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01.
arXiv (CS.AI) 2026-06-12

A Quantitative Experimental Repeated Measures Study of Training Dynamics in a Small Llama Style Language Model Under a Compute-Aware Token Budget

作者:

arXiv:2606.13370v1 Announce Type: new Abstract: This study examines training dynamics in a small Llama-style language model trained under a fixed, compute-constrained token budget. Rather than evaluating efficiency solely through endpoint performance, the study uses a quantitative experimental repeated measures design to analyze how validation loss, validation perplexity, rolling volatility, backslide behavior, spike behavior, and between-seed variability change across token-based training intervals. Six independent training runs were conducted on a 4.26-million-parameter model using the TinyStories corpus, CPU-based full-precision training, and a target budget of approximately 20 million cumulative training tokens. Metrics were collected across 21 intervals, producing 126 seed-by-interval observations. Repeated measures ANOVA showed statistically significant interval effects for validation loss, validation perplexity, and rolling volatility. Descriptive trajectories revealed rapid early improvement followed by non-monotonic degradation during later training intervals. Mean validation loss decreased from 8.3552 at initialization to 2.7996 near 4 million tokens, but increased to 3.9010 by the final checkpoint. Validation perplexity followed the same pattern, falling sharply early in training before rising later. Derived telemetry further showed recurrent validation-loss backslides and no interval-summary evidence of a stable phase under the predefined criteria. These findings suggest that compute-aware language model evaluation should examine training trajectories rather than endpoint metrics alone. In constrained compute settings, additional token exposure may increase computational cost without producing proportional generalization gains, and interval-level telemetry can reveal instability, regression, and diminishing returns that final metrics may obscure.

02.
arXiv (CS.AI) 2026-06-16

From Correlation to Causation in Lane Change Prediction for Automated Driving: A Causal Explanation Framework

arXiv:2606.15756v1 Announce Type: cross Abstract: Lane-change prediction is a central task in intelligent vehicles, where early maneuver anticipation can support safer decision-making. However, many existing approaches mainly learn statistical associations between observed driving variables and future maneuvers, while overlooking the causal dependencies among the input variables themselves. This limits interpretability, especially when physically related variables such as longitudinal gap, relative longitudinal velocity, and Time-To-Collision (TTC) are treated as independent flat inputs. This article presents a causal-inference-based framework for lane-change prediction and explanation. The proposed approach combines linguistic feature construction, expert-constrained causal discovery, deep structural causal modeling with Deep End-to-end Causal Inference (DECI), intervention-based effect analysis, refutation testing, and recursive causal-chain explanation. The objective is not only to predict the future maneuver, but also to identify candidate variables that directly contribute to the prediction, the upstream factors influencing them, and the causal chains through which these effects propagate. The framework achieves average F1-scores above 95% during the first three seconds before the lane-marking crossing event. Beyond prediction accuracy, the framework uses intervention-based effect analysis to distinguish influential from weakly influential variables under the learned causal structure. It further distinguishes candidate direct contributors from mediated effects and generates contrastive causal-chain explanations that clarify why the predicted maneuver is favored and why the alternative maneuvers are less supported. The main contribution is therefore a mechanism-aware lane-change prediction pipeline that moves beyond correlation-based classification toward more interpretable causal reasoning for maneuver prediction.

03.
arXiv (CS.AI) 2026-06-11

Sovereign Assurance Boundary: Certificate-Bound Admission for Agentic Infrastructure

arXiv:2606.11632v1 Announce Type: cross Abstract: Agentic infrastructure introduces a critical control-plane authorization problem: non-deterministic reasoning systems can propose high-stakes mutations to production resources, yet existing security mechanisms – such as identity and access management (IAM), policy engines, consensus protocols, and audit logs – either enforce static, context-unaware permissions or merely record actions post-execution. This paper introduces the Sovereign Assurance Boundary (SAB), a certificate-bound runtime admission layer for autonomous execution authority. SAB intercepts agent proposals at an assurance airlock, compiles them into typed execution contracts $C$, and binds these contracts to cryptographic evidence digests $H(E)$ and policy versions. The contracts are then routed through consequence-aware certification paths. Upon successful admission, the system emits a signed Sovereign Assurance Certificate ($\Omega$) that is strictly scoped to a specific execution identity, revocation epoch, and validity window. Finally, a sovereign execution broker verifies $\Omega$ and performs fresh pre-execution revocation and drift checks before invoking infrastructure APIs. We detail the airlock-broker architecture, formalize its admission and revocation invariants, and report preliminary feasibility measurements from a Go prototype evaluated over 2,500 admission attempts. Ultimately, this broker-enforced model prevents autonomous reasoning from directly mutating state, transforming delegated execution authority into a cryptographically verifiable, evidence-bound, revocable, and replayable runtime artifact.

04.
arXiv (quant-ph) 2026-06-17

Unveiling Hierarchical Invariants in Multiphoton Linear Optics

arXiv:2506.12857v2 Announce Type: replace Abstract: Linear optical networks driven by quantum states of light are important building blocks of photonic quantum technologies. They access large bosonic Hilbert spaces through multiphoton interference. At the same time, their dynamics are generated by single-particle mode transformations, thereby defining a highly structured subset of multiphoton unitaries and setting boundary on linear optics capability. To elucidate this boundary, we reveal an underlying fine-grained symmetry structure that partitions the multiphoton operator space into invariant subspaces and generates a hierarchy of invariants. We experimentally confirm the conservation of high-order invariants and demonstrate their operational utility in characterizing state reachability and the metrological capability of multiphoton probes. Our framework provides a symmetry-based perspective for understanding and harnessing structured multiphoton dynamics across photonic quantum technologies.

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

Text-Driven Fusion for Infrared and Visible Images: Achieving Image Scene Adaptation on Hyperbolic Space

Infrared and visible image fusion aims to integrate complementary modalities, while existing Euclidean methods impose rigid distance metrics that distort multi-modal interactions and parent-to-child semantic hierarchies. To overcome these limitations, we introduce a text-driven fusion framework empowered by hyperbolic manifold learning. During training, BLIP-extracted text prompts serve as topological anchors within the hyperbolic space, guiding vision-attribute alignment through hyperbolic embeddings that naturally accommodate varying semantic granularities. By exploiting the exponential volume growth dictated by the Poincaré ball's negative curvature, this approach seamlessly embeds hierarchical trees to encode coarse-to-fine semantics without metric saturation, while the vast peripheral space prevents texture distortion during cross-modal fusion. At inference, the fusion process autonomously adapts to input content using the learned text-attribute priors, completely eliminating the need for textual input. Experimental results show our method outperforms state-of-the-art approaches on benchmark datasets, with code available at https://github.com/Shaoyun2023/TEDFusion.

06.
medRxiv (Medicine) 2026-06-22

Between Patterns and Predictions: Interpretable Latent EEG Representations for Clinical Insights

Electroencephalography (EEG) captures rich brain dynamics, yet in clinical practice this complexity is often reduced to simplified summaries or categorical labels, limiting its interpretability for decision-making. We tested the hypothesis that a pretrained latent embedding framework, the Universal Map of EEG (UM-EEG), can preserve clinically meaningful structure across heterogeneous datasets and provide a generalizable representation of brain states. We applied UM-EEG, without retraining, to three independent cohorts spanning distinct clinical contexts: long-term EEG recordings from cardiac arrest patients (n = 576), subarachnoid hemorrhage (n = 100), and routine clinical EEG recordings containing physiological and pathological patterns (n = 141). EEG segments were projected into a shared 128-dimensional space anchored by expert-derived reference states, including wakefulness, sleep stages, ictal-interictal continuum activity, and burst suppression. Across datasets, favorable outcome or physiological recordings were consistently located closer to healthy reference states, whereas poor outcome and pathological recordings shifted toward pathological regions of the embedding space. Trajectory-derived geometric and temporal features discriminated outcome in cardiac arrest (ROC-AUC 0.83) and subarachnoid hemorrhage (ROC-AUC 0.76), and distinguished physiological from pathological routine EEGs (ROC-AUC 0.93). In routine EEG, similarity relationships derived from embedding trajectories correlated with those derived from structured clinical reports, indicating that the latent space recapitulates clinically relevant organization. These findings show that a fixed, semantically structured EEG embedding generalizes across etiologies and recording settings, enabling prognostic stratification and contextual interpretation while preserving the relational structure of brain states.

07.
medRxiv (Medicine) 2026-06-10

Prediction of immunotherapy response using live tumor fragments from routine clinical biopsies

Functional ex vivo assays using live tumor tissues have demonstrated strong predictive accuracy for response to immune checkpoint inhibitors (ICIs) but are not scalable, requiring manual processing of large resections collected at academic centers. Here, an ex vivo live tumor fragment (LTF) platform was developed using standard-of-care biopsies from 228 patients with suspected malignancy collected across prospective, multicenter observational trials and biobanks. Hierarchical clustering of ICI-mediated changes in cytokine production identified two groups: responders and nonresponders. A binary classifier (elive index) using 8 cytokines achieved an AUC of 0.99 for cluster prediction. elive index correctly predicted clinical benefit in 93% (26/28) of patients (P = 3.2x10-5) and accurately identified 83% (10/12) of objective responders. Critically, elive responders were identified among biomarker-negative patients, highlighting the platform as a scalable approach that complements existing companion diagnostics and expands the population of patients identified to benefit from ICI therapy.

08.
Science (Express) 2026-05-28

A Hormone Cell Atlas maps the human endocrine system at cellular resolution | Science

作者: 未知作者

Hormones act across tissues and organs to coordinate physiological functions. Drawing inspiration from the Human Cell Atlas, we analyzed expression of 379 hormone and receptor genes in a transcriptomic dataset comprising 14 million single cells and nuclei across 47 human tissues. Using hormone2cell, we mapped putative hormone-producing and hormone-receiving cell types, defining tissue-specific and cross-tissue endocrine signatures. We predicted non-classical sites of hormone expression, including secretin in plasmacytoid dendritic cells, inferred convergent hormone action and endocrine feedback loops, and implicated cell populations in monogenic endocrine disorders. In a cross-tissue integration of adipocyte datasets, we uncovered dynamic endocrine programs across depots, within adipocyte subtypes and through adipogenic differentiation. Cumulatively, the Hormone Cell Atlas ( hormonecellatlas.org.uk ) provides a comprehensive framework for dissecting hormonal impact on health and disease.

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

RC-GeoCP: Geometric Consensus for Radar-Camera Collaborative Perception

Collaborative perception (CP) enhances scene understanding through multi-agent information sharing. While LiDAR-centric systems offer precise geometry, high costs and performance degradation in adverse weather necessitate multi-modal alternatives. Despite dense visual semantics and robust spatial measurements, the synergy between cameras and 4D radar remains underexplored in collaborative settings. This work introduces RC-GeoCP, the first framework to explore the fusion of 4D radar and images in CP. To resolve misalignment caused by depth ambiguity and spatial dispersion across agents, RC-GeoCP establishes a radar-anchored geometric consensus. Specifically, Geometric Structure Rectification (GSR) aligns visual semantics with geometry derived from radar to generate spatially grounded, geometry-consistent representations. Uncertainty-Aware Communication (UAC) formulates selective transmission as a conditional entropy reduction process to prioritize informative features based on inter-agent disagreement. Finally, the Consensus-Driven Assembler (CDA) aggregates multi-agent information via shared geometric anchors to form a globally coherent representation. We establish the first unified radar-camera CP benchmark on V2X-Radar and V2X-R, demonstrating state-of-the-art performance with significantly reduced communication overhead. Code will be released soon.

10.
arXiv (CS.AI) 2026-06-16

Learning to Share: Selective Memory for Efficient Parallel Agentic Systems

arXiv:2602.05965v2 Announce Type: replace-cross Abstract: Agentic systems solve complex tasks by coordinating multiple agents that iteratively reason, invoke tools, and exchange intermediate results. To improve robustness and solution quality, recent approaches deploy multiple agent teams running in parallel to explore diverse reasoning trajectories. However, parallel execution comes at a significant computational cost: when different teams independently reason about similar sub-problems or execute analogous steps, they repeatedly perform substantial overlapping computation. To address these limitations, in this paper, we propose Learning to Share (LTS), a learned shared-memory mechanism for parallel agentic frameworks that enables selective cross-team information reuse while controlling context growth. LTS introduces a global memory bank accessible to all teams and a lightweight controller that decides whether intermediate agent steps should be added to memory or not. The controller is trained using stepwise reinforcement learning with usage-aware credit assignment, allowing it to identify information that is globally useful across parallel executions. Experiments on the AssistantBench and GAIA benchmarks show that LTS significantly reduces overall runtime while matching or improving task performance compared to memory-free parallel baselines, demonstrating that learned memory admission is an effective strategy for improving the efficiency of parallel agentic systems. Project page: https://joefioresi718.github.io/LTS_webpage/

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

{\alpha}-Fair Insurance Pricing: A Fairness Continuum

arXiv:2606.14898v1 Announce Type: new Abstract: Fairness in insurance pricing remains a long-standing and deeply debated puzzle. On one hand, insurers, driven by profitability considerations, set premiums that differentiate across individual risks to achieve actuarial fairness. On the other hand, insurance serves a critical societal function by pooling risks across a population, motivating cross-subsidization among groups to promote solidarity fairness. The tension between these two competing notions of fairness makes insurance pricing inherently complex, particularly in modern settings where granular data allow for increasingly fine risk differentiation and regulators face growing pressure to protect vulnerable groups. To address this challenge, we propose an $\alpha$-Fair Individual Solvent Premium ($\alpha$-FISP) framework for insurance pricing that explicitly captures the trade-off between actuarial and solidarity fairness while guaranteeing solvency, a fundamental requirement in insurance operations. We formulate the pricing problem as a constrained optimization task, where actuarially fair premiums are adjusted subject to budget constraints on cross-subsidization within each risk class. This formulation naturally yields a family of solutions parameterized by $\alpha$, tracing a continuum between purely actuarial and purely solidarity-based pricing and enabling decision-makers to select an operating point along this fairness spectrum. We derive theoretical guarantees for the proposed framework. Numerical experiments show that $\alpha$-FISP is computationally tractable and aligns well with the U.S. regulatory regimes featuring heterogeneous state-level fairness requirements.

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

ROSA-RL: Uncertainty-Aware Roundabout Optimized Speed Advisory with Reinforcement Learning

arXiv:2606.16558v1 Announce Type: new Abstract: Roundabouts challenge automated driving in mixed traffic, as heterogeneous and non-deterministic human behavior, unknown driving intentions, and high interaction complexity create uncertainty about whether the conflict zone will be blocked or available at the moment of entry. We present ROSA-RL – uncertainty-aware Roundabout Optimized Speed Advisory with Reinforcement Learning. It enables safe and efficient roundabout entry for automated and human-driven vehicles in mixed traffic through probabilistic conflict forecasting. A Transformer-based model predicts conflict zone occupancy over a five-second horizon, capturing multi-agent interactions to anticipate upcoming conflicts and available gaps. The prediction outputs encode uncertainty in future motion and intent, and augment the state of a classical RL framework, enabling uncertainty-aware speed coordination. Evaluated in simulations grounded in real-world data, ROSA-RL can effectively handle uncertainty and outperform a comparable model-based baseline, closing the gap to an ideal setting assuming fully known occupancy while improving traffic efficiency and safety. The source code of this work is available under: github.com/urbanAIthi/ROSA-RL.

13.
arXiv (quant-ph) 2026-06-15

Computational regimes in matrix-product-state-based quantum trajectory simulations

arXiv:2606.13779v1 Announce Type: new Abstract: Efficient simulation of open quantum systems is central to modeling noisy quantum hardware and many-body dynamics. In trajectory-based tensor network methods, cost is often associated with trajectory-level quantities such as entanglement growth or bond dimension. However, the total cost of a fixed-accuracy simulation also depends on statistical sampling, and the interplay between per-trajectory complexity and sampling effort remains poorly understood. Here we introduce a cost-resolved framework for matrix product state (MPS)-based quantum trajectory simulations that decomposes total cost into memory per trajectory, runtime per trajectory, and sampling effort. We show that physically equivalent stochastic unravelings of the same Lindblad dynamics do not necessarily reduce total cost, but instead redistribute cost between trajectory complexity and statistical convergence. This trade-off is quantified by two dimensionless inflation factors: a bond dimension inflation $\alpha$ and a sampling inflation $\kappa$, which together determine the preferred unraveling under hardware-dependent memory and parallelism constraints. We provide a practical protocol for extracting $(\alpha,\kappa)$ from modest pilot simulations and demonstrate it using benchmarks across multiple noise channels. The resulting decision maps show that the computationally favorable unraveling can change with noise strength, time-step resolution, system size, and available parallelism. These results establish unraveling choice as a hardware-aware simulation design problem rather than an intrinsic optimization of trajectory entanglement alone.

14.
arXiv (CS.CL) 2026-06-17

PseudoBench: Measuring How Agentic Auto-Research Fuels Pseudoscience

As Large Language Model based agents enter autonomous scientific research, their ability to resist pseudoscience becomes increasingly important. Otherwise, such systems may rapidly generate plausible yet misleading studies that contaminate academic literature and erode trust in science. We present PseudoBench, an adversarial benchmark for evaluating whether agentic auto-research systems can identify and resist pseudoscientific narratives. PseudoBench contains 200 curated pseudoscientific claim-evidence pairs across five domains and evaluates agents through an end-to-end research pipeline from experiments to writing. Testing seven state-of-the-art agents, we find that current systems readily produce persuasive reports that align with pseudoscientific premises with near-zero refusal rates and the highest resistance of only 27.4%. Stronger agents risk packaging pseudoscience in more sophisticated scientific language, increasing its apparent credibility. These findings reveal an alarming capacity to fuel pseudoscience, calling for scientific alignment before widespread deployment.

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

EmbodiTTA: Resource-Efficient Test-Time Adaptation for Embodied Visual Systems

Continual Test-time adaptation (CTTA) continuously adapts the deployed model on every incoming batch of data. While achieving optimal accuracy, existing CTTA approaches present poor real-world applicability on resource-constrained edge devices, due to the substantial memory overhead and energy consumption. In this work, we first introduce a novel paradigm – on-demand TTA – which triggers adaptation only when a significant domain shift is detected. Then, we present OD-TTA, an on-demand TTA framework for accurate and efficient adaptation on edge devices. OD-TTA comprises three innovative techniques: 1) a lightweight domain shift detection mechanism to activate TTA only when it is needed, drastically reducing the overall computation overhead, 2) a source domain selection module that chooses an appropriate source model for adaptation, ensuring high and robust accuracy, 3) a decoupled Batch Normalization (BN) update scheme to enable memory-efficient adaptation with small batch sizes. Extensive experiments show that OD-TTA achieves comparable and even better performance while reducing the energy and computation overhead remarkably, making TTA a practical reality.

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

MARIC: Multi-Agent Reasoning for Image Classification

Image classification has traditionally relied on parameter-intensive model training, requiring large-scale annotated datasets and extensive fine tuning to achieve competitive performance. While recent vision language models (VLMs) alleviate some of these constraints, they remain limited by their reliance on single pass representations, often failing to capture complementary aspects of visual content. In this paper, we introduce Multi Agent based Reasoning for Image Classification (MARIC), a multi agent framework that reformulates image classification as a collaborative reasoning process. MARIC first utilizes an Outliner Agent to analyze the global theme of the image and generate targeted prompts. Based on these prompts, three Aspect Agents extract fine grained descriptions along distinct visual dimensions. Finally, a Reasoning Agent synthesizes these complementary outputs through integrated reflection step, producing a unified representation for classification. By explicitly decomposing the task into multiple perspectives and encouraging reflective synthesis, MARIC mitigates the shortcomings of both parameter-heavy training and monolithic VLM reasoning. Experiments on 4 diverse image classification benchmark datasets demonstrate that MARIC significantly outperforms baselines, highlighting the effectiveness of multi-agent visual reasoning for robust and interpretable image classification.

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

Securing Multi-Agent GIS Systems: Risk Evaluation and Prompt Hardening Optimization

Agentic systems are increasingly integrated with geographic information systems (GIS), where multi-agent coordination enables complex conversational and spatial analysis but introduces security risks. This work presents a security-oriented framework for risk identification, evaluation, and mitigation in a multi-agent GIS system while maintaining adaptability to broader agentic architectures. We test the agentic system of a commercial geospatial partner while developing a modular state-machine-based orchestration framework that abstracts agent behavior into reusable components. We evaluate robustness using a red-teaming framework with an adaptive attacker LLM and a deterministic judge that produces binary outcomes with supporting rationales across multi-turn attacks. We further improve resilience with a prompt optimization framework that treats prompts as structured signatures and injects adversarial demonstrations, enabling systematic security improvements without degrading task performance.

18.
arXiv (CS.AI) 2026-06-12

Arbor: Tree Search as a Cognition Layer for Autonomous Agents

arXiv:2606.12563v1 Announce Type: new Abstract: Arbor is a multi-agent framework that introduces structured tree search as a cognition layer for autonomous agents operating in large, stateful action spaces. Prior autonomous optimization systems operate on isolated targets with stateless evaluation. Arbor instead maintains an explicit search tree of scored hypotheses that serves as the shared working memory across agents, evolving with every measurement, treating failures as diagnostic signal that reshapes subsequent exploration, and expanding as prior successes shift the bottleneck distribution. We validate Arbor on full-stack LLM inference optimization, a domain where achieving peak performance has historically required coordinated effort from engineering teams across the application, framework, compiler, kernel, and hardware stack. Arbor pairs an Orchestrator agent, which drives optimization by delegating to Domain Specialists across the inference stack, with a Critic agent that safeguards stability through root-cause analysis, introspection, and measurement validation – a checks-and-balances architecture where neither agent can unilaterally drive the system. Agent capabilities are decomposed into hard skills (domain expertise) and soft skills (coordination protocols that determine how contributions compose), enabling fully autonomous multi-day campaigns. Arbor achieves up to 193% inference throughput-latency Pareto improvement over vendor-optimized baselines, while a single agent without the harness plateaus at +33% throughput improvement and crashes irrecoverably within hours. Arbor generalizes to multiple generations of hardware platform, and run-to-run variance is within 2 percentage points demonstrating that the method is hardware-agnostic and reproducible.

19.
arXiv (math.PR) 2026-06-17

Convergence Analysis of the Random Bisection Method

arXiv:2603.20483v2 Announce Type: replace-cross Abstract: We propose a generalized version of the bisection method where the cutting point between the two subintervals is chosen at random following an arbitrary distribution. We compute expected convergence rates with respect to any arbitrary a priori distribution for the position of the root in the initial interval and proved that it depends only on the the expectation $\mathbb{E}[c(1-c)]$ of the cut $c$. We also provide a generalization of the method for $K$ random cuts and study its convergence properties. Most probabilistic derivations are kept fairly simple for the ease of understanding of a larger audience. Our theoretical results are then validated numerically using statistical simulation.

20.
medRxiv (Medicine) 2026-06-22

Regional Service-System Conditions Associated with Facility-Linked Home-Based Specialist Care in Japan: A Claims-Based Ecological Study of Home Dialysis

Background Complex chronic care is increasingly delivered in patients' homes while remaining linked to specialist facilities for training, monitoring, and backup care. Home dialysis provides a useful case because peritoneal dialysis (PD) and home hemodialysis (HHD) share a home-facility delivery structure but differ in technical and operational requirements. This study examined regional service-system conditions associated with the presence and scale of PD and HHD in Japan. Methods This ecological study used publicly available claims, administrative, census, and geospatial data harmonized to 334 Secondary Medical Areas. Regional indicators were organized into four domains: dialysis service delivery, implementation support for home-based care, hospital backup capacity, and living and sociodemographic context. Diffusion was examined using claims-based indicators of regional presence and post-presence scale, analyzed separately for PD and HHD with Firth penalized logistic regression and zero-truncated negative binomial regression, respectively. Results PD was observed in 271 regions and HHD in 109. Patterns of associated regional conditions differed by modality and stage. PD was associated mainly with existing dialysis-service organization, whereas HHD was associated with broader regional supports, including home-care delivery, living infrastructure, transition support, and hospital-system indicators. Conditions associated with presence differed from those associated with scale. Cross-modality associations suggested that shared regional factors may shape the distribution of both modalities. Conclusions Regional conditions for home dialysis diffusion in Japan differed by modality and stage. PD was linked mainly to existing dialysis-service organization, whereas HHD was linked to multi-domain regional support for technically demanding home treatment. Under standardized reimbursement, local service-system capacity may remain important for modality- and stage-specific diffusion of home dialysis.

21.
bioRxiv (Bioinfo) 2026-06-11

TifBERT: a self-supervised foundation model for normalization-robust bulk RNA-seq representation learning

Bulk RNA sequencing remains central to translational genomics, yet foundation-model development has largely focused on single-cell data. Existing transformer approaches for bulk RNA-seq often rely on expression discretization, numerical reconstruction, external gene embeddings, or restricted gene sets, limiting robustness across normalization schemes and cohorts. Here, we introduce TifBERT, a self-supervised framework for full-transcriptome bulk RNA-seq representation learning. TifBERT converts each unordered expression profile into a sample-specific gene sequence using term frequency-inverse document frequency (TF-IDF) ordering, prioritizing genes that are both highly expressed within a sample and selectively expressed across the cohort. It is then pretrained using masked gene modeling, predicting gene identities from transcriptomic context rather than reconstructing expression values. Pretrained on harmonized TCGA Pan-Cancer data spanning five RNA-seq normalization schemes, TifBERT learns contextual representations across approximately 10,000 genes without expression binning, landmark-gene restriction, or external biological embeddings. Across 33 TCGA cancer types, TifBERT achieved 90.83% accuracy, 0.996 macro AUC-ROC, and 0.903 MCC. It also captured pathway-level biology, achieving mean sample-wise and pathway-wise Pearson correlations of 0.754 and 0.762 across 1,387 PARADIGM pathway activities. Independent evaluation on GTEx healthy tissues showed preservation of tissue-level transcriptomic structure without retraining. In comparison with existing models, TifBERT achieves competitive subtype discrimination with substantially greater stability and produces markedly richer embedding geometry (effective rank 95.6 versus 6.3), without requiring expression discretization or in-distribution pretraining exposure. Together, TifBERT provides a scalable, normalization-independent foundation model for reusable bulk transcriptomic representation learning

22.
bioRxiv (Bioinfo) 2026-06-22

EventHorizon: A Foundation Model for Clinical Flow Cytometry

Flow cytometry is an essential tool for diagnosis of hematologic malignancies, but existing clinical workflows are highly dependent on expert manual interpretation. Existing machine learning approaches typically require extensive labeled data and are sensitive to variability in panel design, instrumentation, and laboratory workflows, limiting their generalizability. We present EventHorizon, a self-supervised foundation model for clinical flow cytometry that produces unified specimen-level representations from heterogeneous multi-panel data. EventHorizon employs a two-stage hierarchical transformer architecture with marker-aware tokenization, enabling seamless integration of cells measured across different antibody panels into a single shared latent space. We pre-train the model using a DINO-inspired self-distillation strategy with a variety of flow cytometry-specific augmentations on a dataset of more than 100,000 clinical specimens across 17 distinct panels. We evaluate the resulting embeddings on three clinically relevant classification tasks spanning common and rare panels, demonstrating that simple k-nearest neighbor probing of frozen EventHorizon embeddings achieves performance comparable to a fully supervised baseline model and a prior panel-specific self-supervised model. To ensure EventHorizon is not simply shortcut learning on features such as the markers/panels run for a given specimen, we perform a graph-theoretic analysis of EventHorizon's latent space which argues that specimen embeddings are organized primarily by biological diagnosis. Taken together, these results demonstrate that EventHorizon produces biologically meaningful, panel-agnostic specimen representations from clinical flow cytometry data which, with further development and validation, could provide a potential basis for scalable, reproducible diagnostic support across diverse clinical laboratory settings.

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

Let LLMs Judge Each Other: Multi-Agent Peer-Reviewed Reasoning for Medical Question Answering

Objective: To enhance the accuracy, interpretability, and robustness of large language models (LLMs) in medical question answering (MedQA). Method: We designed a multi-agent peer-reviewed reasoning method in which multiple LLM agents independently generate chain-of-thought reasoning with candidate answers, then act as peer reviewers to evaluate each other's reasoning for factual correctness and logical soundness. The highest-rated reasoning chain is selected to produce the final answer. Experiments were conducted with five state-of-the-art LLMs (Llama-3.1-8B, Qwen2.5-7B, Phi-4, DeepSeek-LLM-7B, GPT-oss-20B) on three benchmark datasets: HeadQA, MedQA-USMLE, and PubMedQA. Performance was compared against single-model chain-of-thought reasoning and chain-of-thought-based majority voting. Results: Peer-reviewed reasoning consistently outperformed both baselines. The best model combination achieved an average accuracy of 0.820 across datasets, exceeding the strongest single model (0.777) and majority voting ensembles (up to 0.789). The method also scaled effectively with more participating models, while peer assessments reliably distinguished high- from low-quality reasoning chains. Conclusion: The proposed multi-agent peer-reviewed reasoning method enables LLMs to act as both solvers and evaluators, yielding superior performance in MedQA. By emphasizing reasoning quality rather than answer agreement alone, this approach improves accuracy, interpretability, and robustness, offering a promising direction for trustworthy biomedical AI systems.

24.
arXiv (CS.CV) 2026-06-17

Training LLMs with Reinforcement Learning over Digital Twin Representations for Reasoning-Intensive Surgical VideoQA

Surgical video question answering requires multi-step reasoning across semantic, spatial, and temporal dimensions. Existing methods architecturally compress videos into discrete token representations and couple visual perception with reasoning. This approach fragments continuous spatial-temporal relationships and has been shown to restrict multi-step reasoning capabilities. We introduce a reinforcement learning (RL) framework that trains large language models (LLMs) to decouple perception from reasoning by operating over digital twin representations constructed from surgical foundation models. Additionally, we introduce hierarchical representations across frame, temporal window, and procedure levels with probabilistic uncertainty estimates. Finally, we propose a novel reward that combines format validation with accuracy assessment through clinical plausibility evaluation and uncertainty-aware calibration for training. To demonstrate the capabilities of this approach, we introduce REAL-Colon-Reason, a colonoscopic benchmark with 2000 question-answer pairs across three complexity levels. We achieve state-of-the-art performance on REAL-Colon-Reason and two existing surgical VideoQA benchmarks REAL-Colon-VQA and EndoVis18-VQA.

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

GraphWorld: Long-Horizon Planning with World Models for End-to-End Autonomous Driving

End-to-end autonomous driving has made significant progress by unifying perception, prediction, and planning within a single learning framework, achieving strong performance in short-horizon decision making. However, most existing E2E-AD methods remain confined to short-horizon planning and lack the ability to model long-term temporal dependencies, which severely limits their generalization and security in complex and highly interactive driving scenarios. In this work, we propose GraphWorld, an E2E-AD framework that explicitly enhances long-horizon planning through latent world modeling. We introduce an Ego-Centric Interaction Graph, which adaptively models critical neighboring agents based on spatial proximity, and propagates relational context to planning queries via cross-node cross-attention. We present a World-State-Conditioned Planning that learns ego-centric latent world representations by modeling interactions between an ego vehicle and surrounding agents. This latent world state captures key interaction dynamics and safety-relevant semantics, and serves as a conditioning signal to guide long-horizon, safety-aware trajectory planning. Extensive experiments on Bench2Drive, NAVSIMv1/2, and nuScenes demonstrate that GraphWorld significantly reduces collision rates and improves long-horizon planning performance, validating its effectiveness in complex driving environments.