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.CL) 2026-06-24

MEMPROBE: Probing Long-Term Agent Memory via Hidden User-State Recovery

Long-term memory promises LLM agents that grow more capable across sessions, maintaining an accurate, evolving understanding of the user that interaction forms. In practice, however, this memory is evaluated mostly through downstream behavior, such as later answers, personalization quality, or task success, which tests that understanding only indirectly and leaves the memory artifact itself largely unaudited. We argue that long-term memory should instead be evaluated as an auditable post-interaction artifact: after ordinary assistance, what structured user state can be reconstructed from the memory the agent leaves behind? We instantiate this view in MEMPROBE, a benchmark in which a memory-equipped agent assists simulated users, each carrying a hidden, taxonomy-anchored user-state bank, across a trajectory of leak-controlled tasks, after which that bank is reconstructed from the agent's resulting memory under both full-store and top-k access. Built on synthetic ground truth for efficient, scalable measurement, MEMPROBE spans 50 simulated users with 31 hidden dimensions each (1,550 recovery targets) and tests 5 representative memory systems. Testing state-of-the-art memory agents, we find that successful assistance and recoverable memory behave as distinct capabilities. Task completion nearly saturates, even for a memoryless baseline, while category-balanced recovery stays moderate (about 0.6) and drops further under top-k retrieval. MEMPROBE is the first benchmark to study memory recovery directly, reconstructing the user state a system retains and scoring it against ground truth. We see recovery as a concrete objective for future memory agents to optimize, and MEMPROBE as a step toward an environment where agents are trained to remember their users, growing more faithful the longer they know them.

02.
arXiv (CS.CL) 2026-06-12

M\"OVE: A Holistic LLM Benchmark for the German Public Sector

We present M\"OVE (Modelle für die \"Offentliche Verwaltung Evaluieren), a holistic benchmark for evaluating large language models (LLMs) in the context of the German public sector. While LLMs are increasingly adopted in public administration, model selection remains largely ad hoc, and existing benchmarks offer limited guidance: they are predominantly English-centric, US-centric in content, and focus exclusively on task performance. M\"OVE addresses these gaps by evaluating 39 models across two complementary dimensions. Performance criteria cover summarization, question answering, and topic extraction. Governance criteria assess hallucination tendencies, energy consumption, provider transparency, and alignment with German constitutional values and knowledge about positions by German political parties. In total, we utilize ten German-language datasets, including gold- and silverstandard datasets that we constructed to reflect public-administration domains. We employ a multi-metric evaluation strategy combining classical NLP metrics, embedding-based methods, and LLM-as-a-judge approaches. Our results show that no single model dominates across all criteria: top performers differ between tasks, and model size alone is a poor predictor of quality. We further evaluate the benchmark itself, analyzing its statistical precision, LLM judge reliability, the impact of our private datasets on model rankings, the sensitivity of our results to prompt formulation, and the validity of our energy consumption estimates. M\"OVE is designed as a living benchmark under active development; results are publicly available at https://moeve.bundesdruckerei.de/.

03.
arXiv (math.PR) 2026-06-17

Cutoff for asymmetric shelf shuffle

arXiv:2606.18039v1 Announce Type: new Abstract: A mechanical shuffler consists of $m$ shelves. A deck of $n$ cards, arranged in increasing order, is dealt from the bottom sequentially. Each card is assigned a shelf uniformly at random and placed on the top (bottom) of the existing pile with probability $p$ ($1-p$) independently. We refer to this as asymmetric shelf-shuffle. We find the law $\nu_{n, m}^{(p)}$ of the permutation induced by the asymmetric shelf-shuffle and show that the pair consisting of the number of descents and the number of valleys is a sufficient statistic. This generalizes a result of Diaconis, Fulman, and Holmes (Ann. Appl. Prob., 2013) corresponding to the case $p=1/2$. For $p=1/2$, Chen and Ottolini (ECP, 2025) established the cutoff in the total variation distance near $\lfloor n^{5/4}\rfloor$. We establish the cutoff for the asymmetric shelf shuffle. Let $\nu_n$ be the uniform measure on the set of all permutations $S_n$ of $\{1, \ldots, n\}$. For a fixed $p\neq 1/2$ and $c>0$, we show that \[\operatorname{TV}\left(\nu_{n, \lfloor cn^{3/2}\rfloor }^{(p)}, \nu_n\right)=1-2\Phi\left(-\frac{|2p-1|}{4\sqrt{3}c}\right)+O_{c, p}(n^{-1/2})\;.\] We also establish the cutoff in the separation distance near $m\approx n^{2}$ and in the relative entropy near $m=n^{3/2}$. In both cases, we also obtain the cutoff profile explicitly.

04.
medRxiv (Medicine) 2026-06-12

Immunologically Optimized Zmp1 Peptides Reveal a Translational Serological Biomarker Platform for Tuberculosis Diagnosis Across Disease Manifestations

Tuberculosis (TB) diagnosis remains challenging, particularly for extrapulmonary TB (EPTB), where invasive sampling, low bacillary burden, and suboptimal sensitivity of nucleic acid-based tests in peripheral specimens hinder timely detection. Here, we report an immunology-driven strategy for biomarker discovery and development of a peptide-based serological assay targeting Mycobacterium tuberculosis zinc metalloprotease-1 (Zmp1). Leveraging fundamental principles of adaptive immunity that antigenic regions containing overlapping B-cell and CD4 T-helper cell epitopes would preferentially generate high antibody titers through linked recognition and cognate T-cell help, we used an immunoinformatics pipeline to identify two nested immunodominant peptide regions within Zmp1 (Mtb-Zp-NT and Mtb-Zp-CT) enriched for overlapping B- and T-cell epitopes. The diagnostic potential of these peptides was evaluated through ELISA-based serological assays. A blinded pilot study (N=137) demonstrated a clear discrimination between active TB and TB-recovered individuals. The assay was subsequently validated in an expanded cohort (N=875) by screening 6,086 individuals, which identified 457 TB-positive cases. The cohort included pulmonary TB (PTB), EPTB, TB-recovered individuals, household contacts, non-specific infections, and healthy controls. Receiver operating characteristic analyses, supported by DeLong and bootstrap comparisons, revealed superior diagnostic performance of the peptide-based assays relative to full-length Zmp1. Mtb-Zp-CT exhibited the highest accuracy (AUC=0.93; specificity >90%), while Mtb-Zp-NT also demonstrated strong discriminatory power (AUC{approx}0.89). These findings establish that the immunologically optimized Zmp1 peptides are highly promising serological biomarkers for TB and EPTB. More broadly, they demonstrate how mechanistically informed epitope selection can accelerate translation of pathogen-specific immune signatures into sensitive, minimally invasive, and potentially point-of-care diagnostic platforms for resource-limited settings.

05.
arXiv (CS.CV) 2026-06-12

PROBE: Probabilistic Occupancy BEV Encoding with Analytical Translation Robustness for 3D Place Recognition

We present PROBE (PRobabilistic Occupancy BEV Encoding), a learning-free LiDAR place recognition descriptor that models each BEV cell's occupancy as a Bernoulli random variable. Rather than relying on discrete point-cloud perturbations, PROBE analytically marginalizes over continuous Cartesian translations via the polar Jacobian, yielding a distance-adaptive angular uncertainty $\sigma_\theta = \sigma_t / r$ in $\mathcal{O}(R{\cdot}S)$ time. The primary parameter $\sigma_t$ represents the expected translational uncertainty in meters, a sensor-independent physical quantity that enhances cross-sensor generalization while reducing the need for extensive per-dataset tuning. Pairwise similarity combines a Bernoulli-KL Jaccard with exponential uncertainty gating and FFT-based height cosine similarity for rotation alignment. Evaluated on four datasets spanning four diverse LiDAR types, PROBE achieves the highest accuracy among handcrafted descriptors in multi-session evaluation and competitive single-session performance relative to both handcrafted and supervised baselines. The source code and supplementary materials are available at https://sites.google.com/view/probe-pr.

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

Generalized two-qubit Hamiltonian for Projective Quantum Feature Maps

arXiv:2606.13641v1 Announce Type: new Abstract: Projected quantum feature maps provide a strategy for using quantum processors as feature generators for classical machine-learning models. Building on counterdiabatic Ising-glass and one-dimensional Heisenberg PQFMs, we introduce a generalized two-qubit Hamiltonian-based PQFM that provides a unified way to encode classical features through local Pauli fields and pairwise two-qubit Pauli interactions. This construction allows distinct classical variables to be embedded along different Pauli axes of the same qubit, increasing the information density of shallow circuits while remaining compatible with hardware constraints. We develop and implement these methods in pqfmlib, a publicly available Python library for constructing, executing, and benchmarking Hamiltonian-based PQFMs.We then benchmark the generalized Hamiltonian PQFMs against reference PQFMs on four biomedical classification datasets under a nested cross-validation protocol with paired statistical tests. Quantum features are generated using both IBM quantum processors with up to 156 qubits and statevector simulations. Our results show that the generalized two-qubit Hamiltonian family provides the most consistent pattern of statistically supported gains over matched classical baselines, although the performance of all methods depends on the dataset, encoding strategy, measured observables, and hardware conditions. These findings support generalized Hamiltonian PQFMs as a promising route toward near-term quantum utility.

07.
arXiv (CS.LG) 2026-06-12

Variational Graph Neural Networks for Uncertainty Quantification in Inverse Problems

arXiv:2603.29515v2 Announce Type: replace Abstract: The increasingly wide use of deep machine learning techniques in computational mechanics has significantly accelerated simulations of problems that were considered unapproachable just a few years ago. However, in critical applications such as Digital Twins for engineering or medicine, fast responses are not enough; reliable results must also be provided. In certain cases, traditional deterministic methods may not be optimal as they do not provide a measure of confidence in their predictions or results, especially in inverse problems where the solution may not be unique or the initial data may not be entirely reliable due to the presence of noise, for instance. Classic deep neural networks also lack a clear measure to quantify the uncertainty of their predictions. In this work, we present a variational graph neural network (VGNN) architecture that integrates variational layers into its architecture to model the probability distribution of weights. Unlike computationally expensive full Bayesian networks, our approach strategically introduces variational layers exclusively in the decoder, allowing us to estimate cognitive uncertainty and statistical uncertainty at a relatively lower cost. In this work, we validate the proposed methodology in two cases of solid mechanics: the identification of the value of the elastic modulus with nonlinear distribution in a 2D elastic problem and the location and quantification of the loads applied to a 3D hyperelastic beam, in both cases using only the displacement field of each test as input data. The results show that the model not only recovers the physical parameters with high precision, but also provides confidence intervals consistent with the physics of the problem, as well as being able to locate the position of the applied load and estimate its value, giving a confidence interval for that experiment.

08.
arXiv (quant-ph) 2026-06-17

Post-Selection Probability and Fidelity of Bidirectional Teleportation

arXiv:2606.17251v1 Announce Type: new Abstract: Understanding the scrambling of quantum information is central to many areas of quantum physics, including quantum thermalization, entanglement growth, and quantum information processing. Insights from these studies have, in turn, inspired the development of novel quantum protocols and algorithms. Recently, a bidirectional teleportation protocol was proposed to implement a digital SWAP operation between qubits by leveraging chaotic Hamiltonian evolution combined with measurement and post-selection. In this work, we provide a comprehensive study of two central quantities that characterize the protocol, the post-selection probability and the fidelity, taking into account possible errors in time-reversed dynamics. We show that these quantities can be expressed in terms of standard diagnostics in quantum dynamics, including the Loschmidt echo and its subsystem variant. The results unveil (1) the initial-state dependence of the fidelity and (2) the stability of the post-selection probability in integrable models. Our findings offer practical guidance for the implementation of the protocol on realistic quantum devices.

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

Self-Preference Is Weak or Absent in Verifiable Instruction-Following Revision: A Four-Model Test Under Genuine Authorship

Large language models (LLMs) increasingly review and revise text, including their own. A documented self-preference bias (models favoring their own generations when acting as judges) raises the question of whether models also resist valid corrections to their own writing. We test this in a setting where "valid" is decided not by another model but by a deterministic verifier: instruction-following revision on IFEval. A model writes a draft; the official IFEval checker confirms the draft violates a constraint and that a candidate edit fixes it; the model then accepts or rejects that edit either as the genuine in-context author or as a fresh model that sees the draft neutrally. Across four mid-tier model families and 85 author-versus-fresh comparisons, we find no detectable self-preference: authors reject verified-good fixes to their own drafts at essentially the same rate as fresh models judging the same drafts (gap -5.1 pp, 95% CI [-12.9, +2.7]). A self-skepticism hint from a smaller pilot did not replicate at scale. The one robust observation is qualitative: when authors do reject a verified-good fix, 97% of their stated reasons are flaw-catching rather than preference, that is, about the character of rejections, not an elevated rate. Effects smaller than ~13 pp cannot be excluded at this sample size.

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

JourneyFormer: Encoding Airbnb Guest Journey with Sequence Modeling

arXiv:2606.19108v1 Announce Type: new Abstract: Sequence modeling has become increasingly popular in recommendation and ranking algorithms, owing to its capacity to model users' historical behaviors and infer user intentions. Despite its theoretical simplicity, the practical deployment of a sequence model in production is non-trivial due to complexity of the sequence and sparse labels. For example, in Airbnb, guest sequences are often long, exploratory and complex, and we focus on booking labels, which are sparse. As such, we are often required to make various design decisions regarding data and modeling to strike a balance between effectiveness and scalability. This work delved into these production challenges and deployed JourneyFormer, a sequence modeling solution for search ranking at Airbnb. We detail crucial design considerations, covering aspects such as guest event selection, ID embeddings, model architecture, and label attribution. Additionally, we describe several tailored strategies to accelerate model training and inference. JourneyFormer has been successfully deployed within Airbnb's production, where its effectiveness and impact have been evidenced not only by improved offline ranking metrics but also by significant gains in key business metrics through online A/B testing across 2 production surfaces.

11.
arXiv (quant-ph) 2026-06-19

Quantum Entanglement Degree, Mean Positronium Lifetime, and the $3\gamma$/$2\gamma$ Annihilation-Rate Ratio as Novel PET Biomarkers for Hypoxia – Concept, Challenges, and Predictions

Authors:

arXiv:2605.00021v3 Announce Type: replace-cross Abstract: This manuscript introduces a novel method to assess tissue oxygen concentration via the quantum entanglement (QE) of photons originating from positronium which is produced within the patient's body during positron emission tomography. We also investigate the possibility of assessing hypoxia by simultaneously detecting positronium lifetime and the positronium decay rate ratio. We introduce two distinct quantum sensing approaches. Method 1 utilizes the correlation between oxygen concentration and ortho-positronium (o-Ps) decay rates, relying on the simultaneous measurement of the mean o-Ps lifetime ($\tau_{\mathrm{oPs}}$) and the $3\gamma$-to-$2\gamma$ annihilation rate ratio of o-Ps ($R_{\mathrm{oPs-3\gamma/2\gamma}}$). Method 2 introduces a novel hypothesis: that the degree of QE is sensitive to the relative contribution of annihilation mechanisms (pick-off vs. conversion), which in turn depends on oxygen concentration. We derive a formula for partial pressure of oxygen ($p\mathrm{O}_2$) as a function of $R_{\mathrm{oPs-3\gamma/2\gamma}}$ and $\tau_{\mathrm{oPs}}$ and estimate the measurement accuracy required for these parameters - and for the degree of QE - to sense in-vivo oxygen pressure in the range between hypoxic and physoxic conditions. Theoretical models and quantitative estimates for $R_{\mathrm{oPs-3\gamma/2\gamma}}$, $\tau_{\mathrm{oPs}}$ and for the degree of QE ($C_{\mathrm{QE}}$ ) as a function of $p\mathrm{O}_2$ are provided for water, isopropanol, cyclohexane, isooctane, and adipose tissue. In particular, applying the formulas derived under the working hypothesis that in pick-off process the photons are not entangled, we estimated that for $p\mathrm{O}_2 = 0$, the degree of quantum entanglement $C_{\mathrm{QE}}$ is equal to 0.890 for adipose, 0.886 for isopropanol, 0.867 for water, 0.818 for cyclohexane, and 0.784 for isooctane.

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

Geometric Action Model for Robot Policy Learning

Generalist robot policies must follow user instructions while reasoning about how objects, cameras, and robot actions interact in the 3D physical world. Recent vision-language-action models (VLAs) and video world-action models (WAMs) inherit strong semantic or temporal priors from large-scale foundation models, but they still operate primarily on 2D image frames or 2D-derived latent spaces, leaving implicit the 3D geometry required for contact-rich manipulation. We propose the Geometric Action Model (GAM), a language-conditioned manipulation policy that directly repurposes a pretrained geometric foundation model (GFM) as a shared substrate for perception, temporal prediction, and action decoding. GAM splits the GFM at an intermediate layer: the shallow layers serve as an observation encoder, and a causal future predictor inserted at the split layer forecasts future latent tokens conditioned on language, proprioception, and action history. The predicted future tokens are then routed through the remaining GFM blocks for feature propagation and decoding, allowing a single backbone to produce both future geometry and actions. This design equips the GFM with language-conditioned temporal world modeling through minimal architectural modification while preserving its rich geometric priors. Across a broad suite of simulation and real-robot manipulation benchmarks, GAM is more accurate, more robust, faster, and lighter than current foundation-model-scale baselines.

13.
medRxiv (Medicine) 2026-06-15

Identifying the risk profile of anemia subtypes and hemodynamic obstetric complications in relation to peripartum cardiomyopathy

Background: Peripartum cardiomyopathy (PPCM) is a leading cause of maternal mortality worldwide, with worse outcomes associated with African Ancestry and delayed presentation. However, the mechanisms underlying PPCM are incompletely understood. Objective: Use a large, nationwide cohort to explore associations between PPCM and underexplored perinatal risk factors and complications of childbirth. Methods: Public hospital discharge data were obtained from eleven U.S. states between 2003-2019. Delivery hospitalizations, patient characteristics and obstetric complications were identified using ICD-9 and -10 CM codes. Only cases with unique patient identifiers enabling readmission analysis were included. The primary outcome was incident PPCM coded between 30 days antepartum and 150 days postpartum. Results: Of 7,424,916 delivering patients, 5,488 patients were diagnosed with PPCM. Patients with PPCM had higher rates of anemia, anemia of chronic disease (ACD), iron deficiency anemia (IDA), sickle cell disease (SCD), sickle cell trait (SCT), red blood cell (RBC) transfusion, and postpartum hemorrhage (PPH) (p

14.
arXiv (CS.CL) 2026-06-18

ASyMOB: Algebraic Symbolic Mathematical Operations Benchmark

Large language models (LLMs) are increasingly applied to symbolic mathematics, yet existing evaluations often conflate pattern memorization with genuine reasoning. To address this gap, we present ASyMOB, a high-resolution dataset of 35,368 validated symbolic math problems spanning integration, limits, differential equations, series, and hypergeometrics. Unlike prior benchmarks, ASyMOB systematically perturbs each seed problem using symbolic, numeric, and equivalence-preserving transformations, enabling a fine-grained assessment of generalization. Our evaluation reveals three key findings: (1) most models' performance collapses under minor perturbations, while top systems exhibit an apparent regime shift in robustness; (2) integrated code tools stabilize performance, particularly for weaker models; and (3) we identify examples where Computer Algebra Systems (CAS) fail while LLMs succeed, as well as problems solved only via a hybrid LLM-CAS approach, highlighting a promising integration frontier. ASyMOB serves as a principled diagnostic tool for measuring and accelerating progress toward building verifiable, trustworthy AI for scientific discovery.

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

Chemical tuning of magnetic ordering and cryogenic magnetocaloric response in zircon-type Gd1-xErxVO4

arXiv:2606.08916v2 Announce Type: replace-cross Abstract: Chemical substitution offers an effective route to tune magnetic ordering and magnetocaloric performance in rare-earth oxides for cryogenic refrigeration. Here we investigate the structural evo lution, magnetic properties, and magnetocaloric effect of polycrystalline zircon-type Gd1-xErxVO4 (x=0, 0.1, 0.25, 0.5, and 0.75). Powder X-ray diffraction confirms that all samples crystallize in the tetragonal zircon structure without detectable impurity phases. Substitution of Gd3+ by the smaller Er3+ ion produces a systematic lattice contraction and modifies the magnetic behavior of the rare-earth sublattice. In particular, the magnetic ordering temperature is suppressed from 3.65(2) K in GdVO4 to 2.76(2) K in Gd0.9Er0.1VO4 , accompanied by a weakening of the spin-flop-like field-induced anomaly observed in the parent compound. A low Er concentration correspondingly improves the low-temperature magnetocaloric performance, with Gd0.9Er0.1VO4 exhibiting a max imum magnetic entropy change of 45.1 J kg-1 K-1 for mu_0 Delta H=7T. These results demonstrate that weak Er substitution effectively tunes the competition among exchange interactions, dipolar coupling, and magnetic anisotropy, optimizing the balance between magnetic ordering and available spin entropy in zircon-type rare-earth vanadates, which is crucial for developing efficient cryogenic refrigeration materials.

16.
arXiv (quant-ph) 2026-06-24

How Events Separated by a Timelike Interval Can Help Us Understand Quantum Nonlocality

arXiv:2604.03744v2 Announce Type: replace Abstract: Quantum entanglement plays a fundamental role in quantum cryptography and computation. An important example of quantum entanglement can be found in the correlations of Einstein, Podolsky, and Rosen (EPR). However, despite the plethora of articles related to the topic, different interpretations of the EPR correlations coexist, and a consensus has not yet been reached. In this article, we seek to demonstrate, through the simple and direct application of quantum formalism, how events separated by timelike intervals can, strangely enough, help us better understand some aspects of the so-called "quantum nonlocality" associated with EPR correlations.

17.
Nature Medicine 2026-06-17

General-purpose chatbots outperform clinical AI tools on physicians’ real-world questions

Authors: Unknown Author

Specialized clinical AI tools are entering medical practice with little independent testing. In a head-to-head evaluation across two public benchmarks and real questions from physicians, three general-purpose frontier large language models outperformed two leading clinical AI tools, which performed no better than Google search AI overview.

18.
PLOS Computational Biology 2026-06-22

Adhesion and polarity-driven morphogenesis: Mechanisms and constraints in tissue formation

by Yoshiyuki T. Nakamura, Chikara Furusawa, Kunihiko Kaneko Embryonic development in multicellular organisms exhibits diverse morphogenetic patterns, which can generally be categorized into fundamental types such as monolayer and multilayer spheres, as well as cell masses. Furthermore, we identify two distinct processes for the formation of spherical structures. These basic patterns are thought to be governed by the microscopic properties of intercellular adhesion. However, the specific mechanisms linking the microscopic factors to the emergence of distinct macroscopic morphogenetic patterns remain poorly understood. In this study, we explore how different morphogenetic patterns arise by employing a computational model that incorporates intercellular adhesion and polarity. Our results demonstrate that all fundamental morphogenetic patterns can be generated through the interplay of two key parameters: the polarity strength of the cell and the regulation of polarity via mechanical signals. Furthermore, analytical considerations reveal key mechanisms underlying the formation of these patterns. These findings highlight the critical role of physical constraints in morphogenesis and suggest potential applications to the design of artificial tissues and organoids.

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

Mechanisms of Introspective Awareness

arXiv:2603.21396v5 Announce Type: replace Abstract: Recent work has shown that LLMs can sometimes detect when steering vectors are injected into their residual stream and identify the injected concept – a phenomenon termed "introspective awareness." We investigate the mechanisms underlying this capability in open-weights models. First, we find that it is behaviorally robust: models detect injected steering vectors at moderate rates with 0% false positives across diverse prompts and dialogue formats. Notably, this capability emerges specifically from post-training; we show that preference optimization algorithms like DPO can elicit it, but standard supervised finetuning does not. We provide evidence that detection cannot be explained by simple linear association between certain steering vectors and directions promoting affirmative responses. We trace the detection mechanism to a two-stage circuit in which "evidence carrier" features in early post-injection layers detect perturbations monotonically along diverse directions, suppressing downstream "gate" features that implement a default negative response. This circuit is absent in base models and robust to refusal ablation. Identification of injected concepts relies on largely distinct later-layer mechanisms that only weakly overlap with those involved in detection. Finally, we show that introspective capability is substantially underelicited: ablating refusal directions improves detection by +53%, and a trained bias vector improves it by +75% on held-out concepts, both without meaningfully increasing false positives. Our results suggest that this introspective awareness of injected concepts is robust and mechanistically nontrivial, and could be substantially amplified in future models. Code: https://github.com/safety-research/introspection-mechanisms.

20.
arXiv (quant-ph) 2026-06-19

Progress on the Kretschmann-Schlingemann-Werner Conjecture

arXiv:2308.15389v4 Announce Type: replace Abstract: Given any pair of quantum channels $\Phi_1,\Phi_2$ such that at least one of them has Kraus rank one, as well as any respective Stinespring isometries $V_1,V_2$, we prove that there exists a unitary $U$ on the environment such that $\|V_1-({\bf1}\otimes U)V_2\|_\infty\leq\sqrt{2\|\Phi_1-\Phi_2\|_\diamond}$. Moreover, we provide a simple example which shows that the factor $\sqrt2$ on the right-hand side is optimal, and we conjecture that this inequality holds for every pair of channels.

21.
Nature Biotechnology 2026-06-23

Mapping and engineering the human cell–cell interactome

Authors:

Efforts to systematically understand how cell interactions tune tissue-level function have motivated transformative advances in single-cell transcriptomics and spatial profiling. Although these technologies can measure molecular states in individual cells and their spatial mapping within tissues, they also reveal that there exists a fundamental knowledge gap of how cells influence each other in context. In this Perspective, we propose an initiative to map and engineer the human cell–cell interactome: a functional atlas of how all major human cell types communicate. We highlight how recent innovations can make this vision achievable. As a first moonshot, we propose the ‘Billion Cell×Cell Project’, which systematically characterizes the outcomes of defined cell–cell dyads across diverse cell types and conditions. We envision this multistage initiative will produce progressively deeper insights and unlock additional avenues for therapeutic discovery. We call on the scientific community to join us in building the tools, datasets and models that will decode and rewrite the language of life between cells. Di Carlo and colleagues discuss technologies required to map and engineer the human cell–cell interactome and the therapeutic avenues such an atlas could unlock.

22.
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.

23.
bioRxiv (Bioinfo) 2026-06-23

EnrichViz: An Interactive R Shiny Application for Visualization of Pathway Enrichment Results from Omics Data

Authors:

Pathway and functional enrichment analysis is a cornerstone of omics data interpretation, enabling researchers to map differentially expressed proteins or genes onto curated biological processes, signaling cascades, and molecular functions. While tools such as Ingenuity Pathway Analysis (IPA), g:Profiler, and Enrichr are widely used to generate ranked enrichment results, translating these tabular outputs into clear, publication-ready figures remains a time-consuming step that typically requires custom scripting and familiarity with visualization libraries, a significant barrier for researchers without a computational background. Here we present EnrichViz, a self-contained, browser-based R Shiny application that enables interactive, code-free visualization of pathway and functional enrichment results from quantitative proteomics, transcriptomics, and metabolomics experiments. EnrichViz accepts three standard CSV files as input, a normalized abundance matrix, a sample annotation or metadata file, and enrichment results from any platform that exports tabular output, and produces six complementary, publication-ready visualizations: bar and bubble plots for ranking enriched terms by significance, chord diagrams for exploring pathway-molecule connectivity, clustered heatmaps for displaying Z-score normalized expression patterns across experimental groups, and boxplots or violin plots for examining the abundance distribution of individual proteins, genes, or metabolites. The application supports both raw p-values and pre-transformed -log10(p) values through automatic detection, and all plot parameters are adjustable in real time through a graphical sidebar. Every figure can be exported as a high-resolution PNG file at 300 dpi. EnrichViz is implemented in R using the Shiny, ggplot2, pheatmap, and circlize packages, and is freely available at https://rgmilian.shinyapps.io/EnrichViz/

24.
bioRxiv (Bioinfo) 2026-06-08

TRACEY: an updated resource for SNARE protein domain annotation with improved HMMs and expanded sequence coverage

Motivation: SNARE proteins catalyse membrane fusion across the eukaryotic endomembrane system, from synaptic vesicle exocytosis to intracellular trafficking, endosomal and vacuolar transport, and autophagy, and their accurate domain annotation depends on the quality of profile models and the sequence diversity behind them. The original SNARE domain classification predates the recent expansion of eukaryotic sequence data, leaving its HMM profiles and subgroup coverage unable to resolve divergent and lineage-specific paralogs. Results: We present an updated release of TRACEY built on a resynchronized, non-redundant collection of 18,915 curated SNARE proteins spanning 1,188 species, together with a consolidated set of 83 HMM profiles, including 43 models for newly defined subgroups, reconstructed through an iterative, mixture-model-driven procedure. In direct comparison with the legacy models, at least ~75% of sequences in every overlapping group scored better with the new HMMs, indicating systematic gains in domain detection. A redesigned web interface adds multiparameter querying, FASTA download, and direct scanning of user-submitted sequences against the curated profiles. Availability and implementation: TRACEY is freely available at https://tracey.unil.ch.

25.
arXiv (CS.CV) 2026-06-24

Geometry-Instructed Video Editing

Object-level geometric edits, including translating, rotating, scaling, duplicating, or removing an object, are routine operations in digital content creation (DCC) workflows, yet they remain unreliable in generative video editing. The key challenge lies in specifying the target object's 3D state change unambiguously across viewpoint and time, while consistently updating geometry-dependent secondary effects such as shadows and reflections. We introduce GIVE, a geometry-instructed video editing framework that represents edits through a unified object-state formulation. Two video-aligned geometry streams describe the target object before and after editing: a depth-box encoding coarse 3D placement and extent, and an orientation-box providing an appearance-agnostic orientation cue. Together, these streams provide a compact pre/post geometric specification for object-state transitions. To provide paired supervision for learning these edits, we build a scalable graphics-engine pipeline that executes object-level edit programs and renders controlled before/after pairs, isolating the intended geometric edit while keeping secondary effects consistent with the transformation. Experimental results demonstrate that GIVE produces faithful geometric edits with temporal coherence and consistent secondary effects across operators in a unified framework, and shows promising transfer to in-the-wild videos. Project page: https://geometry-instructed-video-editing.github.io/give/