspondence into Stab-QRAM, a compiler mapping a specification $(A,\mathbf{b})$ to an ancilla-free circuit of CNOT and $X$ gates with zero $T$-count. Via K\"{o}nig's edge-coloring theorem, the compiled schedule provably attains the minimum depth for its gate set. Case studies spanning Simon-type oracles, block-encodings of $X$-type coset operators, and syndrome extraction for CSS codes show one compiler serving the algorithm, primitive, and error-correction layers of the quantum stack.

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

BioMamba: Domain-Adaptive Biomedical Language Models

Background. Biomedical language models should improve performance on biomedical text while retaining general-language-modeling fluency. For Mamba-based models, this trade-off has not been systematically studied across biomedical literature and clinical text. Methods. We developed BioMamba, a family of biomedical Mamba2 models at five scales obtained by continued pretraining of released public Mamba2 checkpoints on a balanced 80%/10%/10% mixture of PubMed abstracts, the Colossal Clean Crawled Corpus (C4), and Wikipedia. The contribution is the adaptation recipe and the accompanying open-weight checkpoints. Results. Across five scales, BioMamba consistently lowered PubMed perplexity, improved Wikipedia-style held-out perplexity by 1.46-4.72 PPL, and left C4 perplexity essentially unchanged. On six out-of-domain multiple-choice benchmarks, BioMamba stayed within +/-3 percentage points of Mamba2 with no systematic regression. After supervised fine-tuning, BioMamba+SFT matched or exceeded Mamba2+SFT on MIMIC-IV note completion and discharge summary generation at every evaluated scale, and improved PubMedQA at every scale. The strongest model (BioMamba-2.7B) reached a PubMed perplexity of 5.28 and accuracies of 90.24% and 73.00% on BioASQ and PubMedQA, respectively. Conclusions. A balanced domain-adaptive continued pretraining recipe strengthens Mamba2 language models on biomedical literature and clinical text while preserving general-language-modeling fluency.

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

The Insurability Frontier of AI Risk: Mapping Threats to Affirmative Coverage, Silent Exposures, and Exclusions

arXiv:2605.18784v2 Announce Type: replace-cross Abstract: The rapid diffusion of agentic AI has created a new coverage problem for commercial insurance: some AI-mediated losses are now affirmatively insured, some create silent-AI exposure under legacy cyber, technology errors-and-omissions (E&O), directors-and-officers (D&O), employment practices liability (EPLI), crime, and media policies, and others are being actively excluded. This paper maps that emerging boundary by coding 55 AI threat classes against 26 insurance products, endorsements, and exclusion regimes using public carrier materials and OWASP/MITRE threat catalogs. We identify a four-tier insurability frontier: affirmatively insured perils, silent-AI exposures, actively excluded perils, and perils outside conventional private insurance structures. Our coding measures publicly claimed positioning rather than executed contract wording; the headline statistics describe what carriers publicly state about coverage, not what would be paid in any specific claim. Three patterns emerge. First, affirmative AI coverage is beginning to differentiate by primary risk emphasis: public materials often position Munich Re around model performance and drift, Armilla and parts of the Lloyd's market around hallucination and broader AI liability, Tokio Marine Kiln and CFC around IP and technology E&O concerns, Apollo ibott around emerging autonomous system liability, and Coalition around deepfake and AI-enabled cyber response. Second, legacy lines retain silent-AI exposure where AI is an instrumentality rather than the legal cause of loss. Third, foundation model concentration is the clearest genuinely novel insurability frontier because upstream model failure can correlate losses across many cedents at once; the relevant market design question is which insurability constraint each candidate structure relaxes, not merely which systemic risk template exists.

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

Native Active Perception as Reasoning for Omni-Modal Understanding

Passive models for long video understanding typically rely on a "watch-it-all" paradigm, processing frames uniformly regardless of query difficulty, causing computational cost to grow with video duration. Although interactive frameworks have emerged, they often rely on global pre-scanning, and their context cost still scales with video length. We propose OmniAgent, the first native omni-modal agent that formulates video understanding as a POMDP-based iterative Observation-Thought-Action cycle. OmniAgent executes on-demand actions to selectively distill audio-visual cues into a persistent textual memory, effectively decoupling reasoning complexity from raw video duration. To operationalize this, we introduce (1) Agentic Supervised Fine-Tuning to bootstrap native active perception via best-of-N trajectory synthesis with dual-stage quality control, and (2) Agentic Reinforcement Learning with TAURA (Turn-aware Adaptive Uncertainty Rescaled Advantage), which leverages turn-level entropy to steer credit assignment toward pivotal discovery turns. Crucially, OmniAgent exhibits positive test-time scaling, where performance improves as the number of reasoning turns increases, validating the efficacy of active perception. Empirical results across ten benchmarks (e.g., VideoMME, LVBench) demonstrate that OmniAgent achieves state-of-the-art performance among open-source models. Notably, on LVBench, our 7B agent outperforms the 10$\times$ larger Qwen2.5-VL-72B (50.5% vs. 47.3%).

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

Deep Temporal Modeling and Ensemble Fusion for Multimodal Emotion Recognition from Physiological Signals

Physiological stress and emotion recognition are important for health monitoring and affective computing. In this work, we present a comprehensive evaluation of deep learning models such as Long Short-Term Memory (LSTM), Temporal Convolutional Networks (TCN), and Transformer on the WESAD dataset for multimodal affect recognition using wrist and chest sensor signals. We perform ablation studies to assess the individual contributions of each modality by training models on wrist-only and chest-only inputs. In addition, we implement a late-fusion ensemble strategy that combines predictions from all three architectures trained on multimodal input. We also employ early fusion at the sensor level by concatenating wrist and chest signals before feeding them into each model. Our results show that Transformer models consistently achieve the highest accuracy in multimodal settings, while TCN models perform best in the wrist-only configuration. The ensemble method yields the highest overall accuracy (98.91 +/- 0.13%) and macro-F1 score (98.56 +/- 0.17%). These findings demonstrate the effectiveness of sensor fusion and ensemble-based fusion in developing robust systems for physiological emotion recognition.

15.
arXiv (CS.CV) 2026-06-18

Pyramid Self-Contrastive Learning for Single-shot Test-time Ultrasound Image Denoising

The inherent electronic and speckle noise complicates clinical interpretation of ultrasound images. Conventional denoising methods rely on explicit noise assumptions whose validity diminishes under composite noise conditions. Learning-based methods are usually pretrained in a limited image domain using a labeled dataset, which implies inevitable domain shift in complex in vivo environments. This study proposes a Pyramid Self-Contrastive Learning (PSCL) framework for test-time ultrasound image denoising without pretraining. Given multiple noisy samples from only one-shot imaging, PSCL disentangles anatomical similarity and noise randomness into separate pyramid latent spaces. The clean image is then decoded from the anatomy space while discarding the noise space. We first apply PSCL to synthetic aperture ultrasound (SAU), where an Aperture-to-Aperture loop serves as a self-supervised proxy task to ensure denoising fidelity. Simulation experiments, including noise levels from 0 to 30 dB and inclusion geometries from simple to complex, demonstrated improvements of 69.3% in SNR and 34.4% in CNR. The in vivo results showed 84.8% SNR and 25.7% CNR gains using only two aperture data of the heart in six echocardiographic views, liver, and kidney. PSCL delivers clear images across diverse imaging targets and configurations, paving the way for more reliable anatomical visualization without domain shift and pretraining costs.

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

A polarity-aware multi-relational model for the signed interaction prediction in biological networks

arXiv:2407.07357v3 Announce Type: replace Abstract: Predicting signed interactions in biological networks is crucial for understanding drug mechanisms and facilitating drug repurposing. While deep graph models have demonstrated success in modeling complex biological systems, existing approaches often fail to distinguish between positive and negative interactions, limiting their utility for precise pharmacological predictions. In this study, we propose a novel deep graph model, PAMR (polarity-aware multi-relational model), designed to predict both polar (e.g., activation, inhibition) and non-polar (e.g., binding, affect) chemical-gene interactions. Our model integrates graph convolutional networks with tensor decomposition to enhance feature representation and incorporates a conflict-aware sampling strategy to resolve polarity ambiguities. We introduce new evaluation metrics, polarity discrimination score (PDS) and CP@100, to assess the model's ability to differentiate interaction types. Experimental results demonstrate that PAMR outperforms baseline models, achieving superior classification accuracy and improved discrimination of polar edges. Specifically, PAMR-CL attains a Macro AUROC of 0.9072 and CP@100 of 0.974, surpassing RGCN, GraphSAGE, TransE, and BioNet baselines. A case study on nicotine further identifies two novel chemical-gene suppression links, S100A6 and SPP1, that are corroborated by independent experimental literature. Furthermore, we analyze the impact of subgraph components on predictive performance, revealing that additional network structures do not always enhance accuracy. These findings highlight the importance of polarity-aware modeling in drug discovery and network pharmacology, providing a scalable computational framework for polarity-aware chemical-gene interaction prediction and network pharmacology analysis.

17.
arXiv (quant-ph) 2026-06-19

Observation of alignment tensor effects in metastability-exchange collisions with highly polarized 3He ensembles

arXiv:2606.20330v1 Announce Type: new Abstract: Highly polarized 3He ensembles prepared by metastability-exchange optical pumping (MEOP) have been widely used in precision measurements and fundamental physics. Metastability-exchange (ME) collisions, serving as the basis of MEOP, are traditionally described in terms of atomic orientation, while the significant contributions of metastable alignment tensor at high polarization remain unexplored. In this work, we develop a linearized model under mean-field approximation to investigate alignment tensor effects in highly polarized 3He , which originate from the metastable F = 3/2 manifold and are revealed through ME-induced relaxation and frequency shift. By means of free-induction-decay (FID) measurements, a pronounced dependence on nuclear polarization is experimentally observed in the response of the ground-state-metastable hybrid 3He ensembles to the external magnetic field. Furthermore, after obtaining the characteristics of tensor-induced phenomena, we demonstrate good agreement between the experiment and the theory. This work advances the understanding of nuclear spin dynamics in highly polarized 3He using MEOP. It further provides applications in systematic error correction of high-accuracy magnetometry, as well as in optimal protocol for the generation of nuclear spin-squeezed states.

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

Conformalized Quantum DeepONet Ensembles for Scalable Operator Learning with Distribution-Free Uncertainty

arXiv:2605.00330v2 Announce Type: replace Abstract: Operator learning enables fast surrogate modeling of high-dimensional dynamical systems, but existing approaches face two fundamental limitations: quadratic inference complexity and unreliable uncertainty quantification in safety-critical settings. We propose Conformalized Quantum DeepONet Ensembles, a framework that addresses both challenges simultaneously. By leveraging Quantum Orthogonal Neural Networks (QOrthoNNs), we reduce operator inference complexity from O(n^2) to O(n), enabling scalable evaluation over fine discretizations. To provide rigorous uncertainty quantification, we combine ensemble-based epistemic modeling with adaptive conformal prediction, yielding distribution-free coverage guarantees. A key challenge in ensembling is that naive parallelism scales hardware resources linearly with the number of models. We resolve this by using Superposed Parameterized Quantum Circuits (SPQCs), which compress multiple ensemble members into a single circuit and enable simultaneous multi-model execution. Experiments on synthetic partial differential equations and real-world power system dynamics demonstrate that our approach achieves accurate predictions while maintaining calibrated uncertainty under realistic quantum noise. These results establish a practical pathway toward scalable, uncertainty-aware operator learning in quantum machine learning.

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

ArogyaSutra: A Multi-Agent Framework for Multimodal Medical Reasoning in Indic Languages

Multimodal Large Language Models (MLLMs) have shown promising reasoning capabilities in general domains, yet their performance remains limited in specialized settings such as healthcare, especially in multilingual and low-resource scenarios. This gap is critical in regions like rural India, where patients often express complex medical queries in native Indic languages and rely on multimodal inputs such as medical images. Existing English-centric MLLMs struggle to support such use cases, limiting equitable access to AI-driven healthcare assistance. To address this challenge, we introduce ArogyaBodha, a large-scale multilingual multimodal medical question-answer dataset constructed from eight heterogeneous sources, covering 31 body systems, six imaging modalities, and 21 clinical domains across English and seven major Indian languages. We further propose ArogyaSutra, an actor-critic-based multi-agent framework that integrates tool grounding with dual-memory mechanisms for step-wise, reasoning-aware decision making, and uses stored actor-critic simulation trajectories for distillation. Experiments show that our dataset and framework improve multilingual medical reasoning accuracy across all Indic languages, with ablations validating the contribution of each component. The source code and dataset are available at: https://iitp-cse.github.io/ ArogyaSutra/

20.
arXiv (quant-ph) 2026-06-11

Bound State Solutions of the Relativistic Finite-difference Equation for the Ring-shaped Quesne Oscillator Potential

arXiv:2606.12082v1 Announce Type: new Abstract: We solve exactly the relativistic finite-difference equation for the quantum three-dimensional ring-shaped Quesne oscillator potential. Our investigation is based on a finite-difference version of relativistic quantum mechanics. So-called relativistic configurational r-space is a key concept here. We show that the radial wavefunctions and angular wavefunctions are expressed through the continuous dual Hahn polynomials and Jacobi polynomials, respectively. A discrete energy spectrum has been found. The radial wave functions and energy spectrum have the correct nonrelativistic limit. We also build a dynamical symmetry group SU (1, 1) for the radial part of the equation of motion, which allows us to find the energy spectrum purely algebraically.

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.LG) 2026-06-18

From Mechanistic to Compositional Interpretability

arXiv:2605.08934v2 Announce Type: replace Abstract: Mechanistic interpretability aims to explain neural model behaviour by reverse-engineering learned computational structure into human-understandable components. Without a formal framework, however, mechanistic explanations cannot be objectively verified, compared, or composed. We introduce compositional interpretability, a category-theoretic framework grounded in the principles of compositionality and minimum description length. Compositional interpretations are pairs of syntactic and semantic mappings that must commute to enforce consistency between a model's decomposition and its observed behaviour. We deconstruct explanation quality into measures of faithfulness and complexity to cast interpretability as a constrained optimisation problem, and introduce compressive refinement to systematically restructure models into simpler parts without altering their function. Finally, we derive a parsimony criterion under which syntactic compression theoretically guarantees more concise, human-aligned explanations. Our framework situates prominent mechanistic methods as subclasses of refinement, and clarifies why their compressibility heuristics tend to align with human interpretability. Our work provides a measurable, optimisable blueprint for automating the discovery and evaluation of mechanistic explanations.

23.
arXiv (CS.AI) 2026-06-18

From Values to Tokens: An LLM-Driven Framework for Context-aware Time Series Forecasting via Symbolic Discretization

arXiv:2508.09191v2 Announce Type: replace-cross Abstract: Time series forecasting plays a vital role in supporting decision-making across a wide range of critical applications, including energy, healthcare, and finance. Despite recent advances, forecasting accuracy remains limited due to the challenge of integrating historical numerical sequences with contextual features, which often comprise unstructured textual data. To address this challenge, we propose TokenCast, a large language model (LLM) driven framework that leverages language-based symbolic representations as a unified intermediary for context-aware time series forecasting. Specifically, TokenCast employs a discrete tokenizer to transform continuous numerical sequences into temporal tokens, enabling structural alignment with language-based inputs. To effectively bridge the semantic gap between modalities, both temporal and contextual tokens are embedded into a shared representation space via a pre-trained LLM, further optimized with generative objectives. Building upon this unified semantic space, the aligned LLM is subsequently fine-tuned in a supervised manner to predict future temporal tokens, which are then decoded back into the original numerical space. Extensive experiments on real-world datasets demonstrate the effectiveness of our framework and highlight its potential as a generative framework for context-aware time series forecasting. The code is available at https://github.com/Xiaoyu-Tao/TokenCast.

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

Large Language Models as Optimizers: A Survey of Direct vs. Tool-Augmented Approaches and Their Performance Frontiers

arXiv:2606.15577v1 Announce Type: new Abstract: Large Language Models (LLMs) are increasingly involved in complex mathematical optimization, even if the pragmatic user who triggers them is unaware of it. After all, many real-world problems reduce to the search for better or the best solutions. The field of LLM-as-optimizer has three paradigms: direct optimization, tool-augmented optimization, and tool-creating optimization. Direct optimization uses iterative prompting and heuristic generation to navigate solution spaces. Tool-augmented optimization translates natural language problems into formal specifications and orchestrates external solvers. Tool-creating optimization goes further, using LLMs to discover reusable algorithms or heuristics that can be deployed at zero marginal LLM cost. We describe current performance frontiers based on the benchmarks from the literature. We identify the critical reasoning gap in current architectures and argue for trade-offs between the future potential of direct optimization and the auditability of tool-augmented optimization. Even future, more powerful models might opt for tool-making to improve operational efficiency for repetitive families of problems.

25.
medRxiv (Medicine) 2026-06-17

High burden of subclinical TB in Africa revealed from a postmortem cohort.

Tuberculosis (TB) is increasingly recognised as a spectrum of infection and disease, yet the prevalence of viable, asymptomatic Mycobacterium tuberculosis (M.tb) infection remains uncertain. Subclinical Tuberculosis (scTB), defined as microbiologically confirmed M.tb infection in the absence of recognised symptoms, is under detected by symptom, sputum and imaging-based approaches. We conducted postmortem examinations of 94 adults who died from non-infectious causes, none of whom were clinically suspected of TB or reported TB related symptoms prior to death. Lung and extrapulmonary tissues were cultured for M.tb. Viable M.tb was confirmed in six individuals, corresponding to a prevalence of 6.4% (95% CI: 2.4 to 13.4%). These findings provide direct tissue-based evidence that viable, asymptomatic M.tb infection can persist beyond the reach of conventional clinical detection. Our data suggest that a biologically active reservoir of infection may exist undetected within high-burden settings, with implications for surveillance strategies aimed at TB elimination.