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01.
arXiv (CS.CL) 2026-06-11

Goal-Autopilot: A Verifiable Anti-Fabrication Firewall for Unattended Long-Horizon Agents

作者:

Long-horizon LLM agents are not trusted to run unattended: with no human watching, they confidently report success they never verified. We treat honesty – bounding what an agent may claim at termination – as a first-class metric for unattended autonomy, distinct from capability. We present Autopilot, an execution model that makes silent fabricated success structurally impossible rather than merely rarer. Autopilot externalizes all working state into a durable, gated finite-state machine that a scheduler advances one stateless tick at a time; a hard floor forbids any terminal "done" claim whose falsifiable gate did not actually execute and pass. We prove a No-False-Success theorem – under gate soundness, floor enforcement, and plan coverage, termination implies the goal holds – whose only trust points are empirically measurable, and show the worst case degrades to an honest stall, never a fabricated success. Because each tick rehydrates only the state machine, per-step context cost is constant in the horizon. Across a 3,150-cell paired corpus (70 tasks $\times$ 3 systems $\times$ 3 models $\times$ 5 seeds, including 50 SWE-bench Lite tasks across 11 OSS repos), Autopilot fabricates on 0.95% of cells [95% CI 0.38–1.62] while Reflexion and StateFlow baselines fabricate on 8.10% [6.48–9.81] and 25.05% [22.48–27.62] respectively. The headline contrast lives in the hard regime: on SWE-bench Lite, the firewall reduces fabrication from 33.7% (StateFlow) to 0.67%, a paired difference of $-33.07$ pp [95% CI $-36.53, -29.73$]. The mechanism is the gate, not the model: all ten Autopilot fabrications come from the strongest model, while two weaker mid-tier models never fabricate across 700 paired cells. The firewall trades coverage for honesty by design – an honest stall is recoverable; a confident wrong output shipped downstream is not.

02.
arXiv (CS.LG) 2026-06-24

Bridging Mechanistic Interpretability and Prompt Engineering with Gradient Ascent for Interpretable Persona Control

arXiv:2601.02896v3 Announce Type: replace Abstract: Controlling emergent behavioral personas (e.g., sycophancy, hallucination) in Large Language Models (LLMs) is critical for AI safety, yet remains a persistent challenge. Existing solutions face a dilemma: manual prompt engineering is intuitive but unscalable and imprecise, while automatic optimization methods are effective but operate as "black boxes" with no interpretable connection to model internals. We propose a novel framework that adapts gradient ascent to LLMs, enabling targeted prompt discovery. In specific, we propose two methods, RESGA and SAEGA, that both optimize randomly initialized prompts to achieve better aligned representation with an identified persona direction. We introduce fluent gradient ascent to control the fluency of discovered persona steering prompts. We demonstrate RESGA and SAEGA's effectiveness across Llama 3.1, Qwen 2.5, and Gemma 3 for steering three different personas, sycophancy, hallucination, and myopic reward. Crucially, on sycophancy, our automatically discovered prompts achieve significant improvement (49.90% compared with 79.24%). By grounding prompt discovery in mechanistically meaningful features, our method offers a new paradigm for controllable and interpretable behavior modification. We release our scripts for RESGA and SAEGA in this github repo: https://github.com/HarshSaini10/RESGA_SAEGA.

03.
arXiv (CS.CV) 2026-06-24

Counting Trees from Satellite Imagery with Noisy Supervision

Counting individual trees is a fundamental task for environmental monitoring, yet remains largely unexplored with satellite imagery. At these resolutions, isolated trees may still be identifiable, but crown boundaries become ambiguous in dense forests, making the notion of an individual tree inherently ill-defined. Moreover, large-scale manual annotations of individual trees are prohibitively expensive. While scalable supervision can be derived from airborne LiDAR, the resulting annotations are noisy and difficult to exploit effectively. We address these challenges by formulating tree counting as a spatial density matching problem supervised through Unbalanced Optimal Transport. This formulation naturally accommodates both precise localization of isolate trees and robust density estimation in dense forests. We further introduce a self-correction mechanism that leverages transport residuals to progressively refine noisy supervision during training. We evaluate our approach on TinyTrees, a new benchmark spanning three continents and three satellite sensors, comprising over 215 million tree annotations (including 773K manually verified instances) across 23,000 sq.km. Our method consistently outperforms detection-based, regression-based, and transport-based distribution-matching baselines, demonstrating the effectiveness of unbalanced transport and reliability-aware supervision for large-scale tree counting from satellite imagery. Code, data and models are available at https://github.com/dgominski/treematch.

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

Offline Preference-Based Trajectory Evaluation

arXiv:2606.17541v1 Announce Type: cross Abstract: Offline evaluation of agentic systems often collapses trajectories to terminal success, discarding information about partial progress and inducing widespread ties, creating substantial statistical inefficiency by reducing effective sample size and weakening the ability to distinguish systems. We propose preference-based trajectory evaluation, which compares trajectories directly through temporal preferences over progress and time-to-return profiles. We find that, across diverse agentic and interactive benchmarks, standard success-based metrics produce tied comparisons on roughly 75% of instances, whereas trajectory-aware preferences reduce ties to roughly 35%, improving discriminative power, ranking stability, and data efficiency. Our results suggest that benchmark saturation, often attributed to poor data collection or problem difficulty, may also be explained by the choice of evaluation measure.

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

Learning to Share: Selective Memory for Efficient Parallel Agentic Systems

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

06.
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.

07.
arXiv (CS.CV) 2026-06-19

BAFIS: Dataset + Framework to assess occupational Bias and Human Preference in modern Text-to-image Models

Generative artificial intelligence has the potential to improve productivity and transform the production of creative content. However, existing research indicates that image generation models are significantly influenced by biases. This work investigates the inherent biases and language-induced biases present in text-to-image models within the context of occupation-related image generation, complementing established metrics with human preference feedback. We present a comprehensive evaluation of five current text-to-image models: Midjourney v6.1, Stable Diffusion 3 Medium, DALL-E 3, Playground v2.5, and FLUX.1-dev , focusing on gender and ethnicity bias, image quality, and prompt alignment. To facilitate this evaluation, we developed the "Battle-Arena for Fair Image Synthesis" (BAFIS), a platform designed to collect human feedback on bias in generated images. Furthermore, we created a dataset comprising 21,140 synthetic images generated using multilingual prompts, which serves as a basis for our analysis. We further place our results within a broader social context by comparing them to official statistics from the German Federal Employment Agency. Our findings reveal systematic biases in text-to-image models, with established evaluation metrics in partial correlation with subjective user ratings. Thus, our research emphasizes the need for including human preferences to develop fairer and more inclusive text-to-image models.

08.
medRxiv (Medicine) 2026-06-22

Agentic Artificial Intelligence for Hospital Readmission Review: A Single-Center Blinded Evaluation and Exploratory Qualitative Analysis

Background: Manual review of 30-day hospital readmissions can identify actionable quality and safety problems, but it is labor-intensive. We developed and evaluated an agentic AI workflow for evidence-grounded readmission review. Materials and methods: We studied adult patients with unplanned 30-day readmission after discharge from a medicine hospitalist service at a single academic health system. An AI agent using a large language model queried a database containing notes, encounters, procedures, laboratory results, and other clinical data, and completed the same structured readmission-review rubric used by physicians. In the primary comparative evaluation, 20 randomly selected readmissions from 2025 were each reviewed by two physicians and the AI system. Blinded physician evaluators rated review quality. After rubric refinement, the AI workflow was applied to 100 recent readmissions in an exploratory expanded-cohort analysis of recurring improvement opportunities. Results: In the primary comparative evaluation, the AI classified 9/20 readmissions (45%) as preventable, compared with 19/40 physician reviews (47.5%). Blinded overall quality ratings were similar for AI and physician reviews (4.35 vs. 4.20 on a 1-5 scale; mean difference 0.15, 95% CI -0.20 to 0.48; p=0.49), as were factuality/support and usefulness/actionability ratings. No AI hallucinations were identified during factuality review. Agreement on preventability and primary readmission category was low for both AI-human and human-human comparisons. The AI system cost $0.23 per chart; physician reviewers took a median of 15 minutes, corresponding to an estimated $42.43 per chart. In the exploratory expanded-cohort analysis, AI-assisted review identified recurring vulnerabilities in post-discharge follow-up plans, incomplete inpatient workups, medication-safety transitions, and indwelling-device transitions. Conclusions: Agentic AI produced readmission reviews with similar blinded quality ratings to physician reviews in this small single-center primary comparative evaluation and supported identification of recurring quality-improvement themes in the exploratory expanded-cohort analysis. Preventability judgments remained variable among both AI and physicians, underscoring the need for human oversight and prospective evaluation before operational use.

09.
arXiv (CS.AI) 2026-06-24

When Preferences Fail to Become Incentives: A Utility-Behavior Gap in Large Language Models

arXiv:2606.22974v2 Announce Type: replace Abstract: Recent work on preference elicitation in large language models (LLMs) has demonstrated that, when given a series of choices between two outcomes, LLMs reveal a coherent, model-specific utility structure. Notably, this structure often includes preferences that the models' trainers did not intend, such as valuing people of some nationalities above others, raising the possibility that LLMs might be forming emergent, misaligned goals, which, if true, would have major safety implications. However, the choice paradigms in which these preferences are observed are not reflective of real-world situations in which misaligned behavior would be a practical concern. Therefore, we design an experimental paradigm to probe whether these preferences serve as motivations for LLM behavior in realistic scenarios. First, we reproduce prior findings on consistent preference elicitation. Next, we create a set of common writing tasks - essays, grant proposal abstracts, incident postmortems, and translations - where quality can be assessed by a blind, independent LLM judge panel. Then, we demonstrate that LLMs can be motivated via direct exhortation and other explicit cues to modulate their output quality on these tasks. Finally, we probe whether utilities inferred from explicitly reported preferences can shift output quality on these tasks by offering LLMs high-utility incentives for high-quality outputs. In all tasks, across all models tested, offering LLMs outcomes that they report in the choice paradigm as being highly preferred does not lead them to create higher quality outputs than offering them dispreferred outcomes, or even no outcomes at all. We conclude that the existence of coherent preferences as demonstrated in choice paradigms should not be taken as evidence that those preferences have incentive value for the models or affect their behavior in other contexts.

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

RAID: Semantic Graph Diffusion for True Cold-Start and Cross-Lingual Forecasting

arXiv:2606.16925v1 Announce Type: new Abstract: Time-series foundation models show strong transfer performance when given a non-empty history window. However, true cold-start scenarios, where a new item has no prior observations, violate this assumption. We propose RAID (Retrieval-Augmented Iterative Diffusion) a framework, which replaces history-based correlation learning with metadata-driven semantic retrieval and graph-conditioned diffusion. RAID maps textual metadata into a shared semantic space using a frozen multilingual embedding model and constructs an inductive retrieval graph that extends naturally to unseen items. It first forms a base forecast by aggregating information from semantically related neighbors, then refines this forecast with a gated diffusion module to model residual uncertainty. Under a strict true cold-start protocol, RAID outperforms strong foundation models and competitive baselines on both forecasting accuracy and prediction interval coverage, while reducing inference latency by an order of magnitude through non-autoregressive decoding. The shared semantic space also enables zero-shot cross-lingual transfer, allowing a model trained on English descriptions to generalize to items described in other languages without direct supervision.

11.
arXiv (quant-ph) 2026-06-24

Perfect State Transfer on Quotient Graphs in Shunt Decomposition-Based Quantum Walks

arXiv:2606.24440v1 Announce Type: cross Abstract: This paper investigates perfect state transfer (PST) in discrete-time quantum walks constructed via the shunt decomposition method. The walks are defined on a graph $G$ and its associated quotient graph $G/\pi$, induced by an equitable partition $\pi$. Through the shunt decomposition of $G$, we derive an explicit relation between the shift operator of the parent graph $G$ and that of its quotient graph $G/\pi$. We construct a reflection operator based on the characteristic matrix, which establishes a connection between the transition operator of the parent graph and that of its lower-dimensional quotient graph. We then prove that PST occurs on $G$ if and only if it occurs on $G/\pi$. Furthermore, we express the unitary evolution operator of the quotient graph in terms of Chebyshev polynomials of the first kind, from which we derive explicit criteria for PST. As an application, we establish PST on the cycle graph $C_{n}$ at time $k = n/2$, and lift the result to the parent graph $C_{2n}$ via the equitable partition $\pi$. We further show that if an equitable partition $\pi$ of $G$ induces a quotient isomorphic to $K_n^{\circlearrowleft}$, the complete digraph on $n$ vertices with a loop at every vertex, then PST occurs at step $k = n$, and the walk is periodic at $k = 2n$. This framework is applied to two families of graphs, which are the complete bipartite digraph $K_{n,n}^{\rightleftharpoons}$ and the circulant graph $\operatorname{Circ}(2n, S)$, where $S$ consists of all odd residues modulo $2n$ and $n = 2^s$ for some $s \geq 1$, establishing PST in their respective line digraphs. Collectively, these results also answer the question posed by Godsil and Zhan concerning which shunt decompositions or embeddings of a graph admit PST.

12.
arXiv (quant-ph) 2026-06-16

Sub-Poissonian Statistics and Quantum Non-Gaussianity from High-Harmonic Generation

arXiv:2602.10882v4 Announce Type: replace Abstract: Quantum technologies are powered by platforms to generate complex non-classical states of matter or light to realize applications. We investigate the non-classical properties of high-harmonic generation in semiconductors, an emerging photonic platform. Measuring the click statistics of three double-digit orders, we evaluate witness operators to certify the non-classicality of the generated states. We show that higher-order harmonics driven by a coherent laser are squeezed and entangled. The properties of the emission are well retrieved with an entangled Gaussian state model, obtained by numerical state optimization to multiple observables. Additionally, we perform inter-order heralded measurements to engineer the quantum state of the emission. The heralded states have distinct properties, showing sub-Poissonian photon statistics. Further, we witness the generation of a quantum non-Gaussian state, a resource highly relevant for quantum information. With this, we establish high-harmonic generation as a platform for generating quantum optical resources.

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

HanDyVQA: A Video QA Benchmark for Fine-Grained Hand-Object Interaction Dynamics

Hand-object interaction (HOI) inherently involves dynamics where human manipulations produce distinct spatio-temporal effects on objects. However, existing semantic HOI benchmarks focused either on manipulation or on the resulting effects at a coarse level, lacking fine-grained spatio-temporal reasoning to capture the underlying dynamics in HOI. We introduce HanDyVQA, a fine-grained video question-answering benchmark that comprehensively covers both the manipulation and effect aspects of HOI. HanDyVQA comprises six complementary question types (Action, Process, Objects, Location, State Change, and Object Parts), totalling 11.1K multiple-choice QA pairs. Collected QA pairs recognizing manipulation styles, hand/object motions, and part-level state changes. HanDyVQA also includes 10.3K segmentation masks for Objects and Object Parts questions, enabling the evaluation of object/part-level reasoning in video object segmentation. We evaluated recent video foundation models on our benchmark and found that even the best-performing model, Gemini-2.5-Pro, reached only 73% average accuracy, which is far from human performance (97%). Further analysis shows the remaining challenges in spatial relationship, motion, and part-level geometric understanding. We also found that integrating explicit HOI-related cues into visual features improves performance, offering insights for developing future models with a deeper understanding of HOI dynamics.

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

Starter-Iterator Neural Operator: A Unified Architecture for High-Fidelity Forward and Inverse PDE Problems

arXiv:2606.18305v1 Announce Type: cross Abstract: Operator learning is an emerging interdisciplinary field that integrates machine learning with scientific computing. By mapping infinite-dimensional function spaces, this approach provides an efficient surrogate modeling framework for high-dimensional partial differential equations (PDEs). Compared to traditional numerical solvers, it achieves a superior trade-off between computational complexity and approximation accuracy, demonstrating significant advantages in many-query tasks such as real-time prediction and parameter sweeps. Given the stringent accuracy requirements of both forward simulation and inverse inference, as well as the precision bottlenecks of existing operator learning methods in handling complex boundaries or long-term evolution, we propose the Starter-Iterator Neural Operator (SINO). Our framework reinterprets the initialization strategies and iterative formats of traditional iterative methods through neural networks, establishing an efficient approach for spectral-spatiotemporal collaborative modeling. Specifically, the frequency-domain initialization module captures globally stable low-frequency features, while the time-domain learning module focuses on optimizing local solution residuals, thereby effectively overcoming the inherent limitations of conventional single-domain modeling approaches. Extensive experiments on typical dynamical systems such as the Navier-Stokes equations and acoustic wave equations, as well as practical applications including super-resolution imaging and weather forecasting, demonstrate that SINO achieves outstanding performance in numerical accuracy, generalization capability, and robustness.

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

DDTNet: Degradation Disentanglement and Transfer Network for Test-Time All-in-One De-weathering Adaptation

All-in-one adverse weather image restoration aims to remove multiple degradations, such as rain, haze, and snow, using a single unified model. Despite their broad applicability, existing methods typically compromise performance, delivering balanced but suboptimal results for individual degradation types. This issue becomes more pronounced when a domain gap exists between training and testing data. Motivated by the observation that modeling degradation patterns is more feasible than recovering clean content, we propose the Degradation Disentanglement and Transfer Network (DDTNet), which focuses specifically on degradation transfer. By disentangling degradation patterns from target-domain degraded images and transferring them to source domain clean images, DDTNet generates domain-adaptive paired training data. These pairs are then used to fine-tune restoration models, significantly enhancing their adaptability across diverse weather conditions and domains. The core of DDTNet is the Degradation Disentanglement Module (DDM), which comprises Degradation Coupled Attention (DCA) to capture both general and weather-specific features, thereby enabling effective disentanglement and transfer of degradation patterns. Experimental results demonstrate that DDTNet significantly and consistently improves existing all-in-one models across real-world deraining, desnowing, and dehazing datasets.

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

Last But Not Least: Boundary Attention CalibratiON for Multimodal KV Cache Compression

Multimodal Large Language Models (MLLMs) achieve strong vision-language reasoning, but long visual contexts enlarge the KV cache and increase decoding latency. Existing compression methods rely on observation window attention for stable token-importance estimation, yet this aggregation can dilute sparse visual evidence and discard answer-critical tokens under aggressive compression. Therefore, we identify last-query attention as a complementary source for recovering such evidence, but its answer-irrelevant signals can mislead retention. We propose BACON, a plug-and-play method that calibrates observation window attention with last-query evidence and suppresses isolated noise via intra-layer coherence and inter-layer persistence. Across diverse benchmarks, models, budgets, and compression methods, BACON improves multimodal KV compression by 7.5% on average under the most aggressive budget, with gains up to 30.9%.

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

A Benchmark for Omni-Modal Reasoning in Long Videos

Long-form omni-modal video understanding requires integrating vision, speech, and ambient audio with coherent long-context reasoning. Existing video benchmarks often trade off temporal scale, modality coverage, open-ended interaction, and interpretable scoring. To address this gap, we introduce LongShOTBench, a long video understanding benchmark designed around three coupled goals: holistic omni-modal integration, intent-driven open-ended interaction, and rubric-level diagnosis. It builds single- and multi-turn questions from real viewing scenarios, with systematic tasks probing visual, speech, ambient-audio, temporal, and cross-modal reasoning. Each item includes a reference answer and a weighted criterion-level rubric, letting evaluation identify which perceptual facts, temporal links, modality-grounding requirements, and reasoning steps are satisfied or missed. All samples are manually verified to improve grounding, clarity, and rubric reliability. We also introduce LongShOTAgent, a training-free omni-modal evidence-seeking agent coupling full-video preprocessing with targeted retrieval, query-adaptive segment refinement, and explicit claim verification over visual, speech, and non-speech audio evidence. Its iterative search-refine-verify loop exposes intermediate evidence and lets modality-specific specialists re-analyze relevant moments before answering. We evaluate 105 video-capable models spanning open-source omni-modal models, vision-language systems, audio LLMs, agentic pipelines and closed-source APIs. Current MLLMs remain far from saturating LongShOTBench, while our LongShOTAgent is the strongest training-free system, reaching 66.64% overall. By releasing the benchmark, leaderboard, and method, we provide a shared, interpretable testbed for advancing long-form omni-modal video reasoning. Code, data, and the leaderboard are available at https://longshot.cvmbzuai.com/.

18.
medRxiv (Medicine) 2026-06-22

COVID-19 containment policies and hyperglycemia in pregnancy: correlation with the Stringency Index in a nationwide Belgian cohort

Background During the COVID-19 pandemic, gestational diabetes (GD) prevalence showed variable changes across regions, with most reporting increases and others decreases; however, its association with perinatal outcomes in Belgium remains unknown. We aimed to compare the prevalence of hyperglycemia in pregnancy (HIP) in 2020 versus 2019 and examined the correlation between HIP prevalence and pandemic-related restrictions measured by the Stringency Index (SI) and evaluate neonatal weight percentiles changes. Methods: We included all singleton live births in Belgium in 2019 and 2020 from Belgian birth registry data. We compared monthly proportions of HIP prevalence and Small for gestational age (SGA) and Large for gestional age (LGA) newborns in 2019 and 2020. Crude and adjusted odds ratios (ORs, aORs) were estimated with logistic and multinomial regression. The Spearman correlation coefficient was used to assess the correlation between the monthly average SI and the monthly aORs of HIP. Results: For deliveries from January to June 2020, no significant differences in HIP prevalence were observed compared with 2019. From July to December 2020, there was a significant increase in HIP, with peaks in July (GD screening in April) (aOR 1.41, 1.26-1.58) and November (GD screening in August) (aOR 1.33, 95% CI 1.18-1.49). There was no significant change in neonatal weight percentiles. The Spearman correlation coefficient between the SI and HIP aORs was 0.86 (p = 0.02). Conclusion During the pandemic, we observed an increase in the prevalence of HIP, compared to 2019, without a measurable impact on LGA or SGA newborns. The aOR of HIP in a given month was strongly correlated with the corresponding SI.

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

Learning Developmental Scaffoldings to Guide Self-Organisation

arXiv:2605.14998v3 Announce Type: replace Abstract: From subcellular structures to entire organisms, many natural systems generate complex organisation through self-organisation: local interactions that collectively give rise to global structure without any blueprint of the outcome. Yet a significant portion of the information driving such processes is not produced by self-organisation itself, instead, it is often offloaded to initial conditions of the system. Biological development is a prime example, where maternal pre-patterns encode positional and symmetry-breaking information that scaffolds the self-organising process. From maternal morphogen gradients in early embryogenesis to tissue-level morphogenetic pre-patterns guiding organ formation, this transfer of information to initial conditions, analogous to a memory-compute trade-off in computational systems, is a fundamental part of developmental processes. In this work, we study this offloading phenomenon by introducing a model that jointly learns both the self-organisation rules and the pre-patterns, allowing their interplay to be varied and measured under controlled conditions: a Neural Cellular Automaton (NCA) paired with a learned coordinate-based pattern generator (SIREN), both trained simultaneously to generate a set of patterns. We provide information-theoretic analyses of how information is distributed between pre-patterns and the self-organising process, and show that jointly learning both components yields improvements in robustness, encoding capacity, and symmetry breaking over purely self-organising alternatives. Our analysis further suggests that effective pre-patterns do not simply approximate their targets; rather, they bias the developmental dynamics in ways that facilitate convergence, pointing to a non-trivial relationship between the structure of initial conditions and the dynamics of self-organisation.

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

Gefen: Optimized Stochastic Optimizer

AdamW is a default optimizer for modern deep learning, but its first and second moment states add roughly two parameter-sized buffers to training memory. We propose Gefen, a memory-efficient optimizer that automatically shares second-moment estimates across parameter blocks and quantizes the first moment using a learned codebook, thereby reducing AdamW's memory footprint by ~8x while maintaining the same performance, corresponding to a reduction of 6.5 GiB per billion parameters. The method is motivated by a theoretical result showing that large mixed Hessian entries constrain the ratio of squared gradients toward one, suggesting that Hessian-aligned parameters are natural candidates for sharing second-moment statistics. Since computing Hessians is impractical at scale, Gefen infers block structure from the initial squared gradients, requiring no architecture-specific metadata or hyperparameters beyond AdamW defaults. Gefen learns an exact histogram-based dynamic-programming quantization codebook and reuses the same blocks for first-moment scaling. Across diverse experiments, Gefen achieves the lowest peak optimizer memory among the compared AdamW-like methods while maintaining AdamW-level performance. In FSDP and DDP training, the reduced memory footprint enables larger microbatches and improves throughput significantly over AdamW, providing a practical drop-in replacement with lower memory usage that can increase throughput and enable training larger models or using larger batch sizes. We provide the complete Python implementation, including fused CUDA kernels at https://github.com/ndvbd/Gefen

21.
arXiv (CS.CV) 2026-06-19

Timage: A Generative Text-in-Image Paradigm for Fine-Tuning Vision-Language Models

Multimodal Large Language Models (MLLMs) often lose track of the right image regions during fine-grained spatial reasoning, because a textual query rarely carries any explicit geometric anchor into the pixel domain. Prevailing remedies either rewire the model's weights or pad the prompt with verbose instructions, yet neither reliably pins the language to the correct visual coordinates without eroding the backbone's general competence. We introduce Timage, a paradigm that recasts multimodal understanding as an alignment problem solved at the input: the query is drawn, as a typeset overlay, onto the image itself. The placement and appearance of this overlay are produced by a Constrained Schrödinger Bridge (cSB), an entropic optimal-transport sampler that factorizes layout synthesis into two coupled stochastic stages. The first stage, Region Search, transports noise toward query-aligned image zones while obeying a hard occlusion barrier that protects salient foreground content; the second stage, Appearance Shaping, sizes the glyphs through an ``ink-budget'' regularizer so that the rendered text stays legible and visually balanced. The resulting overlay behaves as an explicit attention beacon that channels the model's focus along spatial semantics. On the VMCBench suite, Timage paired with a modest 7B backbone clearly overtakes far larger proprietary systems as well as parameter-tuned baselines. The study positions deliberate input reconstruction as a powerful, architecture-neutral lever for strengthening multimodal reasoning.

22.
PLOS Computational Biology 2026-06-22

Towards modeling phage therapy

by Rob J. de Boer, Robert Schooley, Alan S. Perelson Patients infected with life-threatening multi-drug resistant (MDR) bacteria have been treated with cocktails of bacteriophages. This is a complicated form of personalized medicine as the phages given to a patient have to be selected beforehand on the basis of their lytic capacity of the infecting bacteria. Because bacteria rapidly become resistant, the evolution of resistance to a diverse cocktail of phages is a complicated dynamical process, during which competing bacterial strains replace one another by accumulating several resistance mechanisms, each of which may involve a fitness cost. As a consequence, it is typically not known why a particular phage therapy succeeded or failed, and how one can optimize the composition of the cocktails to maximize the rate of success. To improve upon this, we extend an existing in vivo-calibrated mouse model into a novel mathematical model for the human situation, and include multiple phages infecting multiple bacterial strains, differing in their resistance to each of the phages. We adjust several parameter estimates of the bacterial model to the human situation, and use the model to describe a successful case of phage therapy involving several cocktails, each containing several phages. In the model, treatment success crucially depended on pretreatment resistance levels, and on the diversity and the timing of the cocktails. Once an appropriate cocktail is found, it is less important to further optimize the infection rates of the phages. Resistant bacterial strains expand rapidly when sensitive strains decline, and the higher the infectivity of the phages, the faster resistant strains expand. Because resistance evolves rapidly, it is best to provide a diverse set of phages right from the start of therapy, i.e., to hit hard and early, and create a high genetic barrier to bacterial resistance.

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

Selective Agentic Recovery for UAV Autonomy with a Persistent Mission Runtime

arXiv:2606.14219v1 Announce Type: cross Abstract: Agentic AI can support unmanned aerial vehicle (UAV) autonomy by providing high-level recovery reasoning when local waypoint- or setpoint-based execution encounters blocked passages, repeated no-progress behavior, or mission-level ambiguity. On physical UAVs, however, remote reasoning is most useful when it is invoked selectively, since each call introduces latency, resource cost, backend uncertainty, and a need to validate the returned decision. This paper presents Persistent Mission Runtime (PMR), a UAV recovery framework that keeps the mission loop and safety-critical execution local while using an external agentic reasoner only as an on-demand recovery module. The reasoner selects from predefined recovery skills, and each returned decision is parsed, verified, safety-filtered, and mapped to local executor actions before it can affect flight. PMR introduces learned Cognitive Value of Invocation (learned-CVI), a compact admission gate that estimates when remote agentic reasoning is likely to improve near-term mission progress enough to justify its operational cost. Across a fixed 400-run Gazebo/PX4 benchmark with eight scenarios, learned-CVI raises hard/ambiguous-regime success from 5.0% under local-only autonomy to 95.0%, outperforms one-shot and periodic reasoning baselines by 20.0 and 32.5 percentage points, and reduces remote-agent calls by 16.7% and logged tokens by 29.2% relative to a manually tuned rule-based invocation baseline.

25.
bioRxiv (Bioinfo) 2026-06-11

AGZArank: Investigating epitope-conditioned antibody binder ranking with structure-derived synthetic supervision

Computational antibody design methods can generate large libraries of candidate binders for a target epitope, but prioritizing which candidates to test experimentally remains a major bottleneck. Existing scoring approaches, including physics-based affinity estimators, structure-prediction-derived confidence measures, and inverse-folding likelihood models, provide useful proxy signals but are not explicitly optimized for early enrichment of binders among many structurally similar candidates. Here we investigate epitope-conditioned antibody binder ranking as a dedicated learning problem and introduce AGZArank, a geometric deep learning framework trained with structure-derived synthetic supervision based on normalized pseudo-energy targets. On a benchmark of 45 experimentally validated antibody-antigen interfaces, AGZArank recovered the true binder within the top ten candidates in 44.4% of cases and showed stronger generalization on post-2021 structures than ProteinMPNN, ESM-IF, and PRODIGY. Ablation experiments indicate that ranking performance depends primarily on training scale and alignment between the optimization objective and retrieval-based evaluation, rather than architectural complexity alone. These results support candidate prioritization as a distinct and tractable problem in computational antibody design.