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01.
arXiv (CS.CV) 2026-06-18

APT: Atomic Physical Transitions for Causal Video-Language Understanding

Physical events are not understood by their names alone, but by the causal state changes that compose them. A clip-level label such as "bounce" can be correct while hiding the process that makes the event physically valid, from support loss and contact onset to rebound and settling. To make this hidden process explicit, we introduce Atomic Physical Transitions (APTs): minimal, temporally localized state changes that bind a visible cue to an active physical mechanism and before/after dynamical regimes. An APT chain represents a video as an ordered causal transition sequence rather than a single aggregate event label: event labels tell what happened; APT chains explain why it happened. To make APTs learnable by VLMs, we construct mixed-source APT data from human annotations and simulator ground truth, covering 14 transition types across contact, gravity, friction, and rotation/stability, with 27,303 timed instances over 1,246 trials. Using this data, we find that current VLMs miss transition-level physics, with zero-shot recall at most 14% and errors dominated by missed transitions. Direct fine-tuning on APT chains improves transition detection but causes event-level forgetting, indicating that the model learns a specialized answer format rather than a reusable physical representation. We therefore propose APT-Tune, a parameter-efficient recipe that teaches VLMs to use causal transitions without forgetting how to answer video questions. It combines image-pad-aware supervision, format-conditional co-training, and mechanism-conditioned domain-to-type decoding to make APT learning format-robust and physically grounded. With only 11 M LoRA parameters on Qwen3-VL-2B, APT-Tune substantially improves APT recall while also improving event-level video transfer. These results show that APTs are not a new answer format, but a human-aligned causal supervision signal for physical video understanding.

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

Inflationary branch decoherence and the cosmological arrow of time

Authors:

arXiv:2602.21263v3 Announce Type: cross Abstract: We analyze branch decoherence in inflationary quantum cosmology by computing reduced density matrices and branch-overlap factors for long-wavelength perturbations. The Hartle-Hawking no-boundary state is real in the semiclassical regime and contains both expanding and contracting WKB components, whereas the tunneling state is selected as an outgoing complex WKB branch; expanding-contracting decoherence is therefore central for the former and mainly diagnostic for the latter. Using the influence-functional formalism, we derive the noise kernel for a light spectator environment and evaluate decoherence under horizon-based and EFT-motivated coarse grainings. We then compute the single-mode branch overlap directly from the Bunch-Davies mode functions, obtaining $|\mathcal{D}_k(z)|=[z^2/(z^2+1)]^{1/4}$ in the massless limit and $|\mathcal{D}_k(z)|\sim z^\nu$ on superhorizon scales for massive fields, where $z=-k\eta$ is the dimensionless wavenumber with $\eta$ the conformal time. In the massless case, the accumulated geometric branch functional is evaluated in closed form, with a leading cutoff-sensitive phase-space term and a universal subleading contribution. The calculation provides an explicit quantitative bridge between quantum-cosmological boundary conditions, inflationary squeezing, and the emergence of effectively classical cosmological histories.

03.
arXiv (quant-ph) 2026-06-11

PHASE: Pauli Hierarchical Assembly on Subdivided Elements for Quantum-Compatible Operator Synthesis

arXiv:2606.11478v1 Announce Type: new Abstract: Efficiently decomposing finite element stiffness matrices into the Pauli basis is challenging due to the exponential growth of Pauli strings with problem size. A naive Pauli expansion requires $\Theta(8^{\lceil \log_2 N \rceil})$ operations, where $N$ denotes the number of degrees of freedom, rendering direct decomposition infeasible for large systems. Existing approaches exploit algebraic sparsity or operator structure but do not incorporate the geometric organization intrinsic to finite element discretizations, and consequently exhibit poor scaling for stiffness matrices. To address this problem, we introduce PHASE, a hierarchical, geometry-aware Pauli decomposition algorithm that leverages recursive mesh partitioning to organize element contributions across multiple spatial scales. PHASE employs a hybrid strategy that combines full- and reduced-space Tensorized Pauli Decomposition with Fast Walsh-Hadamard Transform-based aggregation to assemble global Pauli coefficients efficiently. We show that this approach yields a dimension-dependent reduction in the exponential scaling exponent of Pauli assembly asymptotic complexity relative to existing methods, reducing the cost from $2^{2{\lceil \log_2 N \rceil}}$ to $2^{\gamma_d{\lceil \log_2 N \rceil}}$ with $\gamma_d < 2$ under standard mesh regularity and balanced partition assumptions. These results substantially improve the feasibility of quantum-compatible operator synthesis for large-scale finite element models.

04.
medRxiv (Medicine) 2026-06-15

Non-invasive intracranial pressure waveform reconstruction with deep learning

Purpose: Continuous intracranial pressure (ICP) monitoring requires invasive instrumentation, reaching only a narrow subset of critically ill patients. We tested whether deep learning models trained on routinely acquired extracranial signals can reconstruct continuous ICP waveforms at clinically relevant accuracy in an independent external cohort. Methods: In adults admitted to the ICU at a single quaternary health system, five deep learning architectures were trained on high-frequency arterial blood pressure (ABP), photoplethysmography (PPG), and electrocardiography (ECG) waveforms, using invasive (intraparenchymal) ICP as ground truth. Two fusion strategies (early and late) and three training objectives (waveform-morphology, baseline robust regression, and weighted robust regression) were evaluated. Models were externally validated on the held-out MIMIC-III Waveform Database. Performance was assessed by mean absolute error (MAE) and waveform similarity by Pearson correlation (r). Results: We analyzed data from 158 critically ill adults (~5,322 hours) across two quaternary health systems (Johns Hopkins Hospital, Baltimore; Beth Israel Deaconess Medical Center, Boston). Validation MAE ranged from 4.276 mmHg [95% CI 4.269, 4.283] (gated recurrent, late fusion) to 4.946 mmHg [95% CI 4.938, 4.956] (attention-based, early fusion), with Pearson r ranging from 0.599 [95% CI 0.599, 0.600] to 0.722 [95% CI 0.722, 0.723]. The multiscale encoder-decoder model demonstrated the most favorable MAE-correlation tradeoff. Conclusion: This is the first demonstration that continuous ICP waveform reconstruction from bedside signals generalizes across institutions at clinically relevant accuracy, establishing a foundation for non-invasive ICP monitoring and motivating validation across broader populations and ICP ranges.

05.
Nature (Science) 2026-06-23

Daily briefing: NASA to launch satellite-rescue mission

Authors:

The space agency will lift the orbit of a falling satellite by around 200 kilometres. Plus, Europe’s efforts to take on the US and China as a science superpower and the narcissism of bosses who want to nix remote working. The space agency will lift the orbit of a falling satellite by around 200 kilometres. Plus, Europe’s efforts to take on the US and China as a science superpower and the narcissism of bosses who want to nix remote working.

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

Benchmark of quantum algorithms for ground state preparation in the presence of noise

arXiv:2606.20551v1 Announce Type: new Abstract: We compare the performance of representative cooling, adiabatic, and optimization algorithms for ground-state preparation in the presence of noise. Using an exactly solvable family of quadratic fermionic Hamiltonians subject to depolarizing noise, we derive the scaling of the achievable relative energy as a function of the noise rate and support these results with numerical simulations. The Hamiltonian exhibits two phases, separated by a quantum phase transition. As expected, the performance of the different algorithms depends on the phase: adiabatic evolution is favorable in the trivial phase, while a multi-frequency cooling algorithm, as proposed in [1], becomes competitive or superior in the topological phase, where gap-closing limits adiabatic protocols. We further present numerical results for the quantum approximate optimization algorithm [2], showing that it performs competitively with cooling in the trivial phase but is typically outperformed in the topological regime. Finally, we show that for this model the cooling protocol exhibits enhanced robustness to parameter imperfections, highlighting its potential advantage for realistic implementations of noisy quantum state preparation. The analytical approach developed here, in conjunction with numerical validation, establishes an extendable approach to benchmarking ground-state preparation algorithms.

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

Speculative Rollback Correction for Quality-Diverse Web Agent Imitation

arXiv:2606.12485v1 Announce Type: cross Abstract: Training interactive web agents through imitation learning from expert trajectories has emerged as a highly effective approach. However, determining the optimal timing for expert intervention presents a critical challenge in this context. Delayed intervention often leads to the accumulation of early-stage errors, pushing the page state into an irrecoverable regime. Conversely, premature or excessive intervention causes the agent to become overly reliant on expert policies, trapping the model in local optima characterized by a single, rigid trajectory. We propose Speculative Rollback Correction (SRC), a branch-level imitation framework for resettable agent environments. Instead of requesting teacher labels at every visited state or correcting only after a completed trajectory, SRC uses fixed-horizon branch review: the student executes a short speculative segment before teacher review, and the teacher localizes the first harmful deviation only when local progress breaks. Rollback preserves useful prefixes, while successful rollouts are filtered by a hard verifier and retained in a lightweight quality-diversity archive. The resulting data supports next-action supervised fine-tuning on both localized corrections and verifier-passing trajectories. On WebArena-Infinity, SRC collects 977 verifier-passing trajectories and 9,183 next-action examples; fixed-horizon review improves the recovery-versus-query tradeoff over step-level review while retaining verifier-passing solution variants. Code is available at https://github.com/LongkunHao/SRC_gui_agent.

08.
arXiv (CS.LG) 2026-06-19

An Information Theoretic Framework for Graph Novelty Generation via Latent Mixture Modeling

arXiv:2606.19770v1 Announce Type: new Abstract: We propose an information-theoretic framework for graph novelty generation, which aims to generate data that are distinct from existing patterns while preserving global structural consistency. Our approach embeds data into a latent space, models the latent distribution using finite mixture models, and generates novel samples by imposing explicit novelty and reliability conditions formulated in terms of description length. Specifically, novelty is enforced by requiring generated samples to be poorly explained by all existing mixture components, while reliability constrains their impact on the overall mixture structure under the Minimum Description Length (MDL) principle. We provide a theoretical analysis showing that, with appropriate threshold choices, the probabilities of misclassifying non-novel or unreliable samples converge to zero with explicit rates. Experiments on synthetic and benchmark graph datasets demonstrate that the proposed method enables principled novelty generation with quantifiable risk.

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

IHUBERT: Vector-Based Semantic Deduplication and Domain-Balanced Pretraining for Persian Resources

Persian pretrained language models (PLMs) are still limited by the scarcity of large-scale, high-quality pretraining corpora and by insufficient evaluation beyond standard classification and NER tasks. We present IHUBERT, a monolingual Persian PLM trained from scratch with the RoBERTa-base encoder (125M parameters) on a 45 GB curated subset of the Sepahr-Danesh collection (about 7-8B tokens). To improve corpus quality and reduce redundancy, we employ a multi-stage preprocessing pipeline that includes normalization, exact and near-duplicate removal, anonymization, and vector-database-based semantic deduplication for distribution balancing control across domains and registers. We additionally train a 139k-vocabulary BPE tokenizer on the full pretraining corpus to better capture Persian morphology and orthographic variation. IHUBERT is evaluated on seven Persian NLU benchmarks covering NER, sentiment analysis, topic classification, NLI, extractive question answering, and relation extraction, using task-standard metrics (entity-level F1, Macro-F1, EM/F1). IHUBERT achieves its strongest gains on extractive QA, ranking first on both PQuAD (F1 88.3542) and ParsiNLU-RC (F1 49.0987), and attains the best result on FarsTail (Macro-F1 0.8350). On NER and topic classification, it remains competitive (e.g., 0.8308 F1 on ParsTwiNER; 0.7953 Macro-F1 on DigiMag), while relation extraction remains the main remaining gap (0.6684 Macro-F1 on PERLEX). A controlled tokenizer ablation on the IHUBERT pretraining corpus shows that BPE yields slightly lower subword fragmentation than WordPiece at matched vocabulary size, supporting our tokenization design. Overall, IHUBERT advances Persian language modeling through semantically curated large-scale pretraining and broad evaluation across both classification and comprehension-oriented tasks.

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

The Algebra of Units: From Buckingham's Pi-grec Theorem to Latent-Variable Learning

arXiv:2606.16737v1 Announce Type: cross Abstract: Engineers often measure many quantities-speed, pressure, temperature, length-expressed in different physical units. The Buckingham Pi-grec theorem states that these variables can always be combined into a smaller set of dimensionless numbers whose values fully determine the system's behaviour. Identifying the appropriate dimensionless groups has traditionally required expert knowledge and physical insight. This paper shows that they can instead be discovered automatically from data, without prior knowledge of the governing physics. The key observation is that, after logarithmic transformation, measurements collected under different scalings of the same system lie on a low-dimensional manifold whose geometry is determined by the underlying dimensionless groups. Singular value decomposition (SVD) identifies this manifold directly from data. A subsequent search over integer-exponent combinations recovers candidate dimensionless quantities, while a repeating-variable filter retains only those constructed from the machine's characteristic scales. This procedure recovers familiar engineering groups, including the flow coefficient, head coefficient, and Mach number, while excluding equivalent but less interpretable alternatives. The method is demonstrated on a synthetic compressor dataset containing 16,000 measurements. Starting from raw dimensional variables and no physics input, it recovers the correct dimensionless groups to numerical precision and reproduces the compressor performance map with an error below 0.01%. More broadly, the work reveals a close connection between classical dimensional analysis and modern data-driven learning. Both rely on the same underlying algebraic structure, suggesting new approaches for building physical models that are simultaneously interpretable, scalable, and data-efficient.

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

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

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

12.
arXiv (math.PR) 2026-06-11

On Skorokhod Problems for Reflected and Singular Stochastic Heat Equations

arXiv:2606.11951v1 Announce Type: new Abstract: We prove a Skorokhod decomposition for the Markov processes $X^a$ and $X$ associated to the gradient Dirichlet forms with respect to the measures $\rho^a\mu^{\beta}$ and $\rho\mu^{\beta}$, respectively. Here, $\mu^{\beta}$ is the law of the standard Brownian bridge $\beta$, while $\rho^a$ and $\rho$ denote densities which are given by $\rho^a(z) := \mathbf{1}_{[0,\infty)}(\bar{z}_a)$ and $\rho(z) := \int_0^1 \mathbf{1}_{[0,\infty)}(\bar{z}_x) \, dx$, respectively, for all $z\in L^2(0,1)$ which have a (unique) continuous representative $\bar{z}$ which vanishes at zero and one. To this end, we derive infinite-dimensional integration by parts formulas (IbPFs) w.r.t. $\rho^a\mu^{\beta}$ and $\rho\mu^{\beta}$, which contain Hida distributions alongside the usual drift terms. We represent these Hida distributions by integration w.r.t. vector measures of bounded variation. The vector measures in question are constructed via an approximation argument, making use of a generalization of Prokhorov's theorem for vector measures. We further prove that, almost surely, the sample paths of $X^a$ and $X$ take values in the equivalence class of continuous functions vanishing at zero and one for all and $dt$-almost all times, respectively. The main motivation for studying $\rho^a\mu^{\beta}$ and $\rho\mu^{\beta}$ lies in the fact that the distributional terms in their IbPFs are simplifications of the distributional term in the IbPF w.r.t. the law of the reflected Brownian bridge on the unit interval $\mu^{|\beta|}$. Representing the latter by integration w.r.t. a vector measure of bounded variation is still an open problem.

13.
arXiv (CS.AI) 2026-06-17

Detecting and Mitigating DDoS Attacks with AI: A Survey

arXiv:2503.17867v3 Announce Type: replace-cross Abstract: Distributed Denial of Service attacks represent an active cybersecurity research problem. Recent research shifted from static rule-based defenses towards AI-based detection and mitigation. This comprehensive survey covers several key topics. Preeminently, state-of-the-art AI detection methods are discussed. An in-depth taxonomy based on manual expert hierarchies and an AI-generated dendrogram are provided, thus settling DDoS categorization ambiguities. An important discussion on available datasets follows, covering data format options and their role in training AI detection methods together with adversarial training and examples augmentation. Beyond detection, AI based mitigation techniques are surveyed as well. Finally, multiple open research directions are proposed.

14.
arXiv (CS.CV) 2026-06-15

StereoGeo: an end-to-end stereo camera calibration method

In this work, we propose StereoGeo, an end-to-end network-based approach for stereo camera calibration. Our method estimates the focal lengths and gravity directions of the left and right cameras, as well as the relative extrinsic transformation relating them. Existing methods often rely on calibration patterns in structured environments or address only a single camera configuration, being limited to either intrinsic or extrinsic estimation, and depending on a multi-view setups. StereoGeo extends the GeoCalib algorithm, integrating deep neural network feature extraction with a differentiable optimizer. Extensive experiments on real-world benchmarks demonstrate that StereoGeo achieves competitive performance for intrinsic calibration and provides accurate stereo extrinsic estimation, outperforming existing methods that are limited to monocular settings. The dataset used in this work is partially publicly available at https://github.com/meddourimane/StereoGeo-dataset.

15.
arXiv (math.PR) 2026-06-18

First to reach $n$ game

arXiv:2506.08782v4 Announce Type: replace Abstract: We consider a game with two players, consisting of a number of rounds, where the first player to win $n$ rounds becomes the overall winner. Who wins each individual round is governed by a certain urn having two types of balls (type 1 and type 2). At each round, we randomly pick a ball from the urn, and its type determines which of the two players wins. We study the game under three regimes. In the first and the third regimes, a ball is taken without replacement, whilst in the second regime, it is returned to the urn with one more ball of the same colour. We study the properties of the random variables equal to the properly defined overall net profits of the players, and the results are drastically different in all three regimes.

16.
bioRxiv (Bioinfo) 2026-06-19

Sanjeevani: A manually curated anti-cancerous phytochemical database integrated with downstream analysis tools.

Background: Cancer continues to pose a massive global health burden. While plant-derived phytochemicals offer promising therapeutic leads, existing natural product databases often lack cancer specificity, dataset downloadability, and integrated screening tools. Methods: We developed Sanjeevani, an integrative web platform cataloguing 4,823 curated anticancer phytochemicals. Using a balanced dataset of 9,646 molecules, we trained Support Vector Machine (SVM), Random Forest, and K-Nearest Neighbours classifiers using a hybrid feature representation of RDKit descriptors and 2048-bit ECFP4 fingerprints. The platform also integrates AutoDock Vina for web-based molecular docking for binding affinity, poses prediction and ADMET-AI for pharmacokinetics estimation. Results: The SVM model demonstrated the strongest predictive capability, achieving a top test accuracy of 0.966 and a ROC-AUC of 0.992. Benchmarking across five docking tools confirmed that AutoDock Vina successfully balanced computational automation with literature-consistent binding affinity replication. The final architecture provides rapid interactive 2D/3D visualizations integrated with downstream analysis tools. Conclusion: Sanjeevani provides an open-access, one-stop pipeline that bridges the gap between raw natural product data and actionable computational screening, accelerating natural product-based oncology drug discovery.

17.
arXiv (math.PR) 2026-06-16

Effective Resistances and Commute Times in Sparse Random Geometric Graphs

arXiv:2606.14895v1 Announce Type: new Abstract: The commute time between two nodes in a network - the expected number of steps for a random walk to travel from one node to the other and then return - is a metric of broad importance arising in community detection, network routing, dimensionality reduction, and diffusion modeling. For random geometric graphs (RGGs), in which nodes are placed at random in a spatial domain and connected pairwise wherever their Euclidean distance is below a threshold radius, the relationship between commute times and the embedding geometry remains poorly understood outside very dense settings (where the role of the geometry disappears and commute times degenerate to a sum of inverse degrees). We develop and numerically validate a model for approximating commute times in sparse RGGs on a torus by combining theoretically motivated geometric contributions with an inverse degree sum. The geometric terms include a universal logarithmic contribution from the Laplacian, a quadratic correction encoding the compact topology of the torus, and a quartic angular term reflecting the square anisotropy of the domain. We fit this model to samples of node pairs across a range of graph sizes and mean degrees, demonstrating good predictive performance and that the geometric terms contribute significantly to model fit. We then study the continuous perturbation of the model from a regular square lattice to a fully random geometric graph, further validating the functional model form through this transition and showing how commute times in sparse RGGs retain meaningful geometric information about the embedding space.

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

U$^2$Mamba: A Two-level Nested U-structure Mamba for Salient Object Detection

Mamba-based models have emerged as a promising alternative for salient object detection (SOD), offering significant advantages in modeling long sequences. However, existing models often fail to explore contextual information and the depth of the entire architecture. This paper introduces U$^2$Mamba, a powerful and innovative U-structured network for salient object detection. We propose multiscale Mamba U-blocks (MMUBs) that enhance the model depth to improve local feature extraction capabilities. Our newly developed nested U-structure, incorporating MMUBs, enables the network to integrate various receptive fields from shallow and deep layers, thereby collecting richer contextual information and longer-range data without being constrained by resolution. Instead of using the traditional deep supervision scheme and top-level supervised training, we propose a hierarchical training supervision method where the loss is computed at each level during the training process. Extensive experiments demonstrate that U$^2$Mamba achieves highly competitive performance against state-of-the-art methods. The source code is available at \url{https://github.com/JL021/U2Mamba}.

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

Mitigating Disparate Impact of Differentially Private Learning through Bounded Adaptive Clipping

arXiv:2506.01396v2 Announce Type: replace Abstract: Differential privacy (DP) has become an essential framework for privacy-preserving machine learning. Existing DP learning methods, however, often have disparate impacts on model predictions, e.g., for minority groups. Gradient clipping, which is often used in DP learning, can suppress larger gradients from challenging samples. We show that this problem is amplified by adaptive clipping, which will often shrink the clipping bound to tiny values to match a well-fitting majority, while significantly reducing the accuracy for others. We propose bounded adaptive clipping, which introduces a tunable lower bound to prevent excessive gradient suppression. Our method improves worst-class accuracy by over 10 percentage points on Skewed and Fashion MNIST compared to unbounded adaptive clipping, 7 points compared to Automatic clipping, and 5 points compared to constant clipping. The code is available at https://github.com/TrustworthyMLHelsinki/adaptive-clipping-fairness.

20.
arXiv (CS.AI) 2026-06-12

EpiBench: Verifiable Evaluation of AI Agents on Epigenomics Analysis

arXiv:2606.13602v1 Announce Type: new Abstract: We introduce EpiBench, a verifiable benchmark for short-horizon epigenomics analysis. EpiBench evaluates whether agents can make well-defined analysis decisions from realistic workflow states and return deterministically gradable answers. The benchmark includes 106 evaluations across CUT\&Tag/CUT\&RUN, ATAC-seq, ChIP-seq, and DNA methylation workflows. Across 5,088 valid trajectories from 16 model-harness pairs, no system passed a majority of attempts: GPT-5.5 / Pi led at 45.0\% (143/318 attempts; 95\% confidence interval (CI), 36.3–53.7), followed by GPT-5.5 / OpenAI Codex at 39.9\% (127/318 attempts; 95\% CI, 31.6–48.3). Claude Opus 4.8 Max / Pi and GPT-5.4 / Pi each passed 39.0\% (124/318 attempts; 95\% CI, 30.2–47.8 and 31.0–47.0, respectively). Performance varies across assay types, and many failed runs still contain parts of the correct answer. Agents often found the right files and computed useful intermediate results, but failed when the task required deeper, assay-specific scientific judgment.

21.
medRxiv (Medicine) 2026-06-10

Global and local genetic overlap among ME/CFS, irritable bowel syndrome and psychiatric traits: a hypothesis-generating analysis

Authors:

Background. Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and irritable bowel syndrome (IBS) frequently co-occur following infection, yet shared genetic architecture at the locus level has not been systematically characterised. Aims. To estimate global and local genetic correlations between ME/CFS (including infection-onset subgroup), IBS, major depressive disorder (MDD) and loneliness/isolation, and characterise ME/CFS cell-type heritability enrichment. Method. GWAS summary statistics: DecodeME (15,579 ME/CFS; 9,738 infection-onset), FinnGen R9 (9,296 IBS), PGC MDD Wave 2 (45,396) and UK Biobank loneliness (N=455,364). LDSC for global correlations; LAVA for local correlations across 2,495 loci; MAGMA for cell-type enrichment (Descartes Human atlas); coloc.abf for colocalisation. Results. All pairwise global correlations were significant after Bonferroni correction, including ME/CFS-all-MDD (rg=0.598, 95% CI 0.46-0.74) and ME/CFS-all-IBS (rg=0.573, 0.39-0.75). Of 4,232 local tests, 16 reached FDR

22.
arXiv (CS.AI) 2026-06-18

UPLOTS: A Unified Pretrained Language Model for Constrained Time-series Generation

arXiv:2606.10466v2 Announce Type: replace-cross Abstract: In time-series generation, existing approaches typically handcraft ortrain a separate model for each dataset, which hinders their scalability and fails to leverage shared temporal structures across domains. To address this fragmentation, we propose UPLOTS, a Unified, Prompt-guided Language model framework fOr constrained Time-Series Generation across diverse domains. Instead of building task-specific models, UPLOTS leverages a single pre-trained transformer backbone guided by learned constraint prompts, enabling on-demand generation with precise pattern control. One key innovation is our dynamic multi-dataset loss re-weighting and prompt-to-pattern mapping, which allows UPLOTS to internalize diverse temporal structures during training and conditionally generate them at inference. We evaluate UPLOTS on four real-world benchmarks and multiple constraint settings, including peak-period, calendar, load-level, and volatility patterns. Additional held-out constraint-combination and downstream forecasting experiments further demonstrate that UPLOTS generalizes beyond the original peak-pattern setting and improves data augmentation under scarce real-data regimes. Our code and baselines are available at anonymous github repo: https://anonymous.4open.science/r/UPLOTS-6C36.

23.
bioRxiv (Bioinfo) 2026-06-16

Orion: Towards Lab Automation with Computer-Using Agents

Laboratory discovery increasingly depends on computational workflows that connect experimental data to analysis, interpretation and follow-up hypotheses. Yet these workflows remain constrained by labor-intensive use of specialized software, visual inspection through graphical user interfaces, and integration of knowledge across multiple sources. Here, we present Orion, a computer-using AI agent for biomedical image analysis and interpretation that moves towards lab automation by automating this computational layer of laboratory work. Orion combines large language models with terminal execution, GUI control and adaptive multi-step reasoning in a shared computing environment. It can inspect visual data, operate standard scientific software, mine web resources and conduct end-to-end analysis and interpretation workflows without requiring bespoke software integrations. Across benchmarks, Orion achieved over 90% accuracy on biomedical database and literature retrieval tasks, learned to use the popular tools CellProfiler and QuPath for quantitative analysis of cellular and tissue images, respectively, and facilitated autonomous discovery in experimental imaging data. In 100 hours of autonomous exploration of a large-scale perturbation imaging dataset, Orion generated 52 research reports, of which human scientist review prioritized 22 plausible mechanistic hypotheses. These results show that computer-using AI agents can substantially expand the reach of laboratory automation, providing a scalable and auditable route from experimental imaging data to quantitative analysis, reports and biologically grounded hypotheses.

24.
arXiv (CS.AI) 2026-06-15

COGNITION: From Evaluation to Defense against Multimodal LLM CAPTCHA Solvers

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

25.
arXiv (quant-ph) 2026-06-24

Introduction to matrix-product states and tensor networks

arXiv:2606.24803v1 Announce Type: cross Abstract: These notes provide an introduction to tensor-network methods in quantum many-body physics, with an emphasis on matrix-product states (MPS). They develop the basic tensor-network language, including graphical notation, virtual indices, bond dimensions, gauge freedom, canonical forms, QR and singular-value decompositions, and the role of entanglement in controlling the efficiency of the representation. The main MPS algorithms are then introduced, including contractions, correlation functions, matrix-product operators, DMRG, and time-evolution methods. The notes also briefly discuss projected entangled-pair states (PEPS) as a higher-dimensional generalization of MPS, together with the basic ideas behind approximate PEPS contraction. Finally, tensor-network representations of mixed states, quantum channels, and Lindblad dynamics are presented, with applications to thermal states and open quantum systems. The presentation is accompanied by short Julia code examples based on ITensor, ITensorMPS, and TensorMixedStates. These notes were written for the 9th Les Houches Summer School on Computational Physics: Open Quantum Systems, held in June 2026.