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01.
arXiv (CS.CL) 2026-06-12

Agent-based models for the evolution of morphological alternation patterns

Why is the past of English "go" the apparently unrelated "went"? Such alternations are frequent in languages. They neither aid communication nor learnability, yet they can be persistent, surviving over centuries or millennia. We present a multi-agent simulation of the emergence of morphological stem and inflection alternations. Alternate forms arise by phonological changes or, as with "go/went", from lexical alternatives associated with a subset of the population. When an agent 'hears' another agent use a novel form for a slot in the paradigm of a word (say, the past tense of go), they will with some probability adopt that form, possibly spreading its use to other slots in the paradigm that shared the same original form. Thus alternative forms can spread through the population and become entrenched as stem or inflectional marker alternants. Unlike many previous computational studies, our system allows for naturalistic lexical forms, realistic phonological rules, lexicons with hundreds or thousands of entries, and agent populations in the tens or hundreds. It supports several network topologies, diffusion patterns and agent adoption policies. One issue with such simulations is evaluation: how realistic is the resulting morphology compared to those of real languages? We introduce the AI Historical Linguist, a novel Large Language Model-driven system that models a debate between two historical linguists. We use this to compare a set of real language morphologies, disguised morphologies, and experimentally evolved morphologies. The results suggest that among the factors that favor more plausible morphologies are scale-free social networks and random Bernoulli adoption of forms. We also present three case studies modeling attested historical changes, allowing us to test what might have happened if history had been different. All code and data are released.

02.
arXiv (CS.AI) 2026-06-19

Computational Identifiability

arXiv:2606.19361v1 Announce Type: cross Abstract: Identification conditions describe the computability of a target query or parameter of interest as a function of the type and amount of information available. In causal identification, this information is often expressed in the form of a causal graph, and data are observed or collected for some subset of variables in the graph. Target queries may be for a single effect alone or for a class of effects in a given model. The derivation of an identification algorithm then defines mathematically the process by which the desired causal effect(s) can be uniquely determined, theoretically, in expectation. Identifiability in expectation, or 'theoretical identifiability,' generally assumes asymptotic properties, infinite data, or other mathematically idealized conditions. In this paper, we explore a fundamental distinction between this theoretical, idealized notion of identifiability and a proposed alternative that is computation-bound. The framework we propose - 'computational identifiability' - is to instead define a finite computational search procedure for an empirical estimator. If this process finds an estimator empirically, within a desired error tolerance, then identifiability is satisfied, conditional on the specified assumptions of the search (i.e., a prior distribution over the parameters) and conditional on the search procedure itself. Through several experiments, we demonstrate how this framework allows us to answer fine-grained, practical identification questions, such as identification with small finite samples, with ambiguous graphical criteria, with mixed observational-interventional data, and across counterfactual data and estimands. Code is available at https://github.com/lbynum/metadentify.

03.
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.

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

Learning What to Remember: A Cognitively Grounded Multi-Factor Value Model for Agentic Memory

arXiv:2606.12945v1 Announce Type: new Abstract: Long-running LLM agents accumulate interaction histories far larger than any context window, forcing a standing decision: what to encode deeply, what to forget, and what to retrieve under a fixed memory budget. Production systems answer with semantic similarity or recency – both mis-specified for the forgetting decision, which is made at consolidation time before the future query is known. We propose a multi-factor memory value function V(m)=\sum_i w_i f_i(m) over seven interpretable factors (emotional intensity, goal relevance, value alignment, self/user relevance, task utility, reliability, and usage history) drawn from cognitive psychology, whose weights are learned from a downstream objective by a gradient-free optimiser, and whose single scalar uniformly controls encoding depth, forget risk, and retrieval rank. We make a methodological point: on LongMemEval, scoring goal relevance against the held-out evaluation question saturates gold-evidence retention at \approx 0.98 – this measures retrieval, not forgetting. In the realistic blind regime, a learned multi-factor value retains 0.770 \pm 0.011 of gold evidence across 479 usable cases, versus 0.657 for uniform weights, 0.518 for the best single factor, and 0.368 for recency; every paired gap's 95% bootstrap CI is above zero, and a neural network over the same factors ties the linear model. The learned weights are interpretable – reliability, emotional intensity, and self/user relevance dominate, while query-time goal similarity is correctly down-weighted for the forgetting decision. A controlled synthetic task with planted confounds confirms the learner recovers a separating weighting (1.00 retention) where uniform weighting fails (0.62). The substrate is open-source; all experiments run on a single CPU with no API calls.

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

SPDA-SAM: A Self-prompted Depth-Aware Segment Anything Model for Instance Segmentation

Recently, Segment Anything Model (SAM) has demonstrated strong generalizability in various instance segmentation tasks. However, its performance is severely dependent on the quality of manual prompts. In addition, the RGB images that instance segmentation methods normally use inherently lack depth information. As a result, the ability of these methods to perceive spatial structures and delineate object boundaries is hindered. To address these challenges, we propose a Self-prompted Depth-Aware SAM (SPDA-SAM) for instance segmentation. Specifically, we design a Semantic-Spatial Self-prompt Module (SSSPM) which extracts the semantic and spatial prompts from the image encoder and the mask decoder of SAM, respectively. Furthermore, we introduce a Coarse-to-Fine RGB-D Fusion Module (C2FFM), in which the features extracted from a monocular RGB image and the depth map estimated from it are fused. In particular, the structural information in the depth map is used to provide coarse-grained guidance to feature fusion, while local variations in depth are encoded in order to fuse fine-grained feature representations. To our knowledge, SAM has not been explored in such self-prompted and depth-aware manners. Experimental results demonstrate that our SPDA-SAM outperforms its state-of-the-art counterparts across twelve different data sets. These promising results should be due to the guidance of the self-prompts and the compensation for the spatial information loss by the coarse-to-fine RGB-D fusion operation.

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

MeiBRD: Meta-Learning Intraoperative Biomechanical Residual Deformation

Accurate intraoperative liver registration is challenging due to substantial soft-tissue deformation yet sparse intraoperative measurements. Biomechanical models regularize this ill-posedness with prior knowledge but exhibit persistent prediction bias due to simplifying assumptions, while data-driven learning solutions struggle with data efficiency, generalization, and physical plausibility. We propose a hybrid registration framework that adapts a biomechanical prior using sparse intraoperative correspondences. Rather than learning a full deformation field, we learn a residual deformation function that corrects linear biomechanical predictions, modeled as a graph neural diffusion function with geometry-aware attention over the 3D liver mesh. To enable long-range information transfer of sparse observations, we take a novel perspective of sparse intraoperative measurements as context samples where input-output pairs of the residual deformation function are fully observed, casting the problem into learning-to-learn this residual function from intraoperative context samples with feedforward meta-learners. Experiments on a deformable liver phantom dataset demonstrate improved registration accuracy and generalization compared to rigid, biomechanical, and data-driven baselines, particularly for out-of-distribution geometries and deformations.

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

DF3DV-1K: A Large-Scale Dataset and Benchmark for Distractor-Free Novel View Synthesis

arXiv:2604.13416v2 Announce Type: replace-cross Abstract: Advances in radiance fields have enabled photorealistic novel view synthesis. In several domains, large-scale real-world datasets have been developed to support comprehensive benchmarking and to facilitate progress beyond scene-specific reconstruction. However, for distractor-free radiance fields, a large-scale dataset with clean and cluttered images per scene remains lacking, limiting the development. To address this gap, we introduce DF3DV-1K, a large-scale real-world dataset comprising 1,048 scenes, each providing clean and cluttered image sets for benchmarking. In total, the dataset contains 89,924 images captured using consumer cameras to mimic casual capture, spanning 128 distractor types and 161 scene themes across indoor and outdoor environments. A curated subset of 41 scenes, DF3DV-41, is systematically designed to evaluate the robustness of distractor-free radiance field methods under challenging scenarios. Using DF3DV-1K, we benchmark nine recent distractor-free radiance field methods and 3D Gaussian Splatting, identifying the most robust methods and the most challenging scenarios. Beyond benchmarking, we demonstrate an application of DF3DV-1K by fine-tuning a diffusion-based 2D enhancer to improve radiance field methods, achieving average improvements of 0.96 dB PSNR and 0.057 LPIPS on the held-out set (e.g., DF3DV-41) and the On-the-go dataset. We hope DF3DV-1K facilitates the development of distractor-free vision and promotes progress beyond scene-specific approaches. The dataset and leaderboard are available at https://johnnylu305.github.io/df3dv1k_web/.

08.
arXiv (CS.AI) 2026-06-16

SpecAlign: Efficient Specification-Grounded Alignment of Large Language Models via Synthetic Data

arXiv:2606.16276v1 Announce Type: new Abstract: As large language models (LLMs) are increasingly deployed in real-world applications, alignment is no longer governed by a single universal notion of safety or helpfulness, but instead by provider- or application-specific model specifications. These specifications are typically long, structured, and frequently updated, yet existing alignment pipelines lack a systematic mechanism to operationalize them as training signals. In this paper, we propose specification-grounded alignment, a new alignment paradigm that treats provider-authored model specifications as the primary alignment target rather than abstract principles or static benchmarks. To instantiate this paradigm, we introduce SpecAlign, a framework that synthesizes alignment data directly from specification documents. SpecAlign combines structured rule annotation, controllable specification instantiation, and multi-agent adversarial data synthesis to generate fine-grained, boundary-aware preference pairs that capture both compliant behaviors and meaningful specification violations. Experiments across multiple model specifications and backbone models demonstrate that training with SpecAlign consistently improves rule compliance while preserving general capabilities and avoiding over-conservative behavior. These results suggest that grounding alignment in explicit model specifications enables rapid, precise, and scalable adaptation of LLM behavior to evolving policy requirements.

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

MotionVLA: Vision-Language-Action Model for Humanoid Motion

Generating realistic humanoid motion from scene images and text involves both low-frequency pose semantics and high-frequency physical dynamics. However, many existing methods tokenize motion with a single shared codebook, forcing heterogeneous motion signals into the same quantization space. Our frequency-domain analysis of human motion data reveals a clear mismatch between single-codebook quantization and motion statistics: five DCT coefficients capture 93% of joint-position energy but only 37% of joint-velocity energy, which can bias quantization toward pose statistics and under-represent high-frequency velocity components. A second challenge lies in adapting a standard autoregressive model to effectively model high-frequency physical signals in motion sequences. Therefore, we propose DSFT, a dual-stream frequency tokenizer that separates motion into Base and physical streams and compresses them independently with DCT truncation and BPE. Furthermore, we present MotionVLA, a Qwen3.5-based model that arranges Base and physical tokens in a unified sequence, where Phys tokens are predicted after Base tokens. Experiments on HumanML3D and MBench show that, despite using a lightweight 2B backbone, MotionVLA reduces the Diversity gap to real data by over 50% on HumanML3D and improves Motion-Condition Consistency by 3.8% on MBench, supporting frequency-aware dual-stream decoupling as an effective formulation for autoregressive motion generation. Code: https://github.com/AIGeeksGroup/MotionVLA. Website: https://aigeeksgroup.github.io/MotionVLA.

11.
arXiv (CS.LG) 2026-06-17

Data augmented bootstrap: Unifying confidence interval construction by approximate invariance

arXiv:2606.09049v2 Announce Type: replace-cross Abstract: We propose the data augmented bootstrap (DAB), a framework for constructing confidence intervals from approximately invariant transformations of the data. As special cases, DAB recovers popular methods that rely on exact group symmetries, such as conformal prediction, wild bootstrap for Maximum Mean Discrepancy U-statistics and the recently proposed SymmPI. Meanwhile, DAB also recovers the classical bootstrap method, which exploits the dataset's approximate invariance under uniform sampling of data indices as the dataset size grows. For all DAB methods, we establish theoretical coverage results that interpolate between finite-sample and asymptotic guarantees according to the strength of the invariance, and without assuming a group structure. The approximate invariance is measured in the Kolmogorov distance and, for statistics that satisfy Gaussian universality, reduces to conditional mean and variance matching. This allows us to incorporate data augmentation (DA), a widely used machine learning heuristic based on approximate invariances, into known statistical methods. We empirically test the performance of incorporating DA into bootstrap, wild bootstrap and conformal prediction for simulated settings as well as for image, language and scientific data.

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

Fantastic Pretraining Optimizers and Where to Find Them II: Hyperball Optimization

arXiv:2606.16899v1 Announce Type: new Abstract: Matrix based optimizers such as Muon can substantially speed up language model pretraining, but their gains over AdamW are observed to shrink as model size and data scale grow when using standard constant decoupled weight decay. We propose Hyperball, a simple optimizer wrapper that addresses this issue. Given a base optimizer such as Adam or Muon, Hyperball sets the Frobenius norms of weight matrices and their corresponding optimizer updates to fixed constants. On Qwen3 style models up to 1.2B parameters, Muon Hyperball achieves 20–30% token equivalent speedup over weight decay baselines. Hyperball also improves learning rate transfer across widths and depths compared to decoupled weight decay. This method is motivated by prior theory showing that training with weight decay leads to an equilibrium weight norm that only depends on the training hyperparameters. Through this mechanism, the weight decay then decides the angular learning rate, i.e. how fast the direction of the weight matrix changes.

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

Re-feeding Is Not Replaying: Measuring Replay Noise in Counterfactual Token-Credit Estimation

Per-token counterfactual credit estimation asks which token in a language-model rollout caused the final answer to be right or wrong: cut the transcript at a pivot, substitute an alternative token, replay continuations, and compare outcomes. Published methods re-feed the transcript prefix as a fresh prompt, assuming this reproduces the state the model passed through during generation. We measure what that assumption costs on a stock inference engine, with a three-pass design: continuations resumed from the verified decode-time KV state, an identical second exact pass (a replica noise floor), and a re-feed pass. Across six configurations and three models (including a GRPO-trained checkpoint), at low-margin decision tokens, re-feeding changes the credit estimate at rates 14-28 percentage points above the replica floor (7-21pp under a treatment-independent conditioning; problem-clustered t = 2.9-6.4). Most changes are zero-boundary crossings of the quantized estimator rather than polarity reversals, and the perturbation is consistent with mean-zero, so averaged quantities are largely safe; but selection is not: a critical-token set chosen by thresholding $|\hat{A}_t|$ under re-feed overlaps the exact-resume selection at Jaccard 0.34-0.90, versus a 0.63-0.96 replica ceiling. A causal confirmation closes the loop: under vLLM's batch-invariant kernels all three passes are identical on every measured channel, with both disagreement rates exactly zero. Replica passes themselves disagree on 9-23% of eligible estimates: single-sample credit measurements at decision tokens are unreliable under any replay. Settings were fixed in advance; exact-pass cache hits in the second campaign are instrumented (100% hit rate, 3,434 pivots); total compute was under 10 USD. We recommend that counterfactual credit studies resume decoder state or use batch-invariant kernels, and report a replica floor.

14.
arXiv (quant-ph) 2026-06-16

Controlled Quantum Metrology with Anisotropic Heisenberg Spin Interactions under Intrinsic Decoherence

arXiv:2606.16918v1 Announce Type: new Abstract: We theoretically investigate quantum parameter estimation in a two-qubit anisotropic Heisenberg spin system with Dzyaloshinskii-Moriya (DM) interaction in the presence of intrinsic decoherence described by the Milburn model. Using the Quantum Fisher Information (QFI), we study the estimation of both the uniform magnetic field and the DM interaction strength. Analytical expressions for the time-evolved density matrix are obtained and used to explore the effects of exchange anisotropy, intrinsic decoherence, and probe-state preparation on the achievable estimation precision. Our results show that suitable tuning of the anisotropic exchange coupling and the initial entangled state can considerably enhance the estimation performance, with different optimal parameter regimes emerging for magnetic-field and DM-interaction sensing. To better understand the role of quantum resources in metrology, we also examine the behaviour of concurrence, quantum coherence, and von Neumann entropy. Overall, our findings demonstrate that anisotropic Heisenberg spin systems with DM interaction provide a promising and flexible platform for high-precision quantum metrology even in the presence of intrinsic decoherence.

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

Scaling Adaptive Depth with Norm-Agnostic Residual Networks

arXiv:2606.16112v1 Announce Type: cross Abstract: Residual architectures are ubiquitous in deep learning, but they suffer from a subtle structural limitation: the norm of the residual stream can grow rapidly with depth. As a result, updates from later layers become small relative to the accumulated residual state. This reduces their impact on the representation and limits the benefits of scaling models in depth. To address this, we introduce NAG, a norm-agnostic residual architecture that separates magnitude from directional information in the residual stream, preserving meaningful layer contributions throughout depth and preventing later updates from being systematically suppressed by residual-norm growth. Importantly, NAG introduces only a negligible number of additional parameters and relies on simple operations that are easily kernel-fusible, preserving training efficiency in practice. We show that this architecture outperforms baseline Transformers, with gains that increase substantially as depth grows, enabling effective training of much deeper models. The norm-agnostic formulation also leads to an interpretable Mixture-of-Depths (MoD) mechanism that adaptively skips both attention and MLP layers. Beyond serving as a post-training accuracy-compute tradeoff, this mechanism can be used as a pretraining-time scaling strategy: under iso-FLOP training, compute saved by reducing per-token forward-pass cost can be reinvested into training on more tokens while keeping the total parameter count and KV-cache budget fixed. In our experiments, moderate Mixture-of-Depths rates of approximately 20%-25% match full-depth baseline performance under equal training compute while substantially reducing the number of executed layer parameters and forward-pass FLOPs. These results identify sparsity in depth as a new scaling axis for fixed-compute training, enabling very deep yet FLOP-efficient models.

16.
arXiv (CS.CL) 2026-06-11

Notes2Skills: From Lab Notebooks to Certainty-Aware Scientific Agent Skills

Scientific discovery workflows usually contain and rely heavily on lab notes, where researchers record observations, interpret uncertain results, and plan follow-up experiments. Such informative lab notes preserve evolving scientific reasoning and author uncertainty, rather than polished final results exhibited in publications, providing a valuable opportunity for AI to engage in scientific exploration at a more comprehensive and deeper level. However, most prior work on scientific text focuses on papers, protocols, or structured databases, leaving informal laboratory notes underexplored as inputs to AI agents for science. This gap matters because lab notes often intermingle validated observations, tentative judgments, and possible experimental next steps within the same passage. If these signals are conflated, an AI agent may mistake uncertain scientific judgments for confirmed conclusions or executable actions. To this end, we present Notes2Skills, a two-stage framework for turning lab notebooks into verifiable skills for scientific AI agents while preserving the author's certainty. Across seven conditions and three wet-lab sessions, Notes2Skills is the only configuration that neither mistakes uncertain notes for firm instructions nor discards firm ones. We show that certainty preservation is the missing piece between lab notebooks and reliable agent skills, opening a path toward safer AI co-scientist systems.

17.
arXiv (CS.LG) 2026-06-11

From inverse problems to neural operators: prediction, mechanism, and generalization of data-driven models

作者:

arXiv:2606.08956v2 Announce Type: replace Abstract: Scientists have historically relied on mathematical models based on differential equations to relate system inputs – forces, fluxes, or heat sources – to outputs, such as displacement, velocity, concentration, and temperature. These models rely on deep domain knowledge to determine the form of the governing differential equation, which is then calibrated with data by solving an inverse problem. In recent years, the field of Scientific Machine Learning has introduced a variety of alternative modeling strategies for physical systems. A method called Sparse Identification of Nonlinear Dynamics learns the governing equation as a sparse linear combination of terms in a user-defined library. Neural Ordinary Differential Equations construct the governing equation by taking in the state and its derivatives at the input layer of a neural network. Entirely foregoing the modeling framework of differential equations, neural operators directly learn a non-linear mapping between the system inputs and outputs. From inverse problems to neural operators, all of these modeling strategies can be conceptualized as data-driven machinery to predict a system's response over a range of inputs. It is then natural to wonder how exactly these various strategies relate to each other, and whether they can be neatly taxonomized. Drawing from the philosophical literature on scientific models, we argue that many model types have a common structure, differing only in the assumed model class of the input-output relation they define. Connecting to philosophical ideas on mechanism, and arguing that data from physical systems arises from solutions to parsimonious differential equations, we propose that only certain models are capable of mechanism discovery, and thus generalization. Our analysis is intended to unite apparently disparate modeling strategies and provide insight into their appropriate use cases.

18.
medRxiv (Medicine) 2026-06-16

Deployment-readiness audit of calibration, clinical utility, and fairness in perioperative infection prediction

Objective: Clinical risk scores intended to guide patient-level decisions can show strong average performance. However, predicted probabilities can be systematically too high or too low in specific subgroups even when overall performance is strong. We audited deployment readiness of a strong end-of-surgery postoperative infection model across clinically relevant subgroups and tested mitigation strategies in miscalibrated subgroups. Materials and Methods: We analyzed out-of-fold predictions for 10,719 surgical procedures at a Swiss tertiary hospital, with 504 postoperative bacterial infection events. Prespecified axes were recorded sex, age stratum, and an EHR-derived physiological-reserve proxy. Within subgroups and pairwise intersections, we evaluated discrimination, calibration, threshold-specific errors, and decision-curve net benefit at the prespecified operating threshold. We compared group-specific isotonic recalibration with Wasserstein-barycenter postprocessing and demonstrated portability in SUPPORT2. Results: Overall AUROC was 0.876. While sex-marginal discrimination was similar in women and men (0.878 vs 0.875), age and reserve stratification revealed deployment-readiness failures. Calibration-in-the-large ranged from -0.86 in frail patients to -2.47 in non-frail patients. At the 0.10 operating threshold, decision-curve net benefit was positive in frail patients but negative in pre-frail and non-frail patients. Isotonic recalibration corrected average physiological-reserve-stratified calibration without worsening Brier scores, whereas Wasserstein postprocessing worsened calibration in most procedure clusters. Discussion: Discrimination-only or sex-marginal evaluation would have missed subgroup failures with clinical-utility implications. Conclusion: Subgroup fairness audits for clinical deployment should jointly evaluate discrimination, calibration, and utility. We implemented the audit as the open-source isitfair framework for identifying deployment-relevant subgroup failures, comparing mitigation strategies, and generating structured reports.

19.
bioRxiv (Bioinfo) 2026-06-12

Systematic functional annotation of thousands of BAHD acyltransferases in plant genomes using Protein Language Model and phylogenomic tools

The functional annotation of plant genes lags significantly behind their genomic annotation. Closing this gap requires thorough cataloging of reported protein activities alongside predictive methods that scale beyond sequence-similarity inference. Focusing on the BAHD acyltransferase enzyme family as a model, we assembled FuncZymeDB-BAHD, a large database of 2,705 LLM-retrieved and curated enzyme-acceptor-donor activities covering 336 BAHDs from 156 plant species, a 2-to-6-fold expansion over Swiss-Prot and prior compilations. We further developed FuncPred-OG, which maps queries to orthologous groups and previously characterized enzymes in FuncZymeDB-BAHD, returning hits with high evidence provenance. FuncPred-OG enabled functional prediction of over half of BAHDs across 85 plant proteomes, of which five novel predictions were validated via in vitro assays and recent studies. For the remaining BAHDs without FuncPred-OG annotation, we developed FuncPred-AI, where logistic-regression classifiers trained on protein language model embeddings achieved high Area-Under-the-Precision-Recall-curve (AUPR) scores and correct-hit rates up to 93%. FuncPred-AI yielded >1 probable donor/acceptor annotation for 99.9% (8894/8897) of BAHDs in our pan-plant dataset. Finally, the FuncPred workflow and datasets were deployed on a web portal for broader utilization, potentially reducing experimentalist efforts for selecting candidates from days to minutes. Overall, this framework provides a generalizable template for functional annotation of entire enzyme families.

20.
arXiv (quant-ph) 2026-06-15

Geometric mechanisms enabling spin- and enantio-sensitive observables in one photon ionization of chiral molecules

arXiv:2603.02735v3 Announce Type: replace-cross Abstract: We examine spin-resolved photoionization of randomly oriented chiral molecules via circularly polarized light, and revisit earlier predictions of Cherepkov (J. Phys. B: Atom. Mol. Phys. 16, 1543, 1983). We will show that the dynamical origin of spin- and enantio-sensitive observables arise from two intrinsic mechanisms that are quantified by two pseudovectors stemming from the geometric properties of the photoionization dipoles in spin space and in real space, and an extrinsic mechanism which is a directional bias introduced by the well-defined direction of light polarization. These mechanisms arise solely from electric dipole interactions. Consequently, this means that the ten independent parameters that was earlier predicted by Cherepkov to fully describe spin-resolved photoionization of chiral molecules can be reduced as moments of these three pseudovectors. We also find that the molecular pseudoscalars describing the spin- and enantio-sensitive components of the yield can be described by the flux of these pseudovectors through the energy shell, which changes sign upon switching enantiomers. Our results provide compact expressions for these observables which provide an intuitive picture on what determines the strength of these spin- and enantio-sensitive observables. The approach can be readily generalized to photoexcitation, multiphoton processes, and arbitrary field polarizations. Regardless of the specific driving conditions, the resulting spin- and enantio-sensitive observables are still controlled by the same three pseudovectors, underscoring their universal role as the primary generators of chirality-induced spin asymmetries, emphasizing their fundamental geometric origin and the universality of the mechanism identified here.

21.
bioRxiv (Bioinfo) 2026-06-12

Evaluating cell type annotations in single-cell omics in the absence of ground truth

Accurate cell type annotation is essential for single-cell transcriptomics, directly shaping downstream analyses and biological interpretations. Yet, objective evaluation of annotation quality remains a major challenge. Here, we argue that a cell type or cell state label has practical utility only if it captures a molecular pattern that is reproducible across biological replicates. Based on this principle, we introduce inter-sample consistency (ISC), a quantitative framework to assess annotation quality in single-cell RNA-seq datasets. Unlike existing cluster validation approaches, ISC distinguishes annotations that generalize across samples and individuals from those driven by technical or unwanted variation, thereby providing principled criteria for annotation quality and transferability. When applied to published single-cell atlases, ISC reveals widespread reproducibility gaps and provides actionable guidance for repairing inconsistent annotations. Notably, ISC enables benchmarking of automated cell type annotation tools even when ground-truth labels are unavailable, providing interpretable metrics to guide their development and evaluation. Implemented as the scTypeEval Bioconductor package, this framework offers a broadly applicable resource for evaluating and improving cell type annotations in single-cell RNA-seq experiments.

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

Efficient Reinforcement for Visual-Textual Thinking with Discrete Diffusion Model

RL-based post-training has been widely adopted to enable interleaved visual and textual reasoning in unified multimodal models capable of both text and image generation. However, most existing approaches are built upon autoregressive (AR) unified models, which require full image regeneration during visual reasoning. In this work, we demonstrate that multimodal discrete diffusion models are effective alternatives to AR models for reinforcement learning in interleaved reasoning, owing to their ability to perform efficient visual rollouts via localized visual editing rather than full image-token regeneration. This reduces rollout computation during GRPO by 26.9\% compared to AR baselines, with minimal performance drop. Despite the improved efficiency, we find that joint reward assignment, which employs a shared reward signal across modalities, introduces cross-modal interference between unrelated image and text token sequences during RL updates. To address this issue, we propose factorized reward assignment, a strategy that assigns rewards independently to text and vision segments. With factorized reward assignment, our RL approach achieves an 11.2% improvement over joint reward assignment and a 38.04% improvement over the base model.

23.
arXiv (CS.AI) 2026-06-18

Dynamic In-Group Persona Generation for Enhancing Human-AI Rapport

arXiv:2606.18256v1 Announce Type: cross Abstract: LLM-based chatbots are increasingly applied in interpersonal domains such as counseling and peer support, where establishing human-AI rapport is crucial yet remains challenging. In this work, we introduce a novel approach for conditioning LLMs with in-group personas, which (i) first identifies a user's primary concern and brief personal context (e.g., a computer science undergraduate worried about future career prospects), and (ii) generates a synthetic in-group persona that shares a similar primary concern while differing in background and narrative details, such as age or profession (e.g., a junior researcher at an AI startup). Furthermore, we conduct a human-subject study to systematically evaluate the effectiveness of in-group persona agents in enhancing human-AI rapport. We compare our approach against two baseline conditions: a conventional agent without persona conditioning and an agent exhibiting minimal self-disclosure (e.g., "I've felt that too"). Results from post-task questionnaires assessing rapport and user experience indicate that the in-group persona agent significantly improves perceived rapport and personal relevance compared to the baselines, and also yields more positive user experience-most notably higher engagement.

24.
medRxiv (Medicine) 2026-06-10

Prediction of immunotherapy response using live tumor fragments from routine clinical biopsies

Functional ex vivo assays using live tumor tissues have demonstrated strong predictive accuracy for response to immune checkpoint inhibitors (ICIs) but are not scalable, requiring manual processing of large resections collected at academic centers. Here, an ex vivo live tumor fragment (LTF) platform was developed using standard-of-care biopsies from 228 patients with suspected malignancy collected across prospective, multicenter observational trials and biobanks. Hierarchical clustering of ICI-mediated changes in cytokine production identified two groups: responders and nonresponders. A binary classifier (elive index) using 8 cytokines achieved an AUC of 0.99 for cluster prediction. elive index correctly predicted clinical benefit in 93% (26/28) of patients (P = 3.2x10-5) and accurately identified 83% (10/12) of objective responders. Critically, elive responders were identified among biomarker-negative patients, highlighting the platform as a scalable approach that complements existing companion diagnostics and expands the population of patients identified to benefit from ICI therapy.

25.
arXiv (CS.CV) 2026-06-15

MVAD: A Benchmark Dataset for Multimodal AI-Generated Video-Audio Detection

The rapid advancement of AI-generated multimodal video-audio content has raised significant concerns regarding information security and content authenticity. Existing synthetic video datasets predominantly focus on the visual modality alone, while the few incorporating audio are largely confined to facial deepfakes–a limitation that fails to address the expanding landscape of general multimodal AI-generated content and substantially impedes the development of trustworthy detection systems. To bridge this critical gap, we introduce the Multimodal Video-Audio Dataset (MVAD), the first comprehensive dataset specifically designed for detecting AI-generated multimodal video-audio content. Our dataset exhibits three key characteristics: (1) genuine multimodality with samples generated according to three realistic video-audio forgery patterns; (2) high perceptual quality achieved through diverse state-of-the-art generative models; and (3) comprehensive diversity spanning realistic and anime visual styles, four content categories (humans, animals, objects, and scenes), and four video-audio multimodal data types. Our dataset will be available at https://github.com/HuMengXue0104/MVAD.