Academic Intelligence · Curated Daily

Explore the Frontier of Global Academia

AcademicHub aggregates real-time literature from top journals and preprint platforms. Build your personal research radar and let large language models compile cross-disciplinary analysis briefings automatically.

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

Learning Visually Interpretable Oscillator Networks for Soft Continuum Robots from Video

Learning soft continuum robot (SCR) dynamics from video offers flexibility but existing methods lack interpretability or rely on prior assumptions. Model-based approaches require prior knowledge and manual design. We bridge this gap by introducing: (1) The Attention Broadcast Decoder (ABCD), a plug-and-play module for autoencoder-based latent dynamics learning that generates pixel-accurate attention maps localizing each latent dimension's contribution while filtering static backgrounds, enabling visual interpretability via spatially grounded latents and on-image overlays. (2) Visual Oscillator Networks (VONs), a 2D latent oscillator network coupled to ABCD attention maps for on-image visualization of learned masses, coupling stiffness, and forces, thereby enabling mechanical interpretability. We validate our approach on single- and double-segment SCRs, demonstrating that ABCD-based models significantly improve multi-step prediction accuracy with 5.8x error reduction for Koopman operators and 3.5x for oscillator networks on a two-segment robot. VONs autonomously discover a chain structure of oscillators. This fully data-driven approach yields compact, mechanically interpretable models with potential relevance for future control applications.

02.
arXiv (CS.LG) 2026-06-19

Phase Transition for Stochastic Block Model with more than $\sqrt{n}$ Communities

arXiv:2509.15822v3 Announce Type: replace-cross Abstract: Predictions from statistical physics postulate that recovery of the communities in the Stochastic Block Model (SBM) with a fixed number $K$ of communities is possible in polynomial time above, and only above, the Kesten-Stigum (KS) threshold. This conjecture has given rise to a rich literature, proving that non-trivial community recovery is indeed possible in SBM above the KS threshold. Failure of low-degree polynomials (LDP) below the KS threshold was also proven, as long as $K\ll \sqrt{n}$, where $n$ is the number of nodes in the observed graph. When $K\geq \sqrt{n}$, Chin et al.(2025) recently proved that, in a sparse regime, community recovery in polynomial time is possible below the KS threshold by counting non-backtracking paths. This breakthrough led them to postulate a new threshold for the many-communities regime $K\geq \sqrt{n}$. In this work, we provide evidence supporting their conjecture:\\ 1- We prove that, for any graph density, LDP fail to recover communities below the threshold postulated by Chin et al.(2025) ;\\ 2- We prove that community recovery is possible in polynomial time above the postulated threshold, not only in the sparse regime considered in Chin et al.~(2025), but also in moderately sparse regimes, by counting occurrences of some specific motifs inspired by the LDP analysis.\\ In particular, counting self-avoiding paths of length $\log(n)$, which is closely related to spectral algorithms based on the Non-Backtracking operator, is optimal only in the sparse regime. More complex motifs based on the blow-up of a cycle must be considered in denser regimes.

03.
arXiv (math.PR) 2026-06-16

An Analytical Methodology for Quantifying Airspace Conflict Rate and Complexity

arXiv:2606.14897v1 Announce Type: cross Abstract: Air traffic growth, advanced air mobility, and increasingly autonomous operations are driving the need for scalable and adaptive airspace design methodologies. Central to this challenge is quantifying how traffic flow structure and demand, governed in part by airspace geometry, influence conflict generation and operational complexity. This paper presents an analytical framework for computing conflict rate and conflict probability in structured airspace using stochastic flow models. Traffic streams are modeled as renewal processes with prescribed inter-arrival time distributions, while interactions between flows are captured through geometry-dependent minimum spacing constraints at merges and crossings. Within this formulation, closed-form upper bounds on the expected conflict rate and conflict probability per aircraft are derived as functions of flow configuration and demand. These metrics are interpreted as complementary measures of airspace complexity, reflecting controller workload and per-aircraft operational risk. The methodology is applied to representative hexagonal cell geometries with varying routing structures and flow distributions. Results reveal non-monotonic tradeoffs between routing flexibility, capacity, and conflict generation, with intermediate flow configurations outperforming both highly constrained and highly distributed cases. The proposed framework provides a tractable tool for evaluating airspace design alternatives and complexity-informed traffic management strategies.

04.
arXiv (CS.LG) 2026-06-17

CoCoEmo: Composable and Controllable Human-Like Emotional TTS via Activation Steering

arXiv:2602.03420v2 Announce Type: replace-cross Abstract: Emotional expression in human speech is nuanced and compositional, often involving multiple, sometimes conflicting, affective cues that may diverge from linguistic content. In contrast, most expressive text-to-speech systems enforce a single utterance-level emotion, collapsing affective diversity and suppressing mixed or text-emotion-misaligned expression. While activation steering via latent direction vectors offers a promising solution, it remains unclear whether emotion representations are linearly steerable in TTS, where steering should be applied within hybrid TTS architectures, and how such complex emotion behaviors should be evaluated. This paper presents the first systematic analysis of activation steering for emotional control in hybrid TTS models, introducing a quantitative, controllable steering framework, and multi-rater evaluation protocols that enable composable mixed-emotion synthesis and reliable text-emotion mismatch synthesis. Our results demonstrate, for the first time, that emotional prosody and expressive variability are primarily synthesized by the TTS language module instead of the flow-matching module, and also provide a lightweight steering approach for generating natural, human-like emotional speech.

05.
bioRxiv (Bioinfo) 2026-06-22

Multivariate Random Forests for Cross-Modal Multi-Omics Integration

Multi-omics studies are widely used across many areas of biomedical research. In many diseases, some signals are shared across data types, while others are strongest in a single omics layer. Current multi-omics clustering methods often either merge all data types into a single representation, which can blur biology that is strong in one layer, or rely on linear structure that may miss more complex relationships across data types. We introduce multiRF, a random-forest-based method that handles complex data types and separates shared and modality-specific structure for multi-omics data. multiRF learns sample similarities across omics layers from multivariate random forests, combines them across data types, and uses the resulting weights to estimate the part of each omics layer that is predictable from the others. The remaining residual is treated as modality-specific signal, allowing shared and modality-specific similarities to be clustered separately. In simulations, multiRF recovered shared clusters as well as or better than established integrative methods while more reliably separating modality-specific signal under nonlinear data structures. In TCGA head and neck squamous cell carcinoma, the shared component aligned with the main subtype structure across established reference classifications, while gene- and miRNA-specific components revealed additional immune and developmental biology. In the ADNI cohort with matched blood DNA methylation and structural MRI, the shared cross-modal aging signal was associated with future conversion to mild cognitive impairment or Alzheimer's disease, and a DNAm-specific residual signal showed exploratory additional information. These results show that multiRF can recover a common disease axis while retaining biologically meaningful signals specific to one data type. multiRF is available as an open-source R package at https://github.com/novawz/multiRF.

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

Generating function and Bloch representation for quantum Fisher tensor

arXiv:2603.04615v2 Announce Type: replace Abstract: The Uhlmann relative amplitude between two density matrices is shown to be a generating function, through which the quantum Fisher tensor that contains both the quantum Fisher information matrix and the mean Uhlmann curvature can be obtained via differentiation over system parameters. In the pure state limit, our generating function recovers that of the quantum geometric tensor proposed by Het\'{e}nyi and L\'{e}vay, and also clarifies the fidelity and phase between two quantum states as the generating functions of the quantum metric and Berry curvature, respectively. A generic expression for the quantum Fisher tensor in terms of the Bloch representation of density matrices is derived, which facilitates the calculation of the tensor, mean Uhlmann curvature, and geometric properties derived from the quantum Fisher information matrix. Canonical ensembles of spins are adopted to demonstrate our formalism, which reveals a constant Ricci scalar, a vacuum Einstein equation, and a cosmological constant on the 3D Euclidean manifold of the magnetic field.

07.
medRxiv (Medicine) 2026-06-15

SPIRIT-CONSORT-ELM: Element-Level Assessment of Randomized Controlled Trial Reporting Using Large Language Models

Randomized controlled trials (RCTs) play a central role in assessing the benefits and harms of interventions. Incomplete reporting in RCT publications can compromise the verifiability and usefulness of RCTs. SPIRIT and CONSORT reporting guidelines aim to improve the completeness of RCT protocols and results publications, respectively. However, many RCTs are not reported completely. Checking manuscripts automatically could help authors improve the completeness of reports prior to publication. We previously annotated SPIRIT-CONSORT-TM, a corpus of 200 articles (comprising 100 protocol-results publication pairs) using 83 checklist items drawn from SPIRIT 2013 and CONSORT 2010. We also trained machine learning models to automatically assess reporting at the item level. Each checklist item can include multiple constituent elements (i.e., specific details required for that item), and an item might be considered fully reported when all of its elements are present. However, prior work does not explicitly capture or evaluate reporting at the element level. To address this gap, we extended SPIRIT-CONSORT-TM by incorporating element-level annotations and using them to assess reporting completeness (SPIRIT-CONSORT-ELM). We formulated element-level assessment as a machine reading comprehension task, operationalized through 119 questions, where each question targets a specific reporting element within a checklist item. Using the 200 articles included in SPIRIT-CONSORT-TM, two annotators independently answered 119 questions for 50 articles (25 protocol-results pairs) and resolved any discrepancies through discussion; the remaining 150 articles (75 protocol-results pairs) were assessed by a single annotator. We then developed an automated pipeline for element-level assessment using SPIRIT-CONSORT-ELM. The pipeline first applies a PubMedBERT-based model to identify sentences containing item-level reporting information, then it uses a generative large language model (LLM; GPT-5) with chain-of-thought reasoning to answer element-level questions based on the retrieved evidence. Agreement between the two annotators was high (Gwet's AC1: 0.782) and our pipeline achieved high accuracy in identifying element-level reporting evidence (F1: 0.822, Gwet's AC1: 0.796). Ablation studies indicate that chain-of-thought reasoning and the inclusion of illustrative in-context examples modestly improve LLM performance on the machine reading comprehension task. SPIRIT-CONSORT-ELM provides a benchmark for evaluating reporting guideline completeness at the element level, enabling assessment of RCT transparency beyond the simple presence or absence of checklist items and is publicly available at https://osf.io/kznx4/. The automated pipeline establishes a robust baseline for assessing RCT reporting and demonstrates potential as a practical aid for authors, reviewers, and editors to identify and address gaps in completeness and transparency of RCT reports.

08.
arXiv (CS.LG) 2026-06-12

Ride, Track, and Recover: Pilot Randomized Trial of a Wearable Digital Self-Management Intervention During a Veteran Endurance-Cycling Program

arXiv:2606.13529v1 Announce Type: cross Abstract: Post-traumatic stress disorder (PTSD) in veterans is characterized by persistent hyperarousal and comorbid anxiety and depressive symptoms that are difficult to monitor and manage outside clinical settings. Thirteen veterans participating in a Project Hero cycling event in Texas were randomized by computer-generated sequence in a naturalistic setting to two arms: (1) digital intervention plus physical activity, or (2) physical activity only, plus a third at-home monitoring control cohort consisting of 7 veterans selected from the broader Project Hero veteran community. Continuous smartwatch sensing combined heart rate and accelerometer features to detect hyperarousal events, which were confirmed in real time by participants. Weekly self-report measures of anxiety, depression, and PTSD severity were collected. Generalized additive mixed models characterized nonlinear trajectories over time. Baseline-normalized hyperarousal trajectories differed significantly across conditions, with the digital intervention group (n=7) showing structured stabilization compared to late-study escalation in the physical-only group (n=3). Both cycling groups exhibited acute symptom improvements during the endurance event; however, the digital intervention group demonstrated a higher overall maintenance of gains. The at-home control group (n=4) showed gradual symptom declines. Perceived precision of ML detections varied substantially across individuals and was positively associated with symptom severity, with higher-severity participants confirming a greater proportion of detected events. These results suggest that coupling wearable detection with digital self-management tools may support stabilization of hyperarousal and symptom improvement while emphasizing the importance of personalization and human-centered design in wearable mental health systems.

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

Bridging Information Asymmetry: A Hierarchical Framework for Blind Face Restoration with Reduced Uncertainty

Blind face restoration remains a persistent challenge due to the inherent ill-posedness of reconstructing holistic structures from severely constrained observations. Current generative paradigms, while capable of synthesizing realistic facial details, remain limited by the under-constrained nature of blind restoration, where severely degraded inputs can be mapped to plausible yet identity-inconsistent outputs. To address this issue, we present Pref-Restore, a hierarchical framework for BFR with reduced restoration uncertainty. Our design is organized around three complementary principles: (1) Semantic Information Augmentation, where an auto-regressive semantic branch converts image and text cues into structured tokens that provide a stable high-level anchor; (2) Texture-level Fidelity Alignment, where the diffusion generator is trained under this anchor to recover identity-relevant details; and (3) Fidelity-constrained Preference Optimization, where a face-aware reward refines the diffusion trajectory while controlling the quality–fidelity trade-off. Extensive experiments on synthetic and real-world benchmarks show that Pref-Restore achieves state-of-the-art performance, with stronger identity-sensitive fidelity and lower restoration uncertainty across repeated sampling. Systematic ablations further attribute these gains to the proposed hierarchical design, showing the necessity of staged training, the robustness and quality dependence of the text pathway, and the benefit of fidelity-constrained preference optimization.

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

X+Slides: Benchmarking Audience-Conditioned Slide Generation

arXiv:2606.19256v1 Announce Type: new Abstract: Automatically generating slide decks from source documents is an important application of large language models (LLMs). Existing benchmarks primarily assess slide completeness and technical depth, while overlooking the target audience as a critical real-world factor. For instance, specialists demand rigorous proofs, whereas decision-makers prioritize actionable conclusions. To bridge this gap, we introduce X+Slides, a benchmark specifically designed for audience-conditioned slide generation. Built on a diverse corpus spanning 113 topics and seven presentation scenes, X+Slides employs a dynamic evaluation framework constructed from 8,133 deduplicated, source-grounded probes. By assigning audience-specific utility weights to the same source-grounded probes, X+Slides reports four complementary metrics: Audience Coverage measures how much audience-essential information is conveyed, Domain-wise Coverage shows which information types are covered, Efficiency measures delivered utility per unit of attention cost, and Correctness verifies whether slide claims are supported by the source. Experiments on DeepPresenter, SlideTailor, and NotebookLM show that current systems can recover a substantial but still incomplete part of audience-essential information: at $\tau_A=0.7$, DeepPresenter reaches a best Audience Coverage of 0.714, SlideTailor reaches 0.594, and the NotebookLM ablation reaches 0.853 while showing clear grounding differences. These results indicate that visual quality and broad topic coverage should not be treated as evidence support without source-grounded evaluation.

11.
arXiv (CS.LG) 2026-06-12

Deep Learning-based Algebraic Reynolds Stress Closures for RANS Simulations of Turbulent Flows

arXiv:2605.26358v2 Announce Type: replace-cross Abstract: Turbulence is ubiquitous in engineering and science, yet direct simulation is prohibitively expensive. The Reynolds-averaged Navier-Stokes (RANS) equations provide savings exceeding ten orders of magnitude but introduce unclosed terms (the closure problem). Offline-trained machine-learning (ML) closures suffer distribution shift in predictive simulations, while ML methods that bypass the governing equations struggle to generalise from scarce high-fidelity data. We develop a physics-derived deep learning closure model for RANS, the Deep Algebraic Reynolds Stress Model (DARSM), which can be trained on small datasets and accurately generalise across Reynolds numbers, to unseen geometries, and to different flow regimes. A neural network maps flow invariants to empirical parameters in an implicit algebraic Reynolds stress equation, derived from the Reynolds stress transport equations under the weak-equilibrium assumption, imposing physics-based structure on the ML closure. End-to-end optimisation through the governing PDEs and the coupled implicit closure eliminates distribution shift, but both unrolled and implicit automatic differentiation fail on the stiff coupled solver. We derive adjoint equations that exploit the solver's implicit-explicit structure for efficient optimisation. On canonical square-duct and periodic-hill benchmarks, DARSM reduces average test velocity error over baseline RANS by $2$-$4\times$ across Reynolds number, geometries, and flow regimes, with peak case-level reductions of $12\times$. The model trained on attached, anisotropy-dominated flows (square duct) accurately generalises without retraining to separated flows (periodic hills), a regime change in the underlying physics. DARSM also outperforms five established ML methods: offline training, tensor-basis neural networks, field-inversion machine learning, DeepONets, and physics-informed neural networks.

12.
arXiv (math.PR) 2026-06-16

Atypical Decay Rates for Atypical Heights in Random Recursive Trees

arXiv:2604.20139v2 Announce Type: replace Abstract: We establish the large deviation probabilities for the height of random recursive trees, revealing polynomial upper-tail decay and stretched-exponential lower-tail decay. Remarkably, the lower tail features an atypical prefactor that grows to infinity more slowly than any $n$-fold iterated logarithm.

13.
arXiv (CS.CV) 2026-06-16

Reasoning in Computer Vision: Taxonomy, Models, Tasks, and Methodologies

Visual reasoning matters for many computer vision tasks that go beyond surface-level object detection and classification. Despite progress in relational, symbolic, temporal, causal, and commonsense reasoning, existing surveys typically cover only one part of the problem, such as visual question answering, scene-graph generation, neuro-symbolic AI, or multimodal chain-of-thought, and rarely analyze reasoning types, methodologies, and evaluation protocols together. This survey addresses that gap. Following a structured literature review, we group visual reasoning into five major types (relational, symbolic, temporal, causal, and commonsense) and examine how each is implemented across methods that range from graph-based models, memory networks, attention mechanisms, and neuro-symbolic systems to reasoning with vision-language models (VLMs) and multimodal large language models (MLLMs), including visual chain-of-thought, visual programming, and tool-augmented and test-time reasoning. We then review evaluation protocols for functional correctness, structural consistency, and causal validity, and we analyze their limits in generalizability, reproducibility, faithfulness, and explanatory power. We also identify open challenges: scaling to complex scenes, integrating symbolic and neural paradigms more deeply, the shortage of comprehensive benchmarks, language-prior shortcuts and hallucination in foundation models, and reasoning under weak supervision. Finally, we set out a research agenda for vision systems and argue that connecting perception and reasoning is necessary for transparent, trustworthy, and cross-domain models, especially in high-stakes settings such as autonomous driving and medical diagnostics.

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

Do Large Language Models Always Tell The Same Stories?

Recent advances in large language models (LLMs) have enabled the generation of high-quality prose, yet the question of whether these models are capable of generating diverse outputs remains contested. In this work, we investigate the diversity of LLM-generated stories through the framework of narrative similarity. Using a contrastive framework and a dataset of human-written stories and prompts from r/WritingPrompts, we collect narrative similarity judgments across 10 representative LLMs, utilizing both human evaluations and three different automatic annotation methods. Our findings reveal a consistent trend: LLM-generated narratives are consistently more similar to each other than human-written stories are. We demonstrate that frontier models in particular converge on a ``mean'' generic narrative that approximates individual human stories but lacks the collective diversity of human authors. Finally, we show that common mitigation strategies, including negative prompting and temperature scaling, fail to meaningfully address this homogeneity.

15.
bioRxiv (Bioinfo) 2026-06-15

VrySure: A Multi-Task AI Scientific Fraud Detection Platform for Identifying Manipulated and AI-Generated Biomedical Research Images

Integrity of scientific data is critical in biomedical research, where images often serve as primary evidence for experimental observations and conclusions. Advances in image-editing technologies and generative artificial intelligence (AI) have increased the accessibility and realism of visual manipulation, making detection through manual review increasingly challenging. To empower our laboratory researchers to continuously monitor and uphold scientific rigor and data integrity, and serve the global scientific community, we developed VrySure, an easy-to-deploy, AI-driven multi-task platform for automated image-integrity screening in biomedical research. VrySure integrates four detection modules: cross-image transformation detection, within-image copy-move detection, splicing detection in blot and gel images, and AI-generated image detection. The system identifies potentially manipulated images and, when possible, localizes suspicious regions using bounding-box outputs to support downstream verification. To support development and evaluation, we constructed task-specific datasets by combining public biomedical image resources, curated manipulated examples, and synthetic images generated by multiple generative AI systems. We evaluated VrySure using region-level F1 score, recall, precision, false negative rate (FNR), and false discovery rate (FDR) across multiple manipulation categories and compared its performance with two commonly used commercial image-integrity screening platforms under a predefined benchmark protocol. Under the tested conditions, VrySure achieved a higher F1 score and recall, lower FNR, and maintained a low FDR for within-image copy-move detection, splicing detection, and AI-generated image detection, while showing comparable performance in transformation detection. Beyond automated screening, VrySure is designed to support source-data comparison and evidence-based assessment in scientific integrity investigations. By integrating multiple detection capabilities into a unified and scalable workflow, VrySure provides a practical framework to improve the efficiency and consistency of image-integrity screening in biomedical research.

16.
arXiv (CS.LG) 2026-06-15

Decoupled Latent Optimization of Diffusion Models for Full Waveform Inversion

arXiv:2606.14139v1 Announce Type: new Abstract: Full waveform inversion (FWI) recovers subsurface velocity from seismic recordings by solving a severely ill-posed, nonconvex PDE-constrained optimization. Classical regularizers stabilize the inversion but fail to reproduce realistic geological structures; recent diffusion-prior methods improve realism at the cost of a fragile trade-off between data fidelity and prior consistency. We propose Decoupled Latent Optimization (DLO), which relaxes the standard latent-optimization formulation into a quadratic-penalty objective over an auxiliary physical variable and a latent variable. The data-fidelity gradient acts in physical space, the diffusion sampler contributes only through a decoded prior sample, and the standard smoothed-velocity initialization of classical FWI is preserved. On the OpenFWI benchmark, DLO outperforms classical regularizers and existing diffusion-based methods under clean, noisy, and missing-trace acquisitions. The prior, trained on 70*70 OpenFWI models, transfers directly to the Marmousi and Overthrust benchmarks, where DLO recovers intricate fault structures and remains robust to initialization smoothing and measurement noise.

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

TA-RAG: Tone-Aware Retrieval-Augmented Generation for Peer-Support Health Communication

Retrieval-augmented generation (RAG) successfully grounds large language model (LLM) outputs in trusted documents, but factual grounding alone is insufficient for sensitive peer-support health communication. In domains such as HIV peer support, responses must also be accessible, stigma-free, empathetic, and tailored to the recipient. This paper presents TA-RAG, a lightweight, prompt-based tone-aware RAG framework that embeds explicit tone control into a RAG pipeline without requiring model fine-tuning. We operationalise tone across four core components: stigma-free rewriting, readability adjustment, recipient adaptation, and empathy rephrasing. We evaluate TA-RAG through component-level tests using questions derived from HIV Online Learning Australia (HOLA), UNAIDS terminology guidance, readability metrics, peer-support standards from National Association of People with HIV Australia (NAPWHA), and a public empathy dataset. Results show that the TA-RAG's components improve their targeted communication quality while preserving key content. These findings emphasise that prompt-based tone control is a potential direction for making RAG outputs suitable for sensitive peer-support health communication.

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

Off-Policy Evaluation for Missingness-Aware Policies in MDPs with Rewards Missing Not at Random

arXiv:2606.20206v1 Announce Type: cross Abstract: In offline Reinforcement Learning, immediate rewards in logged batch data are often unobserved due to sparse or irregular record-keeping, or censored beyond certain reward values. This issue arises in practical settings, including health care and marketing. We investigate off-policy evaluation (OPE) in finite-horizon Markov decision processes when rewards are missing not at random (MNAR), which breaks ignorability and induces selection bias even after conditioning on states and actions. To address this, we formalize a reward-dependent propensity model and use future states as shadow variables to identify the full-data conditional mean reward. We further introduce a bridge function that recovers the conditional mean reward without explicitly modeling the MNAR mechanism, and estimate it via a min-max procedure to avoid double sampling. Building upon these identification results, we propose an Fitted-Q-Evaluation-style estimator that propagates the recovered rewards while allowing target policies to depend on past missingness indicators. Finally, we establish consistency and finite-sample error bounds for our OPE estimator, and show through experiments the strong performance of our method compared to existing methods on simulated and MIMIC-III Sepsis data.

19.
bioRxiv (Bioinfo) 2026-06-22

When Less Is Not More: DICEPro Mitigates the Impact of Incomplete Reference Matrices on Cellular Frequency Deconvolution.

Cellular deconvolution aims to estimate the frequencies of different cell populations from gene expression measurements in a biological sample. Supervised approaches, such as CIBERSORTx and DISSECT, critically depend on the reference signature matrix, which encodes the gene expression profiles of cell-types based on prior knowledge. Despite numerous deconvolution methods, the impact of missing cell populations in the reference matrix remains understudied. Here, we evaluate the robustness of state-of-the-art deconvolution approaches using simulations based on real dataset examples combined with statistical modeling, validated against published data, and multiple real benchmark datasets. Results show that deconvolution performance remains stable when the reference matrix includes most cell-types, but declines sharply as the matrix becomes incomplete, especially for abundant cell populations. To address the limitations of incomplete reference matrices, we introduce DICEPro, an optimization-based framework designed to enhance existing deconvolution methods. By systematically adjusting the reference signatures, DICEPro better accounts for missing or underrepresented cell populations, leading to improved precision and robustness. We show that DICEPro consistently boosts deconvolution performance across both simulated datasets, derived from real data examples, and multiple real biological datasets, offering a practical solution when standard methods are hindered by incomplete references.

20.
arXiv (CS.AI) 2026-06-15

Actionable Interpretability Must Be Defined in Terms of Symmetries

arXiv:2601.12913v4 Announce Type: replace Abstract: This paper argues that interpretability research in Artificial Intelligence (AI) is fundamentally ill-posed as existing definitions of interpretability fail to describe how interpretability can be formally tested or designed for. We posit that actionable definitions of interpretability must be formulated in terms of *symmetries* that inform model design and lead to testable conditions. Under a probabilistic view, we hypothesise that four symmetries (inference equivariance, information invariance, concept-closure invariance, and structural invariance) suffice to (i) formalise interpretable models as a subclass of probabilistic models, (ii) yield a unified formulation of interpretable inference (e.g., alignment, interventions, and counterfactuals) as a form of Bayesian inversion, and (iii) provide a formal framework to verify compliance with safety standards and regulations.

21.
arXiv (quant-ph) 2026-06-12

Scalar Quantum Fields: Theory Space and its Geometry

arXiv:2606.12580v1 Announce Type: cross Abstract: Scalar fields provide perhaps the simplest playground in which to develop our understanding of quantum field theory. In this lecture, we consider what it means to write down a scalar quantum field theory and how we can give geometrical interpretations to the space of such theories: the theory space.

22.
arXiv (CS.LG) 2026-06-19

Integrating national forest inventory, airborne lidar, and satellite imagery for wall-to-wall mapping of forest structure with computer vision

arXiv:2606.20291v1 Announce Type: new Abstract: Remote sensing is increasingly relied upon to deliver actionable science for forest and wildfire risk management across large landscapes. Wall-to-wall, annually updated maps are a persistent need for effective forest management. Many planning systems and data collections combine disparate data sources with different purposes, vintages, and prediction quality, which leads to confounding behavior in operational planning systems. We introduce the VibrantForests framework, developed and applied to map forest attributes and provide a coherent foundation for effective forest and wildfire planning. VibrantForests includes a satellite-based forest structure model trained on lidar-derived samples and applied across the contiguous United States to concurrently generate estimates of canopy cover, canopy height, aboveground live tree biomass, basal area, and quadratic mean diameter at 10-meter resolution. We demonstrate predictive capability spanning the full spectrum of forest conditions ranging from sparse-canopy/low-biomass to dense-canopy/high-biomass. Results show that our model extends the range at which saturation is commonly encountered in comparable passive-sensor models, and reduces regression-to-mean behavior that commonly produces overestimation of forest attributes in small/sparse conditions and underestimation in large/dense conditions. The VibrantForests framework addresses a key limitation in large-area forest and wildfire planning by delivering coherent wall-to-wall estimates of management-relevant attributes at annual cadence and 10m resolution.

23.
arXiv (quant-ph) 2026-06-15

Extending Covariant Fluctuation Theorems into Quantum Regime through Quasiprobability Approach

arXiv:2606.14519v1 Announce Type: cross Abstract: The covariant formulation of stochastic thermodynamics requires treating the stochastic work as a 4-vector, posing significant challenges for quantum systems due to the non-commutativity. We introduce a new quasiprobability distribution for the work 4-vector, which combines the Wigner and Margenau-Hill quasiprobabilities. This extends the covariant fluctuation theorems from classical to quantum regime. We illustrate our findings with a scalar field driven by classical particles with a generalized version of trace formula. Our work establishes a quasiprobability approach to studying relativistic quantum thermodynamics in a covariant way.

24.
bioRxiv (Bioinfo) 2026-06-22

Reference-guided immune recovery matching prioritizes traditional Chinese medicine ingredients

Therapeutic prioritization from single-cell transcriptomes requires a target that is closer to treatment response than disease-signature reversal. In immune diseases, post-treatment recovery may follow patient- and cell-type-specific trajectories rather than a simple return along the pretreatment disease axis. We developed ImmuneNavi, a healthy-reference-anchored recovery-matching workflow for ranking traditional Chinese medicine ingredients from paired PBMC data. The workflow maps heterogeneous PBMC cohorts to a common healthy immune coordinate system, constructs patient-cell-type disease and recovery states, and processes ITCM treated-control profiles into a fixed ingredient perturbation bank. Patient and ingredient states are represented in matched gene, pathway and transcription-factor views, allowing the model to combine local transcriptional direction with more stable program-level features. A matcher trained on one paired treatment cohort preserved recovery-aligned ingredient rankings in independent PBMC cohorts without redefining the feature space, candidate set or preprocessing procedure. This provides a reusable transcriptomic pipeline for moving from paired immune-state measurements to prioritized natural-product candidates for experimental follow-up.

25.
arXiv (CS.CL) 2026-06-15

ADORE: Iterative Query Expansion with Retrieval-Grounded Relevance Feedback

LLM-based query expansion improves retrieval by enriching the original query with additional context. Yet most methods remain generation-driven, producing plausible pseudo-documents or expansions without checking how the target corpus responds. This can introduce retrieval drift, amplify misleading vocabulary, or miss terms that distinguish relevant from non-relevant documents. We argue that effective expansion requires retrieval-grounded feedback, not just single-pass generation or unverified iteration. We introduce ADORE (ADapt, Observe, Relevance Evaluate), an iterative framework that turns retrieval outcomes into feedback for the next expansion. At each round, an LLM generates pseudo-passages, a retriever exposes the corpus response, and a relevance assessor evaluates retrieved documents against the original query. These judgments identify what to reinforce, what remains undercovered, and what to suppress. Across TREC Deep Learning, BEIR, and BRIGHT, ADORE consistently outperforms strong query expansion baselines with notable improvements across nearly all evaluation settings, improving average nDCG@10 by 24.5% over BM25 and 3.6% over the strongest prior query expansion method on BEIR, and by 122.9% over BM25 and 9.2% over the best query expansion baseline on BRIGHT. Our code and data are publicly available.