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

Seed-Guided Semi-Supervised Clustering by A-Contrario Anomaly Detection

arXiv:2606.18833v1 Announce Type: new Abstract: This paper introduces a semi-supervised clustering framework grounded in the statistical duality between grouping principles and anomaly detection. We address the challenge of robust cluster definition in noisy environments – a task where partitioning algorithms often over-assign outliers and density-based methods remain sensitive to heuristic global parameters. Drawing on a-contrario statistical reasoning and Gestalt proximity principles, we define a cluster as a maximal subset of data points containing no anomalies relative to a null hypothesis of uniform randomness. Central to this approach is the Perception algorithm, which utilises a principled expectation-based threshold ($\mathbb{E} < 1$) to identify outliers without manual parameter tuning. By treating clustering as the dual of anomaly detection, we employ an iterative ``clustering-by-exclusion'' mechanism. The algorithm is seed-guided, leveraging minimal user-provided labels to initialise robust cluster medians and form initial groups, which are subsequently expanded by admitting non-anomalous points. This approach naturally isolates fringe points, isolated noise, and emerging unknown clusters. We evaluate the method on synthetic and real-world benchmarks, including image and text datasets represented through raw, linear-reduced, and neighbourhood-preserving embeddings. Results demonstrate that with as few as 10–30 seeds per cluster, the proposed method achieves competitive and often very strong performance under a practical low-tuning benchmarking protocol, while maintaining linear scalability with respect to both observations and dimensionality for a fixed number of seeded clusters and iterations.

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

Towards UAV Image Dehazing: A UAV Atmospheric Scattering Model, Benchmark, and Geometry-Aware Deep Unfolding Network

In UAV applications, haze significantly obscures distant details and weaken structural information, hindering the recovery of details. Current UAV scenarios still face two key challenges: (i) paired hazy/clean images from the real world are unobtainable, while the classical atmospheric scattering model is inadequate for modeling the spatially non-uniform haze in UAV imagery; (ii) existing dehazing methods struggle to remove the heavy haze accumulated in the upper regions of UAV images. To address these issues, we first propose a UAV Atmospheric Scattering Model (UASM), which explicitly incorporates flight altitude, viewing pitch, and extinction to characterize the non-uniform haze distribution in UAV imaging. Based on UASM, we develop a physics-driven dehazing framework, termed Geometry-aware Proximal Deep Unfolding Network (GP-DUN). Specifically, GP-DUN consists of three key modules: a Latent Geometry Estimator (LGE) that infers transmittance consistent with UAV imaging geometry, a Geometry-aware Gradient Descent Module (GeoGDM) that embeds UASM into the data-fidelity term and performs physics-consistent closed-form updates, and an Pooling-Expert Proximal Mapping Module (PE-PMM) that learns an implicit prior to restore textures and structures beyond the capability of explicit physical modeling. In addition, we further construct UASM-HazeSet, which provides controllable paired synthetic data together with 2,285 real UAV haze images for testing. Extensive experiments show that GP-DUN consistently outperforms existing methods on both UASM-HazeSet and real UAV haze benchmarks.

03.
arXiv (CS.AI) 2026-06-17

IsabeLLM: Automated Theorem Proving Applied to Formally Verifying Consensus

arXiv:2606.18098v1 Announce Type: new Abstract: Advances in Artificial Intelligence (AI) have led AI for Theorem Proving to become a promising means of formally verifying computer systems. Whilst formal verification is traditionally reserved for safety-critical systems due to the required amount of expertise and effort, AI can help to automate a large amount of this workload and make it far more accessible. Blockchain-based systems are becoming increasingly popular and are frequently targeted by malicious actors, often resulting in huge financial losses, highlighting the need to better verify these systems and mitigate vulnerabilities. Arguably the most important component of these systems is the consensus protocol, which allows nodes to agree on decisions in a potentially adversarial environment. In this paper, we improve upon IsabeLLM, the automated theorem proving tool in Isabelle. Namely, we implement a Retrieval-Augmented Generation framework, Error tracing and counterexample generation for improved context supplied to the Large Language Model. Compatibility with the latest version of Isabelle and Sledgehammer is also implemented for improved efficiency. We compare the performance of the two versions of IsabeLLM in their ability to complete the verification of Bitcoin's Proof of Work consensus.

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

MPMWorlds: Material-Point-Method Simulations for Inferring and Extrapolating Physical Dynamics

To study the ability to infer physical dynamics from videos and extrapolate them forward in time, we assemble a dataset of 2D Material Point Method (MPM) physical simulations covering rich physical phenomena such as deformable objects, fluids, kinetic objects, and emitters. We study code generation and video diffusion approaches on this dataset, identifying their strengths and weaknesses by varying the amount of physically relevant side information. The code generation model, beyond giving a working demonstration of automatic synthesis of MPM simulations, reveals that such an approach struggles with inferring physical parameters from visual input, but relative to video diffusion, produces physically and temporally stable extrapolations forward in time, while the video diffusion model more strongly identifies geometric properties from visual input but produces physically implausible extrapolations.

05.
arXiv (quant-ph) 2026-06-15

Efficient and simple Gibbs state preparation of the 2D toric code via duality to classical Ising chains

arXiv:2508.00126v2 Announce Type: replace Abstract: We introduce the notion of polynomial-depth duality transformations, which relates two sets of operator algebras through a conjugation by a poly-depth quantum circuit, and make use of this to construct efficient Gibbs samplers for a variety of interesting quantum Hamiltonians as they are poly-depth dual to classical Hamiltonians. This is for example the case for the 2D toric code, which is demonstrated to be poly-depth dual to two decoupled classical Ising spin chains for any system size, and we give evidence that such dualities hold for a wide class of stabilizer Hamiltonians. Additionally, we extend the above notion of duality to Lindbladians in order to show that mixing times and other quantities such as the spectral gap or the modified logarithmic Sobolev inequality are preserved under duality.

06.
bioRxiv (Bioinfo) 2026-06-12

Computational Design of Optimal Sequences for Targeted Hypermutagenesis Using Recombination-Coupled Diversity-Generating Retroelements

Diversity-generating retroelements (DGRs) are natural systems that accelerate evolution via targeted hypermutation at adenines. We previously developed DGRec, a system combining DGRs and recombineering for programmable mutagenesis in Escherichia coli. We here address two important issues with DGRec: the dependence of mutagenesis efficiency on the dgrRNA secondary structure and the variability of the reverse-transcription biases with sequence context and position. First, we introduce and validate a method to recode non-functional templates, i.e. with low mutagenesis efficiency, into highly functional ones through synonymous mutations. Second, we develop a Long Short-Term Memory (LSTM) model to predict DGRec mutational profiles for any given template sequence. By integrating this LSTM model with our recoding method, we establish a comprehensive workflow for customized directed evolution, enabling researchers to precisely fine-tune DGRec in vivo mutagenesis to their engineering needs.

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

Structure-Semantic Co-optimized Latent Diffusion Model for Fast Visual Anagram Synthesis

Visual anagram is an intriguing form of art creation wherein a single image presents different conceptual interpretations under transformations such as flipping or rotation. Recent work has achieved visual anagram synthesis by leveraging pretrained text-to-image (T2I) diffusion models, yet still suffers from several key limitations including computational inefficiency, suboptimal aesthetic quality, and weak semantic fidelity and expressiveness. This work focuses on generating visual anagrams with substantially improved visual quality at minimal computational cost, thereby advancing intelligent creation of illusionary digital art. To increase image resolution while reducing time overhead, we adapt the cutting-edge parallel denoising algorithm from pixel-based T2I model to the adversarially distilled latent-based one, and accordingly propose a structure-semantic co-optimization (S2CO) framework to counteract the consequent visual degradation. As the core of our approach, S2CO framework comprises three key innovations: (\romannumeral1) null-text structure alignment optimization; (\romannumeral2) semantic enhancement optimization; (\romannumeral3) attention-guided noise fusion. Building upon these components, our method dubbed S2CO-Anagram is able to generate higher-resolution anagram images with noticeably superior visual harmony and semantic faithfulness than related SOTA approaches, all while achieving substantially faster inference speed. Code will be publicly available.

08.
arXiv (math.PR) 2026-06-16

Large Deviations for the Nonlinear Schrödinger Equation with Randomized Quasi-Periodic Initial Data in Higher Dimensions: Subcritical Case

arXiv:2604.17253v2 Announce Type: replace Abstract: We study the cubic weakly nonlinear Schrödinger equation with randomized spatially quasi-periodic initial data in higher dimensions. Under a polynomial decay assumption in Fourier space, we establish a Large Deviations Principle for rogue waves in the so-called subcritical time regime. The proof proceeds in two main steps. We first characterize the distribution of the linear solution and establish the corresponding linear large deviations principle. The lower bound is obtained via pointwise estimates, while the upper bound follows from a combination of truncation and probabilistic arguments. {The method used in this step appears to be new; compare with [GGKS23].} We then perform a detailed combinatorial analysis of the Picard iteration, deriving an effective bound for the Duhamel term and thereby establishing the nonlinear large deviations principle.

09.
arXiv (CS.LG) 2026-06-18

Investigating Inductive Biases for Machine Learning Emulation of Sudden Stratospheric Warmings in Idealised Isca Simulations

arXiv:2606.18857v1 Announce Type: new Abstract: Machine-learning emulators are increasingly used for weather prediction and have the potential to extend skill on subseasonal-to-seasonal timescales by learning dynamically important sources of predictability. A key challenge is whether the models can exploit predictability anchors, such as stratospheric variability, that influence tropospheric circulation beyond short lead times. We test how architectural inductive bias affects emulation of sudden stratospheric warming (SSW) dynamics using paired idealised Isca simulations that differ only in an imposed wave-2 heating perturbation. Across convolutional, transformer, and graph-based architectures trained for one-step prediction, model differences are modest when the stratosphere is dynamically quiet but widen substantially when SSW-like variability is active. Our results identify explicit three-dimensional vertical coupling as a key inductive bias for machine-learning emulation of stratospheric dynamics. However, Eliassen-Palm flux diagnostics show that low forecast error does not guarantee physically faithful wave-mean-flow interaction, with coherent errors remaining in stratospheric wave-driving structure.

10.
arXiv (CS.CV) 2026-06-12

AudioX-Turbo: A Unified Framework for Efficient Anything-to-Audio Generation

Audio and music generation based on flexible multimodal control signals is a widely applicable topic, with the following key challenges: 1) a unified multimodal modeling framework, 2) large-scale, high-quality training data, and 3) the prohibitive inference cost of multi-step diffusion sampling. As such, we propose AudioX-Turbo, a unified and efficient framework for anything-to-audio generation that integrates varied multimodal conditions (i.e., text, video, and audio signals) in this work. AudioX-Turbo follows a teacher-student paradigm. The teacher AudioX-Base is built on a Multimodal Diffusion Transformer with a Multimodal Adaptive Fusion module that aligns diverse multimodal inputs for high-fidelity synthesis, and is then distilled into the few-step student AudioX-Turbo via Distribution Matching Distillation adapted to flow matching, complemented by a diffusion-based discriminator for high-quality few-step generation. To support the training of AudioX-Turbo, we construct a large-scale, high-quality dataset, IF-caps-Pro, comprising approximately 9.2M samples curated through a two-stage data collection and annotation pipeline. We benchmark AudioX-Turbo across a wide range of tasks, finding that our model achieves superior performance, especially on text-to-audio and text-to-music generation, while operating at only 4 sampling steps and requiring approximately 25x fewer function evaluations (NFE) than multi-step baselines. These results demonstrate that our method is capable of audio generation under flexible multimodal control, showing efficient and powerful instruction-following capabilities. The code and datasets will be available at https://zeyuet.github.io/AudioX-Turbo/.

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

PlaceRep: Geospatial Place Representation Learning from Large-Scale Point-of-Interest Data

arXiv:2507.02921v4 Announce Type: replace-cross Abstract: Learning effective representations of urban environments requires capturing spatial structure beyond fixed administrative boundaries. Existing geospatial representation learning approaches typically aggregate Points of Interest (POIs) into pre-defined administrative regions such as census units or ZIP code areas, assigning a single embedding to each region. However, POIs often form semantically meaningful groups that extend across, within, or beyond these boundaries, defining places that better reflect human activity and urban function. To address this limitation, we propose PlaceRep, a geospatial representation learning method that constructs place-level representations by clustering spatially and semantically related POIs. PlaceRep summarizes large-scale POI graphs from U.S. Foursquare data to produce general-purpose urban region embeddings while automatically identifying places across multiple spatial scales. By eliminating model pre-training, PlaceRep provides a scalable and efficient solution for multi-granular geospatial analysis. Experiments using the tasks of population density estimation and housing price prediction as downstream tasks show that PlaceRep outperforms most state-of-the-art graph-based geospatial representation learning methods and achieves up to a x100 speedup in generating region-level representations on large-scale POI graphs. The implementation of PlaceRep is available at https://github.com/mohammadhashemii/PlaceRep.

12.
arXiv (CS.LG) 2026-06-17

Recursive Scaling in Masked Diffusion Models

arXiv:2606.18022v1 Announce Type: new Abstract: Masked diffusion models (MDMs) have recently emerged as a promising paradigm for sequence generation. Scaling MDMs is conventionally achieved by increasing the parameter count or the number of denoising steps. We introduce Recursive Masked Diffusion Models (R-MDMs), which add recursive depth as a third scaling axis by repeatedly applying the same denoising transformer within each diffusion step. Recursion enables iterative refinement of the output through parameter reuse, increasing effective model depth without increasing parameter count. Across structured generation tasks, including Sudoku and Countdown, we show that R-MDMs achieve substantially improved parameter efficiency: a model with $L$ recursive iterations often matches the performance of non-recursive baselines with roughly $L\times$ more parameters. Moreover, recursive refinement can partially substitute for additional denoising steps, allowing recursive models to reach the same generation quality with fewer forward passes at inference time. These results suggest that recursive depth is a practically useful scaling mechanism for MDMs, improving both parameter efficiency and the allocation of test-time compute.

13.
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.

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

FlowRL: A Taxonomy and Modular Framework for Reinforcement Learning with Diffusion Policies

arXiv:2603.27450v2 Announce Type: replace Abstract: Thanks to their remarkable flexibility, diffusion models and flow models have emerged as promising candidates for policy representation. However, efficient reinforcement learning (RL) upon these policies remains a challenge due to the lack of explicit log-probabilities for vanilla policy gradient estimators. While numerous attempts have been proposed to address this, the field lacks a unified perspective to reconcile these seemingly disparate methods, thus hampering ongoing development. In this paper, we bridge this gap by introducing a comprehensive taxonomy for RL algorithms with diffusion/flow policies. To support reproducibility and agile prototyping, we introduce a modular, JAX-based open-source codebase that leverages JIT-compilation for high-throughput training. Finally, we provide systematic and standardized benchmarks across Gym-Locomotion, DeepMind Control Suite, and IsaacLab, offering a rigorous side-by-side comparison of diffusion-based methods and guidance for practitioners to choose proper algorithms based on the application. Our work establishes a clear foundation for understanding and algorithm design, a high-efficiency toolkit for future research in the field, and an algorithmic guideline for practitioners in generative models and robotics. Our code is available at https://github.com/typoverflow/flow-rl.

15.
medRxiv (Medicine) 2026-06-16

Physiological Aging of the Respiratory System (PARS): from development to application

Background: Aging has a critical role in lung changes and the outcome of lung disease. Several lung aging equations have been proposed to measure deviation from physiological aging of the respiratory system. In this study, we aimed to develop a single measure of accelerated lung aging and show its application as a measure of lung aging. Method: We used a pre-bronchodilator pulmonary function test (PFT) from NHANES adult participants recruited from 2007 to 2011. We applied Klemera-Dubal Method (KDM) to four PFT measurements, FEV1, FVC, FEF25-75, and PEF, to calculate a measure of lung biological aging. Physiological Aging of the Respiratory System (PARS) was calculated from the residual method vs. chronological age. We tested the construct validity of PARS by measuring its association with risk factors of lung health. The prognostic validity was measured using a survival analysis. Sampling weights were applied to all analyses. Results: In 14,123 adult participants, the mean (SD) of accelerated lung age (PARS) was 0 (8.2) years. Participants with a history of asthma and emphysema had 4- and 10-year higher PARS. Cigarette smoking, lower socioeconomic status, black race, higher serum cadmium, and lower serum selenium and magnesium were associated with higher PARS. During 116 months of follow-up, PARS was associated with a higher mortality (HR = 1.06, 95%CI: 1.05-1.07 per year). Females with higher PARS had a higher risk of death (P for interaction < 0.001). Results were consistent across different subgroups and sensitivity analyses. Conclusion: PARS is a noninvasive lung aging marker and can be applied as a single measure of lung accelerated aging in the adult population. Its strong construct and predictive validity support its future application among different populations with and without lung disease.

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

CLAD: Constrained Latent Action Diffusion for Vision-Language Procedure Planning

We propose CLAD, a Constrained Latent Action Diffusion model for vision-language procedure planning in instructional videos. Procedure planning is the challenging task of predicting intermediate actions given a visual observation of a start and a goal state. However, future interactive AI systems must also be able to plan procedures using multi-modal input, e.g., where visual observations are augmented with language descriptions. To tackle this vision-language procedure planning task, our method uses a Variational Autoencoder (VAE) to learn the latent representation of actions and observations as constraints and integrate them into the diffusion process. This approach exploits that the latent space of diffusion models already has semantics that can be used. We use the latent constraints to steer the diffusion model to better generate actions. We report extensive experiments on the popular CrossTask, Coin, and NIV datasets and show that our method outperforms state-of-the-art methods by a large margin. By evaluating ablated versions of our method, we further show that the proposed integration of the action and observation representations learnt in the VAE latent space is key to these performance improvements.

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

Public transit gains and spatially uneven travel demand changes after NYC congestion pricing

arXiv:2606.17530v1 Announce Type: cross Abstract: New York City implemented the nation's first cordon-based congestion pricing program in January 2025, providing an opportunity to evaluate how system-wide urban mobility responds to large-scale pricing interventions. Because such policies generate spillovers across modes and locations, credible control groups are difficult to construct. We address this challenge using time series foundation models to generate probabilistic counterfactual demand forecasts with calibrated uncertainty. Applying this framework to bus, subway, and aggregate trip volume data, we find that post-policy bus and subway ridership increased significantly relative to expected no-policy demand, while overall travel demand decreased modestly. The effects are spatially heterogeneous: while reductions in overall travel demand are concentrated within the Congestion Relief Zone, transit gains extend beyond Manhattan's core. Socio-demographic analyses further reveal uneven adaptation across neighborhoods, highlighting spatial equity implications. Our framework provides a scalable approach for the uncertainty-aware evaluation of system-wide urban interventions when clean control groups are unavailable.

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

Cramér-Type Moderate Deviations for Engel's Series via a Martingale Approach

arXiv:2606.18866v1 Announce Type: new Abstract: Let $x$ be uniformly distributed on $(0,1)$, and let $(q_n)_{n\geq1}$ be the digits of its Engel series expansion. We establish a Cramér-type moderate deviation expansion for $(\log q_n-n)/\sqrt n$. The proof is based on a martingale decomposition and asymptotic results for martingales. As consequences, we obtain a moderate deviation principle over the full range of scales between the central limit theorem and the law of large numbers, without the additional lower rate restriction required in several earlier works. We also derive a uniform Berry–Esseen bound of order $(\log n)/\sqrt n$.

19.
arXiv (CS.AI) 2026-06-15

Can LLMs Accurately Score Medical Diagnoses and Clinical Reasoning?

arXiv:2604.14892v3 Announce Type: replace-cross Abstract: Evaluating medical AI systems using expert clinician panels is costly and slow, motivating the use of large language models (LLMs) as alternative adjudicators. Here, we evaluate an LLM Jury, composed of three frontier AI models, for scoring 3334 diagnoses on 300 real-world low- and middle-income country (LMIC) hospital cases. Both LLM- and clinician-generated diagnoses are scored against expert panel diagnoses across four dimensions: diagnosis, differential diagnosis, clinical reasoning, and negative treatment risk. The LLM Jury scores are compared with expert and independent re-scoring panel scores to assess error metrics, inter-rater agreement, severe-risk errors, and the effect of post hoc calibration using isotonic regression. In our data, we find that: (i) the uncalibrated LLM Jury scores preserve ordinal agreement with the expert clinician panel scores, but are systematically lower; (ii) the probability of severe-risk errors is lower for the LLM Jury than the human expert re-score panels; (iii) the LLM Jury combined with LLM diagnoses can be used to identify diagnoses at high risk of error, enabling targeted expert review and improved panel efficiency; (iv) the calibrated LLM Jury scores and rankings of diagnosing agents show excellent agreement with those of the primary expert panels; (v) LLM Jury models show no self-preference bias, they did not score diagnoses generated by their own underlying model or models from the same vendor more (or less) favourably than those generated by other models. Together, these results provide evidence that a calibrated LLM Jury is a trustworthy and reliable proxy for expert clinician evaluation in medical AI benchmarking. Confirming these findings in other clinical settings is an important direction for future work.

20.
arXiv (CS.AI) 2026-06-19

StaminaBench: Stress-Testing Coding Agents over 100 Interaction Turns

arXiv:2606.19613v1 Announce Type: cross Abstract: We introduce StaminaBench, a benchmark that measures the stamina of coding agents: how many consecutive interaction turns (change requests) they can handle before failing. Unlike the prevailing fraction-of-tasks-solved metric, this matches real vibe-coding where sessions run dozens or hundreds of turns. In StaminaBench, agents implement a REST API server and modify it across a tunable number of procedurally generated follow-up change requests - 100 in our experiments, resulting in codebases of up to 6,000 lines. Tests are generated fully programmatically without LLM involvement, ensuring reproducibility and reliability; change sequences are drawn from either a hardcoded or LLM-driven sampler, both constrained to a structured action space to ensure changes are valid. The agent and the server run in an isolated environment and communicate with the benchmark through HTTP, making testing fully black-box and language-agnostic. We evaluate six agent harnesses paired with seven open-source LLMs across 20 scenarios of 100 turns each and find that: (1) all the tested models fail within 5-6 turns, confirming that vibe-coding-style programming without thorough testing produces bugs; (2) passing test feedback back to the agent and allowing it to retry improves passed turn count by up to 12x; and (3) a good harness is required for strong performance: stronger models exhibit up to a 6x gap between their best and worst harness, while weaker models fail with any harness. We release the benchmark and the generated tasks to enable further research into multi-turn coding agent behavior. Benchmark code and data: github.com/amazon-science/StaminaBench.

21.
arXiv (quant-ph) 2026-06-16

The Quantum Transition State

arXiv:2606.10266v2 Announce Type: replace Abstract: The transition state – the critical configuration separating reactants from products – is the central organizing concept of chemical reaction rate theory, yet for nearly a century it has been thought to have no exact quantum counterpart: the recrossing-free, one-way flux through a transition state appears to demand simultaneous knowledge of position and momentum, in conflict with the uncertainty principle. We show this obstruction is illusory and construct the quantum transition state directly from the exact quantum flow. Its stable and unstable invariant manifolds intersect in a unique bounded trajectory – the quantum transition-state trajectory – anchoring a moving dividing surface that each reactive characteristic crosses exactly once, yielding a one-way flux of the standard quantum probability current. The geometric framework underlying classical transition-state theory thus survives intact in exact quantum mechanics, in a fundamentally quantum form.

22.
arXiv (CS.AI) 2026-06-16

Post-Hoc Merging is Not Enough: Many-Shot Model Merging with Loss-Gap Balancing

arXiv:2606.16501v1 Announce Type: new Abstract: Model merging has become a practical post-training strategy for building a single multi-task large language model (LLM) by combining multiple task-specialized models. However, most existing approaches rely on post-hoc merging, in which task-specific models are merged only once after training. This one-shot aggregation often suffers from task interference, leading to information erasure across individual tasks. In this work, we show that replacing post-hoc merging with an iterative many-shot merging protocol is effective in improving multi-task performance. Building on this insight, we propose METIS, Mitigating Erasure from Task Interference for Stable many-shot merging. METIS is a loss-aware many-shot merging method that addresses information erasure in post-hoc merging through task-wise loss-gap weighting and consensus-based masking. Notably, METIS exhibits significant performance improvement on the worst-performing task, effectively mitigating information erasure. (Project page: https://imkyungjin.github.io/METIS/)

23.
bioRxiv (Bioinfo) 2026-06-16

RetroMol: Parsing a shared encoding from natural products and their biosynthetic gene clusters

Natural products such as polyketides and nonribosomal peptides (NRPs) are important sources of bioactive compounds, including many antibiotics. Many of them are assembled by modular enzyme complexes and further modified and diversified by tailoring reactions encoded by biosynthetic gene clusters (BGCs). Although natural products and their coding BGCs describe different data modalities of the same biochemical process, a unified language to jointly describe their biochemistry is lacking. Here we introduce a sequence-based representation of the core biosynthesis of modular natural products, which we call primary sequences, that bridges chemical structures and BGCs. We also present RetroMol, an algorithm that parses either natural product structures or their encoding BGCs into their primary sequences of natural product building blocks. RetroMol allows for similarity scoring between natural products and BGCs, enabling the retrieval of compounds, BGCs, and a combination of the two, based on their biosynthetic similarity. This can, for instance, be used to retrieve biosynthetically similar but structurally dissimilar compounds, or link natural products to candidate coding BGCs in large experimental datasets. We demonstrate the latter by rediscovering the nocardichelin B BGC as a proof of principle. We also exemplify the utility of biosynthetic similarity by showing various pairs of biosynthetically similar compounds with low structural similarity. Together, these results establish primary sequences as a shared biosynthetic encoding for natural product comparison and BGC prioritization.

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

Learning Survival Models with Right-Censored Reporting Delays

arXiv:2510.04421v3 Announce Type: replace-cross Abstract: Survival analysis provides statistical methods to model the time until an event occurs. Reporting delays arise when event times are not observed at their occurrence but are only revealed upon reporting. This issue is particularly critical for timely risk evaluation when the observation window is short due to administrative censoring. In this study, we incorporate right-censored reporting delays by jointly modeling parametric hazards for the event and reporting processes. We then construct a consistent estimator for the model parameters and develop a Monte Carlo expectation-maximization algorithm to compute it. To address the challenges posed by administrative censoring, we leverage these findings and propose a transfer-learning procedure. Experimental results demonstrate that our method improves the accuracy of timely risk evaluation under administrative censoring.

25.
medRxiv (Medicine) 2026-06-15

Investigation of Intra-Fraction Stability and Inter-Fraction Reproducibility of Deep Inspiration Breath-Hold Across Two Hypofractionated Radiotherapy Regimens in the HYPORT Adjuvant Study.

Background: Deep Inspiration Breath Hold (DIBH) is a widely used respiratory motion management technique for minimizing cardiac dose in left-sided breast radiotherapy. In the Breast HYPORT Adjuvant study, DIBH was employed for cardiac sparing in patients without nodal irradiation using a standardized institutional protocol with the Varian Real-time Position Management (RPM) system. Both moderate-hypofractionation (control arm - 40Gy in 15 fractions) and one-week hypofractionation (experimental arm - 26 Gy in 5 fractions) regimens were delivered using this protocol. This study aimed to evaluate the robustness of DIBH by analyzing intra-fraction stability and inter-fraction reproducibility of breath-hold amplitude across the two treatment regimens. Methods: Respiratory waveforms acquired during each treatment session were analyzed to determine the median breath-hold amplitude and its standard deviation during beam delivery. Intra-fraction stability was assessed from vari- ations within individual treatment sessions, while inter-fraction reproducibility was evaluated relative to the simula- tion waveform amplitude across all treatment sessions. These parameters were compared between the two HYPORT regimens to examine breath-hold consistency during treatment delivery. Moreover, an additional comparison was made between the one-week hypofractionation regimen and the first five fractions of the moderate-hypofractionation regimen to evaluate the effect of treatment duration . Lung volumes from free-breathing and DIBH CT scans were analyzed to assess the effectiveness of patient breath-hold training. Results: Both arms demonstrated an average 1.7-fold increase of air volume in lung during the breath-hold position, confirming the effective implementation of DIBH during treatment planning and delivery. Structured training resulted in increased breath-hold amplitudes, with gains of 22.87% and 24.16% with respect to the first trial session in the experimental and control arms, respectively. Both regimens receive equivalent doses for approximately the same air volume in lung . Despite the different prescription doses in the two arms (26 Gy vs. 40 Gy), the experimental arm achieved an equivalent mean heart dose of 2.91% (75.6 cGy) compared with 2.95% (118.51 cGy) in the control arm, suggesting a similar cardiac preservation protocol adopted during treatment planning. Intra-fraction stability was similar between the control arm and the experimental arm, with median amplitude variations of 1.006 mm (95% CI: [0.998-1.015]) and 1.079 mm (95% CI: [1.067-1.097]), respectively. In contrast, inter-fraction reproducibility improved in the experimental arm, with lower deviation from simulation amplitude (0.44 {+/-} 0.24 mm vs. 0.66 {+/-} 0.25 mm) for the entire treatment schedule. The stability and reproducibility of experimental arm were further compared with the first five fractions of the control arm. The results were similar to those of the experimental arm. Conclusion: In this study, we compared two treatment regimens in terms of intra-fraction stability and inter-fraction reproducibility during DIBH radiotherapy. Both regimens demonstrated comparable intra-fraction stability, indicating effective motion management irrespective of treatment duration. However, the experimental arm showed better inter- fraction reproducibility, suggesting more consistent breath-hold performance throughout the treatment course. Based on stability and reproducibility, a reasonable narrowing of the DIBH gating window may be implemented with minor changes to the institutional protocol. The observed trend highlights the potential for improved consistency with the experimental approach and supports further investigation to better understand the underlying factors and strengthen these findings in future studies.