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01.
arXiv (CS.LG) 2026-06-16

LLM-Based Synthetic Ground Truth Generation for Audio-Based Emotion Classification via In-Context Learning

arXiv:2606.14784v1 Announce Type: cross Abstract: Understanding human states and interaction dynamics is a core goal of human-computer interaction (HCI). As interaction paradigms become more immersive, virtual reality (VR) has emerged as a powerful platform for studying collaborative work. In such settings, evaluating team collaboration states, including team performance and team resilience, requires continuous and reliable inference of latent team-level cognitive and affective states from multi-modal sensor data, such as speech signals. However, generating ground truth labels for these latent states remains challenging due to sensor-induced noise, contextual variability, and sparse expert annotations. Traditional self-reporting approaches provide only static and delayed measurements and are therefore insufficient for capturing dynamic team processes reflected in continuous speech data. In this work, we propose a large language model (LLM)-driven, agentic inference workflow for automated emotion-related synthetic ground truth generation from streaming speech data in multi-user VR environments. Leveraging the generalization capabilities of LLMs, we use In-Context Learning (ICL) with few-shot demonstrations of paired audio-based samples and their corresponding transcriptions. ICL tends to achieve task adaptation comparable to model fine-tuning while circumventing the computational overhead of parameter updates. To construct informative and robust in-context prompts, we adopt a retrieval-based selection strategy that dynamically identifies relevant audio demonstrations based on similarity in the acoustic feature space.

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

BOUTEF: A Multilingual Corpus for FakeNews in North Africa – Language as a Weapon

The rapid spread of fake news on social media has become a major challenge, particularly in multilingual and under-resourced contexts such as North Africa. In this paper, we introduce BOUTEF, a large-scale multilingual corpus designed to study the propagation, characteristics, and impact of fake news in Algeria and Tunisia. The corpus integrates three complementary components: fake narratives, genuine narratives, and associated user-generated comments, along with verified debunking information. It covers a wide range of languages and linguistic varieties, including MSA, Algerian and Tunisian dialects, Arabizi, French, English, and code-switched language. Building on this resource, we conduct a comprehensive empirical analysis combining quantitative and qualitative approaches. We examine thematic distributions, linguistic and rhetorical strategies, sentiment patterns, and social engagement dynamics. Statistical analyses reveal significant associations between thematic categories and message veracity, as well as strong correlations between user engagement and the visibility of fake content. Our findings show that fake news relies heavily on emotionally charged narratives, sensational framing, and hybrid linguistic practices that enhance virality and audience engagement. In contrast, debunking content adopts a more factual and verification-oriented style. Furthermore, a comparative analysis between Algeria and Tunisia highlights both shared dynamics and country-specific characteristics shaped by sociopolitical contexts. The results emphasize the role of informal language practices in the diffusion and reception of misinformation. By providing a rich, annotated, and publicly available dataset, this work contributes to advancing research on fake news detection, low-resource language processing, and the understanding of information disorders in complex linguistic environments.

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

OpenMedQ: Broad Open Pretraining for Medical Vision-Language Models

We present OpenMedQ, a medical vision-language model pretrained on the broadest fully-open medical mix to date: 14 datasets totaling ~3.35M pretraining samples spanning pathology, radiology, microscopy, and text-only clinical QA. OpenMedQ reaches state-of-the-art BLEU-1 on PathVQA (75.9), beating Med-PaLM M variants up to 562B parameters (~80x larger), and matches the best reported VQA-MED BLEU-1 (64.5). Its vision encoder, transferred to 8 unseen medical classification benchmarks under an identical downstream recipe, obtains the highest average macro-F1 (0.757) among BiomedCLIP (0.745), PMC-CLIP (0.745), PubMedCLIP (0.746), and a from-scratch baseline (0.616). We release our code and an interactive demo is publicly available as a reproducible baseline for the community.

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

EPM-JEPA: Operator-Side Experience Modulation in JEPA-Family World Models

arXiv:2606.12979v1 Announce Type: new Abstract: JEPA-family world models use a static predictor whose weights do not adapt when test-time dynamics diverge from training. We compare two mechanisms for incorporating accumulated experience into a JEPA predictor under distribution shift: operand-side injection, where a compressed experience representation is added as a residual to the predictor's hidden state (EI-JEPA), and operator-side modulation, where the same representation generates low-rank weight deltas via LoRA applied to the predictor's weights (EPM-JEPA). On a pre-registered comparison (Moving MNIST, gravity shift), EPM-JEPA (D_shift^{n=50} = 0.7848 +/- 0.0078, three seeds) differs from EI-JEPA (0.8238) by delta = 4.74% - Outcome C: a null result - by our stated criterion, a valid outcome. As a secondary, non-pre-registered observation, EPM-JEPA improves 1.90% over a no-memory baseline (0.8000), consistently across seeds, while EI-JEPA underperforms the baseline, indicating the benefit is specific to weight-level modulation. Our primary contribution is a mechanism analysis: the D_shift^{n=50} trajectory reflects three independent dynamical processes - buffer cycling, EMA target drift, and an intrinsic LoRA settling transient of +0.021 - rather than convergence to equilibrium. These findings motivate PEM-JEPA, a physics-grounded successor addressing this dynamical-peak limitation.

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

Your "Pro" LLM Subscription May Actually Be "Free": Exposing Fingerprint Spoofing Risks in LLM Inference Services

As Large Language Model (LLM) APIs become ubiquitous, users increasingly rely on black-box fingerprinting to verify that providers are serving the advertised premium models. However, these methods may overlook adversarial providers who manipulate model weights to cheat the fingerprint process. We introduce a novel threat termed fingerprint spoofing, where a malicious provider stealthily serves a weaker model that has been parameter-efficiently fine-tuned to mimic a stronger model, thereby evading user-side fingerprinting. We first formally prove that user-side resource constraints (i.e., finite query budgets and weak fingerprinting classifiers) make current fingerprinting vulnerable to fingerprint spoofing. Guided by this theoretical analysis, we propose GhostPrint, a cost-effective attack framework leveraging surrogate modeling, reward-ranked fine-tuning, and knowledge distillation. Extensive evaluations in both static and continual fingerprinting settings demonstrate that GhostPrint allows weak models to consistently bypass representative fingerprint methods while maintaining utility at a low fine-tuning cost, exposing a critical vulnerability in current LLM fingerprinting pipelines.

07.
arXiv (CS.CL) 2026-06-11

Steering the Noise: Turning Random Perturbations into Effective Descent for Memory-Efficient LLM Fine-Tuning

Fine-tuning large language models (LLMs) achieves strong performance but is often limited by the memory overhead of backpropagation. Zeroth-order (ZO) optimization avoids this overhead by estimating gradients through forward passes alone, yet it typically converges slowly because random Gaussian perturbations yield high-variance gradient estimates in high-dimensional parameter spaces. In this paper, we propose a plug-and-play framework that turns random perturbations into more effective descent directions. The key idea is to draw a small pool of candidate perturbations, evaluate their loss values, and then select or combine those that are best aligned with the optimization objective. We develop two instantiations of this idea: MeZO-GV, which forms a guiding vector from the contrast between low-loss and high-loss perturbation groups, and MeZO-Greedy, which keeps the single best perturbation within a fixed evaluation budget. We theoretically show that both strategies yield a larger per-step reduction in the objective than standard ZO estimation, leading to improved convergence rates. Experiments on LLMs of different scales and architectures confirm that the proposed methods integrate naturally with existing ZO optimizers and consistently improve convergence speed and task accuracy. On OPT-13B, our approach outperforms all ZO baselines across 11 benchmarks and exceeds gradient-based methods on 9 of them, while retaining the memory efficiency of forward-only optimization.

08.
arXiv (quant-ph) 2026-06-19

Quantifying Imaginarity in Neutrino Systems

arXiv:2412.01871v2 Announce Type: replace-cross Abstract: It is a fundamental question why quantum mechanics employs complex numbers rather than solely real numbers. In this work, we conduct the first analysis of imaginarity quantification in neutrino flavor and spin-flavor oscillations. As quantum systems in coherent superposition, neutrinos are ideal candidates for quantifying imaginarity within the resource theoretic framework, using measures such as the $\ell_1$-norm and the relative entropy of imaginarity. We show that in the case of two-flavor mixing, these measures of imaginarity are nonzero. The measures of imaginarity reach their extreme values when the probabilistic features of quantum theory are fully maximized, i.e., both the transitional and survival probabilities are approximately equal. Our study reveals that the imaginarity, as a resource, can be harnessed not solely from the presence of a complex phase in the mixing matrix but also from the intrinsic quantum dynamics of time evolution itself. We further extend our analysis to explore the dynamics of three-flavor neutrino mixing, incorporating the effects of a nonzero $CP$ phase.

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

GrowthHacker: Automated Off-Policy Evaluation Optimization Using Code-Modifying LLM Agents

With data-driven development now widely adopted, online A/B testing is an established method for measuring the effects of new technologies. However, deploying online experiments demands resources for design, implementation, and deployment, and may negatively impact users (e.g., unsafe or unethical outcomes) while requiring weeks of data collection. To address this, the growing research area of off-policy evaluation (OPE), or offline A/B testing, assesses new technologies offline using previously collected logged data. OPE is also a fundamental problem in reinforcement learning and is important where online testing is expensive or risky, such as healthcare, recommender systems, education, and robotics. Despite advances in code-generation large language models (LLMs) and agentic workflows, little is known about whether and how LLMs and LLM-based agents can automatically optimize OPE implementations. We propose GrowthHacker, a benchmark that evaluates baseline LLMs and LLM-based agents on large-scale public datasets. GrowthHacker autonomously and iteratively modifies code, runs OPE, and uses the metrics to guide subsequent optimization. We evaluate methods on Open Bandit Pipeline (OBP) and Scope-RL, and develop a two_agent framework that addresses limitations of existing frameworks while reducing complexity. Across both libraries, two_agent shows the highest reliability (98.1%-100% success rate) and positive-outcome rate (78%), with a median improvement of 4.4% among positive outcomes; CrewAI achieves the highest average improvement (37.9%) and is the only framework with zero extreme-value failures. AutoGen and Default each reach 65% positive-outcome rates. These results establish the feasibility of using LLM-based agents as automated "growth hackers" to continuously improve OPE systems, with implications for scaling data-driven decision-making where manual optimization is expensive.

10.
arXiv (CS.AI) 2026-06-17

From Paper to Program: Knowledge Externalization for AI-Assisted Quantum Many-Body Code Generation

作者:

arXiv:2604.04089v3 Announce Type: replace-cross Abstract: Large language models can write scientific code, but direct paper-to-program translation remains fragile when correctness depends on tacit conventions in the literature. We identify this bottleneck as knowledge externalization: converting implicit computational assumptions – index conventions, gauge choices, fermionic signs, contraction order, and memory constraints – into an explicit technical specification before implementation. We evaluate a multi-stage, human-in-the-loop workflow that inserts such a specification, with validation and stop gates, between theory extraction and code generation. The workflow is tested on two algorithmically distinct quantum many-body tasks: variational sweep-based Density-Matrix Renormalization Group (DMRG) from a pedagogical review and constructive Pfaffian conversion of Hartree–Fock–Bogoliubov states to matrix product states from the five-page Letter by Jin et al., Phys. Rev. B 105, L081101 (2022), for which no public code is available. For DMRG, all 16 specification-guided model pairings in a $4\times4$ grid satisfy physics-validation criteria, compared with 6/13 direct attempts. A prose-specification ablation indicates that externalized content, not \LaTeX{} formatting, is the essential ingredient. For Pfaffian-MPS, the workflow succeeds in 11/26 archived attempts, whereas direct prompting yields zero audited passes. Cross-specification transfer is asymmetric: non-GPT specifications implemented by GPT~5.5 pass 4/4, while GPT~5.5 specifications implemented by weaker models fail 4/4, indicating a residual implementation-model bottleneck. The resulting Paper-to-Program Many-Body skill provides an auditable protocol for AI-assisted implementation of many-body algorithms and for diagnosing where externalization succeeds or fails.

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

PianoKontext: Expressive Performance Rendering from Deadpan Context

arXiv:2606.12282v1 Announce Type: cross Abstract: Expressive performance rendering (EPR) aims to generate realistic performances constrained on sequences of notes. However, flow matching audio editing models manipulate only synchronized music samples of the same duration, limiting their understanding of expressive timing. We introduce PianoKontext, a flow matching rendering model for classical piano music that generates variable-length performances in the latent space of a pretrained Music2Latent model. We synthesize MIDI scores into deadpan audio and employ Dynamic Time Warping (DTW) in the latent space to construct paired data for training. The aligned embeddings are concatenated in DiT blocks, allowing for a simple and effective learning of the dependencies between the score and performances. Audio samples are available at our demo page: https://realfolkcode.github.io/pianokontext_demo/.

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

Beyond Parallel Sampling: Diverse Query Initialization for Agentic Search

arXiv:2606.17209v1 Announce Type: new Abstract: Test-time scaling for agentic search typically increases depth (i.e., more turns and tokens per trajectory) or breadth (i.e., more parallel rollouts). Here we focus on breadth scaling, showing that standard parallel sampling yields diminishing returns, tracing this to query redundancy at the first turn. When models issue similar first queries across rollouts, the threads retrieve overlapping evidence, and subsequent turns are conditioned on this shared retrieval. We address this limitation with DivInit, a training-free intervention at the first turn. Rather than sampling k independent first queries, DivInit draws n candidates from a single call, picks k < n diverse seeds, and runs them as parallel trajectories. Across five open-weight models and eight benchmarks, DivInit consistently improves over standard parallel sampling, with average gains of five to seven points on multi-hop QA at matched compute. Code available at https://github.com/cxcscmu/diverse-query-initialization

13.
arXiv (CS.CL) 2026-06-19

A BART-based approach with hierarchical strategy for Vietnamese abstractive multi-document summarization

In this technical report, we focus on solving the challenge of Vietnamese multi-document abstractive summarization, introduced in the International Workshop on Vietnamese Language and Speech Processing (VLSP) 2022. We choose to follow the popular hierarchical approach, i.e. condensing each document followed by aggregation and summarization. We propose a novel yet simple strategy to shorten documents that is driven by the golden summary, thus ensuring high correlation between stages of the hierarchical approach. Our method achieves a ROUGE2-F1 score of 0.2468 on the VLSP's public test set, and can produce fluent and concise summaries. Additionally, we utilize external sources for extra data, which greatly enhances the quantity of data for Vietnamese multi-document summarization. The additional data is made available for the community.

14.
Science (Express) 2026-04-16

Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase | Science

作者: 未知作者

Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two distinct RTs (Drt3a and Drt3b) and a noncoding RNA (ncRNA), synthesizes alternating poly(GT/AC) double-stranded DNA. Cryo–electron microscopy structures at 2.6 Å resolution reveal a D3-symmetric 6:6:6 complex of Drt3a, Drt3b, and ncRNA. Drt3a produces the poly(GT) strand using a conserved ACACAC template within the ncRNA. Notably, Drt3b synthesizes a complementary, protein-primed poly(AC) strand in the complete absence of a nucleic acid template, using conserved active site residues specific to Drt3b to enforce precise base alternation. These findings expand the functional landscape of nucleic acid polymerases, revealing a protein-templated mechanism for sequence-specific DNA synthesis.

15.
arXiv (CS.CV) 2026-06-11

Density Ridge Selective Prediction for LLM and VLM Hallucination Detection under Calibration Label Scarcity

Hallucination detection in large language and vision-language models is increasingly framed as selective prediction, where a detector assigns a confidence score and abstains when confidence is low. Unsupervised sampling detectors (Semantic Entropy) avoid labels but plateau in quality, while supervised probes attain stronger in-distribution scores yet degrade sharply when calibration labels are scarce. We recover the response manifold of an LLM as the density ridge of a kernel density estimate built on a six-dimensional kinematic feature map of hidden state generation trajectories. A test generation is scored by the negated Euclidean distance from its projected feature point to the nearest ridge vertex, yielding a low-dimensional geometric skeleton of the stochastic output distribution. We evaluate against Semantic Entropy, topological methods, and log-probability on six QA benchmarks (HaluEval-QA, TriviaQA, GSM8K, POPE, ScienceQA, A-OKVQA) using eight text and vision LLMs in a deliberately label-scarce protocol ($n_{cal}{=}200$ queries, $N{=}5$ generations). Our ridge-based score beats on AUROC with 5-20 points gain, while demonstrating tempered degradation under calibration-label scarcity.

16.
arXiv (CS.CV) 2026-06-17

Beware of Aliases – Signal Preservation is Crucial for Robust Image Restoration

Image restoration networks are usually comprised of an encoder and a decoder, responsible for aggregating image content from noisy, distorted data and to restore clean, undistorted images, respectively. Data aggregation as well as high-resolution image generation both usually come at the risk of involving aliases, i.e.~standard architectures put their ability to reconstruct the model input in jeopardy to reach high PSNR values on validation data. The price to be paid is low model robustness. In this work, we show that simply providing alias-free paths in state-of-the-art reconstruction transformers supports improved model robustness at low costs on the restoration performance. We do so by proposing BOA-Restormer, a transformer-based image restoration model that executes downsampling and upsampling operations partly in the frequency domain to ensure alias-free paths along the entire model while potentially preserving all relevant high-frequency information.

17.
medRxiv (Medicine) 2026-06-17

The interaction between chronic hepatitis B (CHB) and Metabolic dysfunction-associated steatotic liver disease (MASLD) in a diverse central London population

Introduction: The overlap between chronic hepatitis B (CHB) and metabolic dysfunction-associated steatotic liver disease (MASLD) is an emerging global health challenge. We investigated the impact of MASLD and metabolic comorbidity in a diverse London viral hepatitis clinic. Methods: This retrospective cross-sectional study (May 2018-Feb 2024) included adults with CHB having controlled attenuation parameter (CAP) measurements. MASLD was defined as CAP >264 dB/m plus [&ge;]1 cardiometabolic factor (CMF). We used univariable and multivariable models to examine MASLD's relationship with liver stiffness and hepatitis B viral load (HBV VL). Results: Among 323 individuals (67% male, median age 36), most were from Black (35%) or non-white British/Irish (29%) backgrounds. Overall, 64% had [&ge;]1 CMF, and 20% had MASLD. The CHB/MASLD group was significantly older (median 43 vs 35 years, p

18.
arXiv (math.PR) 2026-06-12

Sphere Packings in Higher Dimension (after Boaz Klartag)

arXiv:2606.13313v1 Announce Type: cross Abstract: Let $\delta_n^L$ be the maximal density of a lattice sphere packing in the $n$-dimensional Euclidean space. We explain how Boaz Klartag proved the inequality $\delta_n^L \geq c n^2 2^{-n}$ where $c>0$ is a universal constant. In higher dimension, even for non-lattice sphere packings, this new lower bound is a substantial improvement. Klartag's proof uses the probabilistic method in two different ways. The first, very standard, relies on the statistical properties of a uniformly chosen random lattice. The second, completely new, studies the stochastic evolution of an ellipsoid constrained to contain non nonzero lattice points in the interior.

19.
medRxiv (Medicine) 2026-06-22

Artificial Intelligence-Enabled Cardiac Function Estimation from Phone Videos of Echocardiograms

Importance: Mobile phone-recorded echocardiogram videos are commonly used in point of care, telemedicine, and resource-limited workflows, but artificial intelligence models for left ventricular ejection fraction (LVEF) estimation have primarily been evaluated on native Digital Imaging and Communications in Medicine (DICOM) videos. Objective: To evaluate whether previously described artificial intelligence models for LVEF estimation retain performance when applied to mobile phone-recorded echocardiographic videos. Design: Multicenter model validation study comparing model-estimated LVEF with clinician reported LVEF. Setting: Three medical centers: Kaiser Permanente Northern California, Beth Israel Deaconess Medical Center through MIMIC-IV-ECHO, and Cedars-Sinai Medical Center. Participants: Source studies with clinician reported LVEF and apical 4-chamber or apical 2-chamber views, yielding 6209 phone-recorded videos from 2648 studies and 2611 patients. Exposures: Mobile phone recording of native echocardiographic videos and fine-tuning of pretrained models using mobile phone-recorded videos from the Kaiser Permanente Northern California training cohort. Main Outcomes and Measures: Mean absolute error in ejection fraction percentage points, R^2 for continuous estimation, and area under the receiver operating characteristic curve for identifying ejection fraction greater than 50%. Results: The study included 6209 mobile phone recorded echocardiographic videos from 2648 studies and 2611 patients; the weighted mean age was 68.4 years, and 1031 patients were male (39.5%). Without phone-video fine-tuning, the primary model achieved a mean absolute error of 7.00 percentage points, coefficient of determination of 0.49, and area under the receiver operating characteristic curve of 0.91 on phone-recorded videos; corresponding native DICOM performance was 6.08 percentage points, 0.60, and 0.93, respectively. On the 2396-video fine-tuning evaluation cohort, fine-tuning improved primary model performance to a mean absolute error of 6.96 percentage points, coefficient of determination of 0.61, and area under the receiver operating characteristic curve of 0.93. Fine-tuning the public EchoNet-Dynamic model improved performance from 9.36 percentage points, 0.37, and 0.84 to 7.86 percentage points, 0.50, and 0.89, respectively. Progressive central zoom preprocessing degraded model performance. Conclusions and Relevance: These findings suggest that artificial intelligence assisted left ventricular ejection fraction estimation from mobile phone-recorded echocardiograms may be feasible when native image export is unavailable, although prospective evaluation is needed before clinical deployment.

20.
arXiv (CS.AI) 2026-06-16

Theorem-Grounded Execution Ontologies for Interpretable Machine Reasoning

arXiv:2606.16010v1 Announce Type: cross Abstract: Large language models have achieved impressive performance on reasoning tasks spanning mathematics, science, programming, and commonsense inference. Despite these advances, their reasoning processes remain largely latent, making them difficult to interpret, verify, replay, debug, and transfer across domains. Existing approaches such as chain-of-thought, tree-of-thoughts, graph-of-thoughts, and tool-augmented reasoning expose intermediate reasoning artifacts but typically lack explicit execution semantics, formal state representations, and verifiable reasoning structures. We introduce Theorem-Grounded Execution Ontologies (TGEO), a framework that models reasoning as an executable state-transition process rather than a sequence of generated tokens. Given an input problem, TGEO identifies relevant theorem families, binds the problem to a domain ontology, discovers semantic objects, instantiates states and operators, constructs predicates and contracts, and synthesizes an executable reasoning graph. The resulting graph provides an interpretable, replayable, and auditable representation of reasoning in which every state transition, operator application, and validation step is explicitly represented. TGEO integrates five architectural components: (1) theorem-grounded reasoning priors, (2) executable ontologies, (3) operator-mediated state transitions, (4) predicate and contract-based execution validation, and (5) architectural auditing and failure localization. We evaluate TGEO on theorem-intensive reasoning tasks derived from mathematical benchmark domains and a curated Golden Execution Suite. Our findings demonstrate the value of executable reasoning representations for interpretable, verifiable, and reproducible AI reasoning systems.

21.
arXiv (CS.AI) 2026-06-17

CMIP-Forge: An Agentic System that Retrieves, Computes, and Self-Reviews Climate Science

arXiv:2606.17076v1 Announce Type: cross Abstract: The Coupled Model Intercomparison Project Phase 6 (CMIP6) has generated thousands of peer-reviewed publications documenting model configurations, evaluation procedures, emergent constraints, and projection uncertainties. As the community transitions toward CMIP7, efficiently extracting and operationalizing this unstructured knowledge alongside live data analysis represents a critical bottleneck. Here we present CMIP-Forge, a hybrid retrieval-augmented generation (RAG) and autonomous analysis system that bridges the gap between scientific literature and Earth System Grid Federation (ESGF) data archives. The system pairs a curated corpus of 6,581 CMIP6-related open-access publications (101,828 indexed chunks) with an agentic pipeline in which a tool-augmented worker plans and executes Python workflows over live climate data, while a panel of independent reviewer models audits its methodology end to end. CMIP-Forge introduces a multi-layered Defense-in-Depth architecture that enforces physical and methodological invariants through executable mechanisms: Abstract Syntax Tree (AST) static analysis, audited scientific primitives, and an autonomous adversarial peer-review protocol. We demonstrate the system's capabilities through end-to-end autonomous research pipelines spanning atmospheric teleconnections, ocean dynamics, regional extremes, and global warming projections. An agentic analysis system grounded in peer-reviewed literature, constrained by automated code guardrails, and audited by an independent adversarial review loop can complete complex climate-research workflows autonomously. The same experiments expose concrete failure modes of the review loop (sycophantic regression, REVISE verdicts that are never resolved, and the submission of stub code for review), each diagnosable from the immutable telemetry and provenance record released with the article.

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

Learning to Distort: Weakly-Supervised Image Quality Transfer for Prostate DWI Correction

Single-shot echo-planar prostate diffusion-weighted imaging (DWI) is frequently complicated by geometric distortions, which impact the ability to derive reliable diagnoses from such images. Developing automated correction methods is challenged by the absence of paired distorted and undistorted clinical scans. In this paper, we first propose a novel weakly-supervised image quality transfer (IQT) framework from undistorted to distorted images that utilizes image quality assessment (IQA) signals to supervise the transfer process. Unlike traditional methods that require expensive, voxel-wise paired data or resort to developing unpaired algorithms, our approach utilizes image-level quality labels (here, distorted vs. undistorted) to establish latent quality prototypes within a pre-trained feature space. Recognizing that simulating realistic distortions is more reliable than direct unpaired correction, we describe a weakly-supervised prototype flow matching algorithm to explicitly regularize generative trajectories towards distorted prototypes, producing realistic susceptibility artifacts that mimic clinical degradations. By synthesizing these realistic pairs, we enable a second IQT model to be trained in the forward direction for distortion correction. Experimental results demonstrate that our generated images successfully mimic the diagnostic interference of real-world artifacts, which leads to more capable distortion correction IQT models. In addition to qualitative comparisons, we also conduct exhaustive quantitative evaluations that compare our approach with existing unpaired approaches (e.g., CycleGAN, UNIT-DDPM, and OT-FM) - as either forward or reverse alternatives - by assessing clinical downstream task performance in PI-RADS and Gleason score classification, using both in-distribution and external data sets.

23.
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.LG) 2026-06-17

Continuous-time Optimal Stopping through Deep Reinforcement Learning

arXiv:2606.17545v1 Announce Type: new Abstract: Simulation based solvers for optimal stopping problems must discretize the stopping decision. Under classical dynamic programming, a coarse exercise grid with only a few stopping opportunities can materially undervalue the optimal expected reward, whereas on a very fine grid, approximation errors accumulate through the backward recursion. To remove this limitation, we develop a new reinforcement-learning inspired algorithm that enables us to learn the exercise rule at arbitrarily fine time resolution. Our CARLOS (Continuous-time Adaptive Reinforcement Learning for Optimal Stopping) algorithm utilizes an aggregate deep neural network (ADNN) to learn a joint space-time decision boundary. Starting from a coarse time grid, we progressively increase the frequency of stopping opportunities, while in parallel training the ADNN to refine its timing-value estimates. We moreover design an adaptive sampling strategy that gradually concentrates training effort near the stopping boundary. Benchmarked results show that CARLOS delivers higher prices than existing Bermudan solvers, approaching the American upper bound, and achieves high computational efficiency relative to non-RL comparators.

25.
arXiv (CS.LG) 2026-06-12

The Metric Picks the Winner: Evaluation Choice Flips Model Rankings for Drug-Response Prediction in Unseen Chemistry

arXiv:2606.12639v1 Announce Type: new Abstract: Predicting how a cell's transcriptome responds to a drug it has never seen is a core, hard problem in computational cell biology: recent benchmarks show complex models often fail to beat trivial baselines once test compounds are held out by chemistry. We study one cell line and assay, THP-1 cells profiled by DRUG-seq, scored by the active-compound weighted MSE(wMSE) of the VCPI prediction contest. We propose a staged approach: dumb baselines (untreated control and mean training-compound response) that the field keeps failing to beat; non-parametric retrieval (a Tanimoto-weighted average of a held-out compound's nearest training compounds); and a fusion stage combining a frozen chemistry embedding with retrieval-support features to predict the residual over the mean, with an uncertainty head and gene programs. On the released VCPI THP-1 drug-seq data (14,026 training compounds), under a Bemis-Murcko scaffold split, the model ranking inverts depending on the metric. Under an inverse-variance per-gene proxy, a regularized linear regression on Morgan fingerprints appears to win over the deep models, retrieval, and ChemBERTa – the textbook "simple baselines win" result. But under the contest's true active-set metric (per-(gene, compound) Mejia weights, validated against the official scorer; mean baseline 0.535 vs the organizers' 0.507 reference), that reverses: the deep models win, our fusion decoder significantly beats the linear fingerprint baseline (-0.012 wMSE, paired bootstrap p < 10^-4), and the proxy's winner becomes the worst chemistry-aware predictor. Picking the metric picks the winner – to our knowledge the first demonstration on real held-out drug chemistry of the metric-calibration effect established largely on genetic perturbation. We release a reproducible pipeline wired to the official scorer that emits a valid submission over the real 1064 x 12,995 grid.