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

P3D-Bench: Benchmarking MLLMs for Parametric 3D Generation and Structural Reasoning

Multimodal large language models can write code to produce complex programs as well as use programs to do 3D modeling, which opens up a new avenue for 3D generation powered by their priors, world knowledge and reasoning. Yet existing benchmarks rarely evaluate 3D modeling through code. Such modeling demands more than runnable code: from a text or visual specification, a model must generate a parametric 3D program that is geometrically precise, semantically aligned and assembly-consistent. We introduce P3D-Bench, a benchmark for parametric 3D generation. Unlike a 3D mesh, a parametric 3D program exposes explicit dimensions, construction operations and part relations, revealing whether a model recovers a design's structure, not just its appearance. Under a unified protocol, P3D-Bench covers three task families (Text-to-3D, Image-to-3D and Assembly-3D) and scores each output for executability, geometric fidelity, topology, text-grounded constraints, multiview semantic alignment and part-level structure. We evaluate frontier MLLMs and text-only LLMs on 400 text cases, 400 image cases and 203 annotated assemblies, with domain-specific models as reference points. Our extensive evaluation yields three findings. First, assemblies are the hardest setting, where models still fail to compose multiple parts into a coherent structure. Second, models can often recover the global shape and semantic identity of the target object, yet fail to reproduce the precise parametric geometry specified by the input. Third, part-level modeling remains weak on assemblies, where models recover neither the geometry of each part nor the right number of parts. These results position P3D-Bench as a benchmark for evaluating precise parametric geometry and part-level structure in parametric 3D generation.

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

Transfer Learning for FHIR Questionnaire Terminology Binding

Electronic prior authorization workflows require FHIR Questionnaire items to carry LOINC codes, yet most items in the HL7 Da Vinci CDS-Library lack these bindings. We treat this as a retrieval problem: given a Questionnaire item's text, find the correct LOINC code in a pool of 97,314 active codes. We compare six methods (TF-IDF, frozen MiniLM, BioBERT, BioLORD, contrastively fine-tuned MiniLM, and a TF-IDF+GPT reranker) on a 54-item evaluation set spanning three query styles (natural question, medium, and terse). No single method wins on every metric. BioLORD, a frozen encoder pre-trained on biomedical ontology definitions, has the best top-rank accuracy (R@1 = 0.185, MRR = 0.246) despite seeing no task-specific data, while a contrastive fine-tune on raw LHC-Forms pairs takes R@5 (0.389) and R@10 (0.426). A distribution-shift ablation shows why the fine-tune in our main table is not the strongest one: adding GPT-generated paraphrases to the raw pairs drops R@5 from 0.389 to 0.296, so the augmented union underperforms raw-only training on every metric except R@1. Performance peaks at 5k training pairs. Error analysis on BioLORD's R@1 failures shows that wrong-specificity and ambiguous-text cases together account for 59% of errors.

03.
arXiv (CS.AI) 2026-06-16

Green AI Carbon Optimizer: Carbon-Efficient Training Location Recommendation and Global AI Energy Demand Forecasting

arXiv:2606.14707v1 Announce Type: cross Abstract: AI training and deployment consume substantial electricity, but carbon outcomes remain weakly integrated into routine model development decisions. This paper presents Green AI Carbon Optimizer with two primary contributions: (i) a carbon aware cloud region recommendation method for training workloads, and (ii) a power law forecasting pipeline for global AI energy demand. For location recommendation, we combine regional grid carbon intensity, renewable share, and data center Power Usage Effectiveness (PUE) into a unified scoring model across 100+ regions from major cloud providers. For a reference workload (8*A100, 100h), estimated emissions in our sampled regions range from 7.74kg to 272.00kg CO2. Selecting the best region instead of the worst corresponds to a 97.2% reduction relative to the worst case. Ablation shows that ranking by renewable share alone can select regions with higher CO2 emissions than rankings that include grid carbon intensity. For forecasting, we fit a power law relation between parameter count and training energy using 26 anchor models. We combine this fit with scenario assumptions on model growth, hardware efficiency, and training frequency, and evaluate sensitivity to inference ratio and ecosystem scaling. Across scenarios, projected 2030 demand ranges from 7TWh to 1,436TWh under the stated assumptions, highlighting the importance of deployment choices, model scaling discipline, and transparent energy reporting.

04.
arXiv (CS.CL) 2026-06-25

The Tatoxa System for Text Detoxification in Low-Resource Languages: The Case of Tatar

Text detoxification, the automated detection and mitigation of abusive and harmful content, is essential for ensuring the safety of online communities and protecting users. However, low resource languages such as Tatar have received little research attention. In this paper we present Tatoxa, a novel state-of-the-art system for text detoxification in the Tatar language. Comparative experiments show that the proposed approach outperforms existing open source and proprietary commercial LLMs on key quality metrics. We also introduce a new dataset for text detoxification in Tatar, designed for fine tuning and evaluation in low resource settings. Finally, cross lingual transfer experiments indicate that transfer from other languages, including the culturally close Russian, performs significantly worse than training on native Tatar data even when a large Russian corpus is available.

05.
arXiv (CS.AI) 2026-06-19

Augmenting Game AI with Deep Reinforcement Learning

arXiv:2606.20210v1 Announce Type: new Abstract: Immersion in video games depends not only on graphics, audio, and game mechanics, but also on the quality of in-game characters. Producing believable characters, or game AI, remains a significant challenge as behavioral complexity is hard to capture with hand-coded systems. Game AI is a source of immersion and engagement; however, the limitations stemming from the challenges of creating game AI often lead to frustration and the breaking of the illusion of realism within the game. The introduction of machine learning models opens the door to creating more believable, authentic, and relatable characters in games. The promise is that they either learn from interacting with the game, or from player data, to develop true human-like behavior. In this paper, we envision more applications of reinforcement learning for game AI in the future. For this to materialize, current research limitations are prohibitive to broad deployment across game genres. Therefore, we propose a framework for training reinforcement learning models with a set of requirements in mind that are suited towards game AI and game development. We present examples of games with reinforcement learning-augmented game AI and describe the practicalities of deploying player-facing machine learning agents in modern games. Furthermore, we identify bottlenecks and hard problems in these areas, which we believe offer promising research directions to accelerate the adoption of machine learning in game AI for the video game industry.

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

Low-rank Updates in Slowly Time-varying Graphs for Spatial-Temporal Signal Interpolation

arXiv:2606.24011v1 Announce Type: cross Abstract: A crucial assumption in graph signal processing (GSP) is the existence of an underlying graph that captures the pairwise similarities between nodes, allowing filters to be designed based on this graph for tasks such as denoising. For spatial-temporal data in which node-to-node similarities evolve over time, a static spatial graph is insufficient. In this paper, to represent slowly time-varying pairwise relationships, we model the graph changes in two consecutive adjacency matrices $P = W^{(2)} - W^{(1)}$ across time as a low-rank matrix. % Specifically, given an initial adjacency matrix $W^{(1)}$ at time $t=1$, we jointly interpolate a signal $x_2$ and estimate $W^{(2)}$ at $t=2$ using both a graph signal smoothness prior for $x_2$ and a low-rank prior on $\P$. We alternate optimization steps. With $W^{(2)}$ fixed, $x_2$ is interpolated by solving a linear system. Alternatively, holding $x_2$ fixed, $W^{(2)}$ is updated via proximal gradient descent (PGD). The proximal mapping of the rank term $Gamma(W^{(2)} - W^{(1)})$ is approximated in linear time using a fast orthogonal matching pursuit (OMP) algorithm that selects a sparse combination of atoms from a dictionary $cR$ formed by the outer products of $W^{(1)}$'s eigenvectors. We unroll iterations of our algorithm into layers to build a lightweight neural network for limited data-driven parameter tuning. Experiments show that our joint optimization achieves better signal interpolation compared to existing time-varying graph models.

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

Spectral DPPs via NEPv: A Scalable Continuous Relaxation of Determinantal MAP for Diversity-Aware Data Selection

arXiv:2606.19411v1 Announce Type: new Abstract: Selecting a small, diverse, high-quality subset from a massive pool of candidates is a recurring primitive in modern machine learning – data curation and coreset selection for training and fine-tuning large models, active-learning batch acquisition, prompt and exemplar selection for in-context learning, retrieval diversification, and experimental design. Determinantal Point Processes (\operatorname{DPP} s) give a principled, well-calibrated notion of diversity for this task, but their MAP objective – pick a size-$k$ subset $S$ maximizing $\logdet(L_S)$ – is NP-hard, and the standard greedy and sampling algorithms scale superlinearly in the ground-set size $n$. This cost is prohibitive precisely in the data-centric regime where diversity matters most, where $n$ ranges over millions to billions of candidate examples, features, or embeddings. We recast \operatorname{DPP}-MAP as a continuous optimization problem over the Stiefel manifold, and show that its first-order optimality conditions form a Nonlinear Eigenvalue Problem with eigenvector dependency (\operatorname{NEP}v) of a previously unstudied form. This \operatorname{NEP}v\ admits a self-consistent field (\operatorname{SCF}) iteration with a spectral-gap-based local contraction guarantee, giving a principled iterative solver where the diversity objective drives an eigenvector-dependent operator. The resulting algorithm, \OurMethod, requires only matrix-vector products with the kernel and runs in time $O\!\big((ndk+nk^2)\,t\big)$ for a small number of iterations $t$, scaling near-linearly in $n$ and integrating directly with low-rank and feature-map kernels common in ML. This paper focuses on the relaxation, solver, and scaling analysis; full real-data benchmarking is left to a planned empirical study.

08.
medRxiv (Medicine) 2026-06-24

Matrix matters: head-to-head concordance of serum and plasma for NULISAseq CNS Disease Panel

Blood-based proteomic profiling is now widely applied in neurodegenerative and neuroinflammatory disease, yet the choice between serum and plasma remains poorly characterised for high-multiplex platforms. Many legacy biobanks hold mainly serum, whereas most current NUcleic-acid-Linked Immuno-Sandwich Assay (NULISA) studies use plasma. We compared the 130-protein NULISAseq central nervous system (CNS) Disease Panel head-to-head in matched serum and plasma collected at the same draw from 62 participants (30 neurodegenerative, 19 demyelinating, 13 healthy controls). Agreement was measured with Spearman correlation (rho), Lin's concordance correlation coefficient (CCC), the intraclass correlation coefficient (ICC) and the mean paired serum-to-plasma difference (dNPQ). Concordance was moderate to high: 123 of 130 proteins reached significance and 18 reached rho >= 0.90, with a median rho of 0.72 (range 0.10-0.988). Proteins fell into three tiers. Cytoskeletal markers (NEFH rho=0.988; NEFL rho=0.947) and glial GFAP (rho=0.949, |dNPQ|

10.
arXiv (CS.CV) 2026-06-25

Hybrid deep learning-based phase diversity method for wavefront reconstruction

The efficiency of high-power laser systems is limited by wavefront distortions in the beam, particularly non-common path aberrations, which reduce the peak intensity at the focal plane. Compensating for these aberrations requires the calibration of the adaptive optics system. Conventional calibration methods rely on a time-consuming iterative optimization that is highly sensitive to initial conditions. While deep learning-based models offer high speed, they often demonstrate insufficient accuracy. In this work, we present a hybrid wavefront reconstruction method that combines a convolutional neural network to generate an initial estimate of the wavefront distortions, with the L-BFGS (Limited-memory Broyden-Fletcher-Goldfarb-Shanno) algorithm for its subsequent refinement. In numerical simulations, the method achieved an efficiency of $\sim 0.99$ in 80% of the cases for a root-mean-square (RMS) of wavefront distortions ranging from 0 to $1.3\lambda$. In a physical experiment, for initial wavefront distortions with RMS values from 0.15 to $0.6\lambda$, the method achieved an efficiency of $\sim 0.75$. As a result, focusing with a Strehl ratio of $0.96 \pm 0.02$ was attained within 2 to 4 iterations of the algorithm, confirming the applicability of the method for the fast and accurate calibration of adaptive optics systems under real experimental conditions.

11.
arXiv (CS.LG) 2026-06-25

ConSolv: Solvent-Conditional Machine Learning Implicit Solvent Potential

arXiv:2606.24983v1 Announce Type: cross Abstract: Implicit solvent machine learning potentials (MLPs) offer a powerful route to bridging the gap between accuracy and efficiency in molecular simulations. However, existing models have largely focused on aqueous environments, overlooking the diverse and important roles of non-aqueous solvents in areas such as organic synthesis and battery technology. Here, we present ConSolv, a solvent-conditional MLP architecture that explicitly incorporates solvent effects on solute interactions through an attention-based solvent-embedding block. By combining experimental solvation free energy data with ab initio data, we train a single implicit solvent MLP that is transferable across 66 common organic solvents. ConSolv outperforms classical explicit solvent methods and selected ab initio implicit solvent approaches across multiple solvation free energy benchmarks, and demonstrates generalization to unseen solvents. Beyond solvation free energies, the model shows close agreement with experimental nuclear magnetic resonance (NMR) data for $\gamma$-fluorohydrin molecules in chloroform. ConSolv's architecture is readily extensible to broader chemical spaces and alternative training strategies, while its attention-based design supports explainable artificial intelligence (AI) analysis that can help elucidate complex, solvent-dependent molecular interactions.

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

Multi-Granular Node Pruning for Causal Circuit Discovery

arXiv:2512.10903v2 Announce Type: replace Abstract: Circuit discovery aims to identify minimal subnetworks that are responsible for specific behaviors in large language models (LLMs). Existing approaches primarily rely on iterative edge pruning, which is computationally expensive and limited to coarse-grained units such as attention heads or MLP blocks, overlooking finer structures like individual neurons. We propose a node-level pruning framework for circuit discovery that addresses both scalability and granularity limitations. Our method introduces learnable masks across multiple levels of granularity, from entire blocks to individual neurons, within a unified optimization objective. Granularity-specific sparsity penalties guide the pruning process, allowing a comprehensive compression in a single fine-tuning run. Empirically, our approach identifies circuits that are smaller in nodes than those discovered by prior methods; moreover, we demonstrate that many neurons deemed important by coarse methods are actually irrelevant, while still maintaining task performance. Furthermore, our method has a significantly lower memory footprint, 5-10x, as it does not require keeping intermediate activations in the memory to work.

13.
arXiv (quant-ph) 2026-06-25

Hodge Spectral Surrogates for Topology-Constrained Optimization

arXiv:2606.25194v1 Announce Type: cross Abstract: Topological information is widely used in data analysis, network design, and machine learning, and topological constraints naturally arise when optimizing or generating objects with prescribed homological structure. However, directly controlling Betti numbers and persistent homology is difficult because they are discrete and combinatorial. We propose a differentiable framework for topology-constrained optimization based on Hodge-spectral relaxations of homological constraints and low-pass spectral filters. From soft graphs and soft clique complexes, we construct Hodge-Laplacian-type spectral relaxations that unify graph clique complexes and Vietoris–Rips filtrations of point clouds. In the hard limit, the penalty-regularized ambient operator recovers the ordinary Hodge Laplacian on the active subcomplex, while in the soft regime it serves as a differentiable low-frequency spectral surrogate. Homological information is represented by zero and near-zero modes, and differentiable topological objectives are defined using heat filters, resolvent filters, and polynomial Laplacian moments. For point clouds, we show that the proposed Hodge spectral-filter losses yield more spatially distributed gradients, smoother scale-normalized behavior under persistence-pairing changes, and geometry-aware update directions than persistent-homology-based losses. For graph clique complexes, Laplacian moments control normalized first-Betti-type quantities and can be combined with ordinary graph-feature objectives. We also discuss connections to trace-based normalized Betti-number estimation, polynomial spectral methods, and possible quantum trace estimation.

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

Training-Free Open-Vocabulary Visual Grounding for Remote Sensing Images and Videos

Remote sensing visual grounding (RSVG) aims to localize a referred target in a remote sensing image or video according to a natural language expression. Existing RSVG methods usually rely on task-specific manual annotations, which are costly to collect and inevitably limited in covering the diversity of real-world geospatial scenarios. As a result, they often struggle to generalize to open-vocabulary queries involving novel objects, fine-grained attributes, complex spatial relationships, and functional semantics. In this paper, we propose RSVG-ZeroOV, a training-free framework that leverages frozen generic foundation models for zero-shot open-vocabulary RSVG. RSVG-ZeroOV follows an Overview-Focus-Evolve paradigm, which exploits the distinct yet complementary attention patterns of vision-language models (VLMs) and diffusion models (DMs) to progressively generate precise grounding results. Specifically, (i) Overview utilizes a VLM to extract cross-attention maps that capture semantic correlations between the referring expression and visual regions; (ii) Focus leverages the fine-grained modeling priors of a DM to compensate for object structure and shape information often overlooked by VLM attention; and (iii) Evolve introduces a simple yet effective attention evolution module to suppress irrelevant activations, yielding purified object masks. To handle video inputs, we further present Video RSVG-ZeroOV, which extends image-level grounding to spatio-temporal grounding through a query-relevant key-frame selector and a temporal propagator, enabling efficient and temporally coherent video grounding without video annotations or fine-tuning. Extensive experiments on six image and video grounding benchmarks show that RSVG-ZeroOV consistently outperforms existing zero-shot baselines and achieves competitive or superior performance compared with weakly- and fully-supervised methods.

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

ScaleToT: Generalizing Structured LLM Reasoning for Billion-Scale Low-Activity User Modeling

arXiv:2606.24605v1 Announce Type: new Abstract: Accurate user modeling often depends on rich interaction histories, which are unavailable for billions of low-activity users. Large Language Models (LLMs) can infer latent user states from static profiles, but this reasoning becomes unreliable when profiles are sparse, and applying an LLM to billions of users is prohibitively expensive. We present ScaleToT, which learns structured reasoning from a small LLM-processed subset and extends it to the broader low-activity user population. To improve reasoning reliability, ScaleToT constructs typed user-state chains with a bounded entropy-guided Tree-of-Thought (ToT) refinement procedure. To make this structured reasoning usable from sparse profiles, the teacher-curated chains are used to train a student model on static profiles through supervised fine-tuning (SFT) and Outcome-Driven Segment-Aware Implicit Reward Policy Optimization (OSIPO). ScaleToT then transfers the student's reasoning representations to a lightweight profile encoder, providing shared reasoning signals for the remaining users without LLM inference. We evaluate ScaleToT on lifetime value (LTV) prediction in a billion-scale advertising deployment. A randomized online A/B test increased LT30 by 6.738\%, while offline reasoning covered only 7.32\% of the potential population, greatly reducing compute cost compared with full-population reasoning.

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

Conformal Path Reasoning: Trustworthy Knowledge Graph Question Answering via Path-Level Calibration

Knowledge Graph Question Answering (KGQA) offers grounded, interpretable reasoning, but existing methods often fail to provide reliable coverage guarantees over retrieved answers. While Conformal Prediction (CP) offers a principled framework for producing prediction sets with statistical guarantees, prior conformal KGQA methods suffer from two critical pitfalls: violated coverage guarantees due to invalid calibration, and weak score discriminability that yields excessively large prediction sets. We propose Conformal Path Reasoning (CPR), a novel trustworthy KGQA framework built on two key innovations. First, query-level conformal calibration over path-level scores preserves exchangeability to ensure valid coverage guarantees. Second, we introduce the Residual Conformal Value Network (RCVNet), a lightweight module trained via PUCT-guided exploration to learn discriminative path-level nonconformity scores. Extensive experiments show that CPR significantly improves the Empirical Coverage Rate by 45% while reducing prediction set size by 52% on average over conformal baselines across benchmark datasets, highlighting its effectiveness for reliable conformal reasoning over knowledge graphs.

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

From Open Waters to Enclosed Cabins: ProteusVPR for Cross-Scene Visual Place Recognition in Maritime Perception and Cabin Inspection

Autonomous robotic inspection in maritime environments presents unique challenges for Visual Place Recognition (VPR) due to cross-scene perceptual shifts. Robots navigating ship-borne environments must transition between visually distinct domains: open decks with sparse textures and severe illumination changes, and enclosed cabins with repetitive structures and high visual ambiguity. Existing VPR methods, designed primarily for urban or indoor scenes, fail to generalize reliably across these starkly different scenarios. To address this, we propose ProteusVPR, a two-stage retrieval-refinement framework. The first stage employs any standard VPR model for initial image retrieval. The second stage introduces a geometric-visual estimation network that fuses the retrieved image with two temporally preceding frames, incorporating geometric descriptors, a local affine coordinate system, and camera azimuth encoding to achieve precise localization. To support this task, we introduce the XHZ dataset, an 8K-panoramic ship-borne dataset collected from an operational vessel, featuring multi-floor cabin structures, deck transition zones, and strict query-database separation for rigorous evaluation. Extensive experiments on the XHZ dataset demonstrate that ProteusVPR consistently improves the localization accuracy across multiple VPR backbones, reducing mean localization error by over 60\% on average and that ProteusVPR offers an effective and robust solution for precise visual localization in challenging, cross-scene maritime environments.

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

Mix-QVLA: Task-Evidence-Aware Mixed-Precision Quantization of Vision-Language-Action Models

We propose Mix-QVLA, a task-evidence-aware mixed-precision PTQ framework for VLA models. Mix-QVLA anchors each quantized variant to the full-precision action-token reference decision and evaluates whether quantization preserves task-relevant evidence across key VLA functional boundaries. It computes normalized gradient-weighted task-evidence maps from boundary activations and compares full-precision and quantized maps using evidence-mass and attribution-distribution distortion, capturing changes in both the strength and allocation of decision-supporting evidence. A soft-bottleneck objective aggregates boundary-level degradation into layer-wise sensitivity scores. Mix-QVLA further models sensitivity throughout task execution, capturing phase-dependent shifts in layer importance rather than assuming a fixed sensitivity profile. The resulting evidence- and time-aware scores guide mixed-precision bit allocation under model-size and BitOps budgets. Extensive evaluations on OpenVLA-style policies show that Mix-QVLA improves the accuracy-efficiency trade-off of low-bit VLA deployment. On LIBERO, Mix-QVLA reduces OpenVLA-OFT memory from 15.4 GB to 4.1 GB, retains 96.3 average success compared with 97.1 for the BF16 model, and achieves a 1.52x inference speedup.

19.
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/.

20.
medRxiv (Medicine) 2026-06-17

Brain age gap correlates with DTI-derived microstructural abnormalities in multiple sclerosis.

Background: Brain age gap (BAG) is increased in multiple sclerosis (MS), but whether it reflects microstructural pathology beyond conventional atrophy remains unclear. Objective: To test whether BAG is elevated in MS and correlates with conventional and diffusion tensor imaging (DTI) abnormalities relative to healthy controls. Methods: A case-control study of 43 people with MS and 18 healthy controls was performed. BAG was estimated from T1-weighted MRI using brainageR. Controls were used as MRI reference distributions. MRI values were expressed as deviation z-scores and correlated with BAG within MS. Conventional MRI and DTI domains were analysed using age/sex-adjusted partial correlations with domain-wise Benjamini-Hochberg FDR correction, where appropriate. Results: BAG was higher in MS than controls (4.79 vs -2.58 years; p

21.
arXiv (CS.AI) 2026-06-25

Learning with a Single Rollout via Monte Carlo Pass@k Critic

arXiv:2606.25451v1 Announce Type: cross Abstract: Estimating token-level advantages in reinforcement learning (RL) for language models remains challenging because scaling up episodic experience collection is expensive. The difficulty intensifies for baseline advantage estimation methods, where repeated sampling causes trajectories to diverge into substantially different reasoning prefixes. In this context, RL algorithms such as GRPO prove limited: an outcome reward is too sparse to be attributed to specific actions like intermediate steps, and comparisons across sampled traces are non-trivial because they are heterogeneous. To mitigate both the computational cost of repeated sampling and the difficulty of credit assignment, we study single-rollout proximal policy optimization (SR-PPO) featuring token-level credit assignment in RL for language models. Instead of estimating advantages by normalizing episodic returns within the candidate group, we train a calibrated token-level credit critic using Monte Carlo outcomes from one rollout per prompt. Specifically, we use the critic to predict the Pass@k success probability at the prompt prefix, which is derived from a Pass@1 attempt. This choice yields a more selective learning signal than Pass@1: it discounts easily solved prefixes while prioritizing hard ones whose success probability remains marginal. We show that as $k$ increases, Pass@k converges to a reachability indicator, reflecting whether a prefix can lead to at least one successful continuation. In an explicit state graph, the limit ($k \rightarrow \infty$) can be computed in $O(|V|+|E|)$ time, offering a promising surrogate for direct credit assignment without the need to sample contrastive traces. As an initial validation, SR-PPO exhibits stable learning dynamics, along with consistent gains in Pass@128 success rates on mathematical reasoning benchmarks such as HMMT26 and AIME24.

22.
arXiv (CS.CL) 2026-06-19

Prompt, Plan, Extract: Zero-Shot Agentic LLMs Workflows for Lung Pathology Extraction from Clinical Narratives

Information extraction from pathology reports is essential for cancer staging, tumor registry population. Yet key data remains embedded in narrative reports, making manual extraction labor-intensive and error-prone. Traditional supervised Natural Language Processing pipelines address this through fully supervised Named Entity Recognition and Relation Extraction, but require expensive manual annotation and suffer cascading failures when upstream entities are missed. In this study, we developed a zero-shot, agentic workflow, and evaluated five open-source generative Large Language Models (LLMs) to populate 13 College of American Pathologists synoptic fields from lung resection pathology reports. We compared them against a state-of-the-art supervised GatorTron NER-RE baseline using a novel, registry-aligned evaluation framework. The baseline achieved Micro-F1of 0.960, while the best zero-shot model (GPT-OSS-20B) achieved Micro-F1 of 0.893 (recall: 0.949), accurately extracting complex relations like Pathologic Stage without task-specific training. These results suggest that open-source, zero-shot agentic LLMs are a low-cost solution for extracting lung pathology information.

23.
arXiv (CS.LG) 2026-06-15

Smoothing Dark Areas in Molecular Latent Diffusion

arXiv:2606.13955v1 Announce Type: new Abstract: Latent diffusion is a promising framework for scalable 3D molecular generation, but it requires a latent space that remains smooth, valid, and navigable beyond posterior samples. Existing molecular VAEs, however, are typically learned through reconstruction-based objectives, which do not guarantee such a latent space. We show that this leads to dark areas: regions of latent space that are reachable during diffusion sampling but decode to disconnected or chemically invalid molecules. Unlike in image generation, molecular decoding requires strict structural and chemical precision, so even small latent perturbations can produce catastrophic failures. We therefore propose TopVAE, a topology-optimized VAE that reduces dark areas by making the decoder internalize structural and chemical constraints during training, eliminating the need for test-time chemical correction. TopVAE greatly improves off-posterior robustness, and when paired with a standard DiT, achieves $77\%$ lower FCD-3D on QM9, the highest V&C, $52\%$ lower FCD-3D on GEOM-Drugs, and $1.29{\times}$ more stable and connected molecules on zero-shot scaffold inpainting.

24.
arXiv (CS.CL) 2026-06-18

Morpheus: A Morphology-Aware Neural Tokenizer and Word Embedder for Turkish

Turkish is agglutinative: meaning is carried by morphemes, yet the subword tokenizers that drive modern language models split words by corpus statistics, fragmenting semantically loaded suffixes and – in the case of WordPiece and rule-based analyzers – failing to decode their output back to the original text. This paper presents Morpheus, a neural morpheme-boundary model for Turkish that is at once a lossless, morphology-aware tokenizer and a word-embedding producer. A differentiable Poisson-binomial dynamic program turns per-character boundary probabilities into soft morpheme memberships during training and exact segments at inference, with no string normalization, so $\mathrm{decode}(\mathrm{encode}(w)) = w$ holds by construction. Because the model is neural, the same forward pass that tokenizes also emits a structured word embedding. Among reversible tokenizers – the only ones valid for generation – Morpheus attains the lowest bits-per-character ($1.425$), roughly doubles the gold morphological alignment of the subword family (MorphScore macro-F1 $0.61$ vs.\ ${\sim}0.32$), and uses ${\sim}19\%$ less GPU memory than 64K-vocabulary subword tokenizers. As an embedder, frozen Morpheus vectors lead on lexical retrieval (root-family MAP $0.85$) and same-root verification (ROC-AUC $1.00$), surpassing the multilingual retriever BGE-M3 and BERTurk; on context- and inflection-dependent tasks (NER, case/number probing) the heavier contextual encoders remain ahead – a trade-off we attribute to Morpheus's root-centric geometry. Code: https://github.com/lonewolf-rd/TurkishMorpheus; model: https://huggingface.co/lonewolflab/Morpheus-TR-50K; interactive demo: https://huggingface.co/spaces/lonewolflab/morpheus-tr-demo.

25.
arXiv (CS.LG) 2026-06-18

Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning

arXiv:2604.14906v3 Announce Type: replace-cross Abstract: The pseudoknot secondary structure in SARS-CoV-2 RNA is essential for regulating protein synthesis through $-$1 programmed ribosomal frameshifting ($-1$ PRF), a mechanism that allows the virus to generate both structural and non-structural proteins from overlapping reading frames. This pseudoknot exhibits both threaded and unthreaded long-lived topologies. The influence of ligand binding on its folding is a process critical for the development of $-$1 PRF small-molecule inhibitors. Understanding this process through unbiased molecular dynamics (MD) simulations can be facilitated by introducing collective variables (CVs) that capture the corresponding slowest dynamical modes. Here, we use spectral map (SM), a thermodynamics-driven machine learning technique, to learn such CVs directly from all-atom MD trajectories of the SARS-CoV-2 RNA pseudoknot in complex with the $-$1 PRF inhibitor merafloxacin and its two structural analogs in neutral and ionized forms. Free-energy landscapes (FELs) derived from the learned CVs indicate that ligand-induced destabilization is topology-selective. In the threaded pseudoknot, the inhibitors destabilize the S2 stem, while in the unthreaded pseudoknot, destabilization occurs in the S1 and S3 stems. Furthermore, the extent to which each ligand reshapes the FEL matches experimentally reported antiviral potency, whereas the protonation state qualitatively alters dynamics within the same RNA topology. Overall, our results show how pseudoknot topology, ligand type, and protonation state collectively influence the slow conformational dynamics of viral RNA and establish physiological protonation as a critical factor for modeling RNA-targeted drug action.