Papers

Cross-language code clone detection (X-CCD) is challenging because semantically equivalent programs written in different languages often share little surface similarity. Although large language models (LLMs) have shown promise for semantic clone detection, their use as black-box systems raises concerns about cost, reproducibility, privacy, and unreliable output formatting. In particular, compact open-source models often struggle to follow reasoning-oriented prompts and to produce outputs that can be consistently mapped to binary clone labels. To address these limitations, we propose a knowledge distillation framework that transfers reasoning capabilities from DeepSeek-R1 into compact open-source student models for X-CCD. Using cross-language code pairs derived from Project CodeNet, we construct reasoning-oriented synthetic training data and fine-tune Phi3 and Qwen-Coder with LoRA adapters. We further introduce response stabilization methods, including forced conclusion prompting, a binary classification head, and a contrastive classification head, and evaluate model behavior using both predictive metrics and response rate. Experiments on Python–Java, Rust–Java, Rust–Python, and Rust–Ruby show that knowledge distillation consistently improves the reliability of compact models and often improves predictive performance, especially under distribution shift. In addition, classification-head variants substantially reduce inference time compared to generation-based inference. Overall, our results show that reasoning-oriented distillation combined with response stabilization makes compact open-source models more practical and reliable for X-CCD detection.

Understanding whether deep neural networks are effectively optimized remains challenging, as training occurs in highly nonconvex landscapes and standard metrics provide limited visibility into layer-wise learning quality. This challenge is particularly acute for transformer-based language models, where training is expensive, models are often reused in frozen form, and poorly optimized layers can silently degrade performance. We propose a layer-wise peeling framework for monitoring training dynamics, in which each transformer layer is locally optimized against intermediate representations of the trained model. By constructing lightweight, layer-specific reference solutions and projecting layers onto multiple intermediate outputs via different permutations, we obtain achievable baselines that enable fine-grained diagnosis of under-optimized layers. Experiments on decoder-only transformer models show that these layer-wise reference bounds can match or even surpass the trained model at various stages of training, exposing inefficiencies that remain hidden in aggregate loss curves. We further demonstrate that this analysis remains effective under binarization and quantized settings, where training dynamics are particularly fragile. Across all numerical results, the proposed bounds consistently separate apparent convergence from effective optimality, highlighting optimization opportunities that are invisible when relying on training loss alone.

Retraction-free approaches offer attractive low-cost alternatives to Riemannian methods on the Stiefel manifold, but they are often first-order, which may limit the efficiency under high-accuracy requirements. To this end, we propose a second-order method landing on the Stiefel manifold without invoking retractions, which is proved to enjoy local quadratic (or superlinear for its inexact variant) convergence. The update consists of the sum of (i) a component tangent to the level set of the constraint-defining function that aims to reduce the objective and (ii) a component normal to the same level set that reduces the infeasibility. Specifically, we construct the normal component via Newton$\unicode{x2013}$Schulz, a fixed-point iteration for orthogonalization. Moreover, we establish a geometric connection between the Newton$\unicode{x2013}$Schulz iteration and Stiefel manifolds, in which Newton$\unicode{x2013}$Schulz moves along the normal space. For the tangent component, we formulate a modified Newton equation that incorporates Newton$\unicode{x2013}$Schulz. Numerical experiments on the orthogonal Procrustes problem, principal component analysis, and real-data independent component analysis illustrate that the proposed method performs better than the existing methods.

We introduce PLACE (Persistence-Landmark Analytic Classification Engine), a closed-form pipeline for classifying point clouds and graphs through their persistent-homology signatures. Three quantitative guarantees – a margin-based excess-risk rate, a closed-form descriptor-selection rule, and a per-prediction certificate – are derived from training labels alone, with no learned weights or held-out calibration. The embedding sums Mitra-Virk single-point coordinate functions over a sparse landmark grid; the closed-form weight rule $w_k^2 \propto (d_{k+1}^2 - d_k^2)/R_k^2$ maximizes the distortion slope in Mitra-Virk's affine certificate under $\nu$-coherence. (i) An $O(kR/(\Delta\sqrt{m_{\min}}))$ margin bound, driven by class-mean separation $\Delta$ and embedding radius $R$, matched in the sample-starved regime $m \lesssim R/\Delta$ by a Le Cam minimax lower bound. (ii) The Mahalanobis margin under Ledoit-Wolf-shrunk covariance is the strongest closed-form ranker on a 64-descriptor chemical-graph pool (mean Spearman $\rho = +0.56$ across 11 benchmarks, positive on 10 of 11); the isotropic surrogate $\Delta/\sqrt{\ell}$ admits a closed-form selection-consistency rate on the homogeneous protein/social pools. (iii) A training-time-decided certificate, with no per-prediction overhead, in three concrete radii (Pinelis, Gaussian plug-in, and variance-aware Pinelis-Bernstein). Empirically, PLACE is the strongest diagram-based method on Orbit5k and matches the strongest topology-based baseline within statistical noise on MUTAG and COX2; remaining gaps fall into two diagnosable regimes (descriptor blindness on NCI1/NCI109; pool-coverage limits elsewhere). The Pinelis-Bernstein radius fires on 8 of the 12 benchmarks; on MUTAG the empirical and population nearest-centroid rules agree on every one of 940 held-out test predictions, validating the certificate's mechanism.

Videos are unique in their ability to capture actions which transcend multiple frames. Accordingly, for many years action recognition was the quintessential task for video understanding. Unfortunately, due to a lack of sufficiently diverse and challenging data, modern vision-language models (VLMs) are no longer evaluated on their action recognition capabilities. To revitalize action recognition in the era of VLMs, we advocate for a returned focus on domain-specific actions. To this end, we introduce VideoNet, a domain-specific action recognition benchmark covering 1,000 distinct actions from 37 domains. We begin with a multiple-choice evaluation setting, where the difference between closed and open models is stark: Gemini 3.1 Pro attains 69.9% accuracy while Qwen3-VL-8B gets a mere 45.0%. To understand why VLMs struggle on VideoNet, we relax the questions into a binary setting, where random chance is 50%. Still, Qwen achieves only 59.2% accuracy. Further relaxing the evaluation setup, we provide $k\in\{1,2,3\}$ in-context examples of the action. Some models excel in the few-shot setting, while others falter; Qwen improves $+7.0\%$, while Gemini declines $-4.8\%$. Notably, these gains fall short of the $+13.6\%$ improvement in non-expert humans when given few-shot examples. Finding that VLMs struggle to fully exploit in-context examples, we shift from test-time improvements to the training side. We collect the first large-scale training dataset for domain-specific actions, totaling nearly 500k video question-answer pairs. Fine-tuning a Molmo2-4B model on our data, we surpass all open-weight 8B models on the VideoNet benchmark.

We present an experimental study of energy-to-solution (ETS) of hybrid quantum-classical applications, enabled by direct instrumentation of power consumption of a Forte Enterprise trapped-ion quantum processor. We apply this methodology to a hybrid quantum-classical pipeline for quantum fine-tuning of foundational AI models, and validate the approach end-to-end on quantum hardware. Despite noise and limited qubit counts, the resulting models achieve accuracy competitive with and exceeding classical baselines such as logistic regression and support vector classifiers. Our results show that QPU energy consumption scales approximately linearly with qubit number for shallow circuits, while classical simulation exhibits exponential scaling, indicating a break-even for ETS around 34 qubits. The classification error improvement of the best quantum fine-tuned model over the best classical fine-tuned model considered in this study is around 24%. We further contextualize these findings with comparisons to tensor network methods. This work establishes energy-to-solution as a measurable and scalable metric for evaluating quantum applications and provides experimental evidence of favorable energy-accuracy trade-offs.

Structure aware graph generation aims to generate graphs that satisfy given topological properties. It has applications in domains such as drug discovery, social network modeling, and knowledge graph construction. Unlike existing methods that only provide coarse control over graph properties, we introduce a novel conditional variational autoencoder for fine-grained structural control in graph generation. The approach refines the decoder's latent space by dynamically aligning graph- and property-driven representations to improve both graph fidelity and control satisfaction. Specifically, the approach implements a mixture scheduler that progressively integrates graph and control priors. Experiments on five real-world datasets show the efficacy of the proposed model compared to recent baselines, achieving high generation quality while maintaining high controllability.

Offline safe reinforcement learning often requires policies to adapt at deployment time to safety budgets that vary across episodes or change within a single episode. While diffusion-based planners enable flexible trajectory generation, existing guidance schemes often treat reward improvement and constraint satisfaction as competing gradient objectives, which can lead to unreliable safety compliance under cost limits. We reinterpret adaptive safe trajectory generation as sampling from a constrained trajectory distribution, where the budget restricts the trajectory region, and reward shapes preferences within that region. This perspective motivates Safe Decoupled Guidance Diffusion (SDGD), which conditions classifier-free guidance on the cost limit to bias sampling toward trajectories satisfying the specified limit, while using reward-gradient guidance to refine trajectories for higher return. Because direct reward guidance can increase return while also steering samples toward trajectories with higher cumulative cost, we introduce Feasible Trajectory Relabeling (FTR) to reshape reward targets and discourage such directions. We further provide a first-order sampling-time analysis showing that FTR suppresses reward-induced cost drift under a prefix-restorative alignment condition. Extensive evaluations on the DSRL benchmark show that SDGD achieves the strongest safety compliance among baselines, satisfying the constraint on 94.7% of tasks (36/38), while obtaining the highest reward among safe methods on 21 tasks.

We consider the infinite-width limit of a fully connected deep neural network with general weights, and we prove quantitative general bounds on the $2$-Wasserstein distance between the network and its infinite-width Gaussian limit, under appropriate regularity assumptions on the activation function. Our main tool is a Lindeberg principle for Deep Neural Networks, which we use to successively replace the weights on each layer by Gaussian random variables.

LLMs are increasingly used for end-user task planning, yet their black-box nature limits users' ability to ensure reliability and control. While recent systems incorporate verification techniques, it remains unclear how users can effectively apply such rigid constraints to represent intent or adapt to real-world variability. For example, prior work finds that hard-only constraints are too rigid, and numeric flexibility weights confuse users. We investigate how interaction workflows can better support users in applying constraints to guide LLM-generated plans, examining whether abstracting strictness into high-level types (i.e., hard and soft) paired with distinct verification mechanisms helps users more reliably express and align intent. We present U-Define, a system that lets users define constraints in natural language and categorize them as either hard rules that must not be violated or soft preferences that allow flexibility. U-Define verifies these types through complementary methods: formal model checking for hard constraints and LLM-as-judge evaluation for soft ones. Through a technical evaluation and user studies with general and expert participants, we find that user-defined constraint types improve perceived usefulness, performance, and satisfaction while maintaining usability. These findings provide insights for designing flexible yet reliable constraint-based workflows.

Molecular property models increasingly support high-stakes drug-discovery decisions, but their outputs are often difficult to audit: classical predictors return scores without rationale, while language models can produce fluent explanations weakly grounded in the input molecule. We introduce Bolek, a compact multimodal language model that grounds natural-language reasoning in molecular structure by injecting a Morgan fingerprint embedding into an instruction-tuned text decoder. Bolek is fine-tuned on molecular alignment tasks, including molecule description, RDKit descriptor prediction, and substructure detection, and on downstream reasoning over 15 TDC binary classification tasks using synthetic chains-of-thought anchored in concrete molecular features. Across these tasks, Bolek outperforms its Qwen3-4B-Instruct base on all endpoints in yes/no mode and on 13 of 15 in chain-of-thought mode, raising mean ROC/PR AUC from 0.55 to 0.76. It also outperforms TxGemma-9B-Chat on 13 of 15 binary classification tasks despite being less than half its size. Bolek's explanations are more grounded than those of the baseline LLMs: it cites numerical descriptors 10-100x more often per chain-of-thought, and the cited values agree strongly with RDKit for key descriptors such as TPSA, MolLogP, and MolWt (Spearman rho = 0.87-0.91). Generalisation extends beyond the training panel: on 15 unseen TDC classification endpoints, Bolek matches TxGemma on five, and it produces non-trivial rank correlations on three held-out regression endpoints despite never seeing downstream regression during training. These results suggest that targeted modality injection and reasoning supervision tied to verifiable molecular features can yield compact, auditable molecular reasoning models.

Motion in-betweening is one of the most artistically demanding and time consuming stages of 3D animation, where the expressivity and rhythm of motion are defined. The level of creative control it requires makes it a major production bottleneck, underscoring the need for intelligent tools that assist animators in this process. Although recent deep learning approaches have achieved strong results in motion synthesis and in-betweening, they assume data characteristics, motion styles, and problem formulations that diverge from professional animation workflows. To bridge this gap, we propose a method explicitly aligned with the constraints of motion in-betweening for keyframe-based animation in production environments. At its core, the Adaptive Interpolation-Synthesis (AIS) layer mirrors the animator's creative process by dynamically balancing learned interpolation and direct pose synthesis. In addition, a domain-based input keypose schedule reflects the distribution of production data, improving stylistic consistency and alignment between training and real-world usage. Our method achieves state-of-the-art performance on production data; when integrated into Autodesk Maya, it enables animators to complete in-betweening tasks with a 3.5x speedup.

Continuous latent-space reasoning offers a compact alternative to textual chain-of-thought for multimodal models, enabling high-dimensional visual evidence to be integrated without explicit reasoning tokens. However, we identify a previously overlooked optimization pathology in existing latent visual reasoning methods: although visual latents become semantically enriched during training, their contribution to final answer prediction is systematically suppressed. Within the shared parameter space, the autoregressive objective favors shortcut reliance on direct visual input, driving latent tokens toward transition-like states rather than informative reasoning content. We term this phenomenon Silenced Visual Latents. To address it, we disentangle the two conflicting objectives by directly optimizing the latent reasoning at inference time, keeping backbone parameters frozen. In Stage I, visual latents are warmed up via query-guided contrastive latent–visual alignment, improving semantic quality while preventing latent collapse. In Stage II, the latent reasoning is further optimized via a confidence-progression reward, which incentivizes predicted token distributions along the latent span to become progressively more concentrated, routing predictions through the latent reasoning rather than bypassing it. Experiments across eight benchmarks and four model backbones show that inference-time latent optimization, without any parameter updates, effectively unleashes the suppressed reasoning capacity of visual latents.

Self-supervised speech models (S3Ms) achieve strong downstream performance, yet their learned representations remain poorly understood under natural and adversarial perturbations. Prior studies rely on representation similarity or global dimensionality, offering limited visibility into local geometric changes. We ask: how do perturbations deform local geometry, and do these shifts track downstream automatic speech recognition (ASR) degradation? To address this, we present GRIDS, a framework using Local Intrinsic Dimensionality (LID) across layer-wise representations in WavLM and wav2vec 2.0. We find that LID increases for all low signal-to noise ratio (SNR) perturbations and diverges at high SNR: benign noise converges toward the clean profile, while adversarial inputs retain early-layer LID elevation. We show LID elevation co-occurs with increased WER, and that layer-wise LID features enable anomaly detection (AUROC 0.78-1.00), opening the door to transcript-free monitoring in S3Ms.

Mobile crowdsensing (MCS) is a distributed sensing architecture that utilizes existing sensors on mobile units (MUs) to perform sensing tasks. A mobile crowdsensing platform (MCSP) publishes the sensing tasks and the MUs decide whether to participate in exchange for money. The MCS system is dynamic: the task requirements, the MUs' availability, and their available resources change over time. The MUs aim to find an efficient task participation strategy to maximize their income while the MCSP focuses on maximizing the number of completed tasks. As optimal strategies require perfect non-causal information about the MCS system, which is unavailable in realistic scenarios, the main challenge is to find an efficient task participation strategy for the MUs under incomplete information. To this end, a novel fully decentralized federated deep reinforcement learning algorithm, FDRL-PPO, is proposed. FDRL-PPO enables every MU to learn its own task participation strategy based on its experiences, available resources, and preferences, without relying on perfect non-causal information about the MCS system. To replenish their batteries, the MUs rely on energy harvesting. As a result, their available energy varies over time, leading to varying availability and fragmented learning experiences. To mitigate these challenges, the proposed approach leverages federated learning, enabling MUs to collaboratively improve their models without sharing private raw data like their own experiences. By exchanging only learned models, MUs collectively compensate for individual limitations, and find more scalable, robust, and efficient task participation strategies. Comprehensive evaluations on both synthetic and real-world datasets show that FDRL-PPO consistently outperforms benchmark algorithms in terms of task completion ratio, fairness in task completion, energy consumption, and number of conflicting proposals.

Effective pair programming depends on coordination of attention, cognitive effort, and joint regulation over time, yet most adaptive learning systems remain individual-centric and reactive. This paper introduces ProPACT, a proactive AI-driven adaptive collaborative tutor that treats collaboration itself as the object of instruction. ProPACT constructs a multimodal dyadic learner model based on Joint Visual Attention (JVA), Joint Mental Effort (JME), and individual mental effort, and employs an XGBoost-based forecasting model to predict emerging suboptimal collaboration states up to 30 seconds in advance. These predictions drive a hierarchical adaptive policy that delivers minimally intrusive scaffolds while fading support during productive collaboration. A within-subject study with 26 pair-programming dyads shows that proactive feedback significantly improves debugging success, task efficiency, feedback uptake, and post-intervention gains in JVA and JME, demonstrating the potential of forecast-driven dyadic adaptivity for real-time collaborative learning regulation.

We propose a robust gradient estimator based on per-sample gradient clipping and analyze its properties both theoretically and empirically. We show that the resulting method, per-sample clipped SGD (PS-Clip-SGD), achieves optimal in-expectation convergence rates for non-convex optimization problems under heavy-tailed gradient noise. Moreover, we establish high-probability convergence guarantees that match the in-expectation rates up to polylogarithmic factors in the failure probability. We complement our theoretical results with multiple numerical experiments. In particular, we demonstrate that PS-Clip-SGD outperforms both vanilla SGD with momentum and standard gradient clipping when training AlexNet on the CIFAR-100 dataset, even after accounting for the additional computational time caused by per-sample clipping. We also empirically show that, in the presence of gradient accumulation, applying clipping at the mini-batch level can improve training performance while incurring virtually no additional computational cost. This finding is particularly interesting, as it contradicts the common practice of applying clipping only after all accumulation steps have been completed.

Learning data-efficient object dynamics models for robotic manipulation remains challenging, especially for deformable objects. A popular approach is to model objects as sets of 3D particles and learn their motion using graph neural networks. In practice, this is not enough to maintain physical feasibility over long horizons and may require large amounts of interaction data to learn. We introduce PIEGraph, a novel approach to combining analytical physics and data-driven models to capture object dynamics for both rigid and deformable bodies using limited real-world interaction data. PIEGraph consists of two components: (1) a Physically Informed particle-based analytical model (implemented as a spring–mass system) to enforce physically feasible motion, and (2) an Equivariant Graph Neural Network with a novel action representation that exploits symmetries in particle interactions to guide the analytical model. We evaluate PIEGraph in simulation and on robot hardware for reorientation and repositioning tasks with ropes, cloth, stuffed animals and rigid objects. We show that our method enables accurate dynamics prediction and reliable downstream robotic manipulation planning, which outperforms state of the art baselines.

Across many scientific disciplines, multiple observations are collected from the same experimental units, and in modern datasets these observations often arise as non-Euclidean random objects. In such settings, the incorporation of random effects is a critical modeling step for efficient estimation and personalized prediction. Although mixed-effects models are well established for scalar outcomes and, more recently, for functional data in Hilbert spaces, general random-effects frameworks for objects in metric spaces remain underdeveloped. In this paper, we propose a nonlinear Fréchet-based algorithm for random-effects modeling of arbitrary random objects defined on a metric space. Using M-estimation theory, we establish conditions under which the proposed metric-space prediction target is consistently estimated under a working random-effects formulation. We then evaluate the empirical performance of the proposed method using both synthetic data and digital health datasets that require practical tools for analyzing random objects in metric spaces, such as multivariate probability distributions and random graphs. We show that, although our method is developed beyond Hilbert spaces, it can outperform existing Hilbert space-based methods.

The proliferation of large-scale and structurally complex data has spurred the integration of machine learning methods into statistical modeling. Recurrent neural networks (RNNs), a foundational class of models for time-dependent data, can be viewed as nonlinear extensions of classical autoregressive moving average models. Despite their flexibility and empirical success in machine learning, RNNs often suffer from limited interpretability and slow training, which hinders their use in statistics. This paper proposes the Parallelized RNN (ParaRNN), a novel model composed of multiple small recurrent units. ParaRNN admits an additive representation that decouples recurrent dynamics into interpretable components, whose behavior can be characterized through recurrence features. This interpretability enables its applications in nonparametric regression for time-dependent data, while the design also allows efficient parallelization. The approximation capacity and non-asymptotic prediction error bounds in a nonparametric regression setting are established for ParaRNN. Empirical results on three sequential modeling tasks further demonstrate that ParaRNN achieves performance comparable to vanilla RNNs while offering improved interpretability and efficiency.

Long-term time series forecasting requires models that simultaneously capture rapid oscillations, medium-range periodicities, and slowly evolving macro-trends from a fixed look-back window. Existing lightweight MLP-based models typically operate on a single temporal resolution, limiting their ability to explicitly model patterns at multiple scales. We propose MSMixer, a channel-independent multi-scale MLP architecture that addresses this limitation through three complementary innovations: (i) three parallel scale branches at down-sample factors {1x, 4x, 16x} with independent MLP blocks, (ii) a learnable softmax gate that dynamically weighs branch outputs, and (iii) a DLinear complementary shortcut that provides full-window trend and seasonality context. MSMixer contains only 112K parameters at H=96 and runs at O(T) complexity. Evaluated on four ETT benchmarks with standard chronological splits and three random seeds, MSMixer achieves the lowest average MSE (0.357) among lightweight models, outperforming DLinear (0.386, -7.4%) and NLinear (0.365, -2.1%), winning 12 of 16 configurations. Against five Transformer-based baselines from the literature, MSMixer achieves best or second-best MSE in 9 of 16 configurations while using 5x fewer parameters than PatchTST. Ablation and sensitivity analyses confirm the complementary contributions of the multi-scale branches and the DLinear shortcut.

Spectral-based machine learning models have been increasingly deployed in chemometrics and spectroscopy, where predictive accuracy is as important as explainability. Current employed eXplainable Artificial Intelligence (XAI) methods are largely adapted from tabular or generic multivariate domains, assigning relevance to isolated spectral variables rather than to the chemically meaningful spectral zones. Widely adopted tools such as SHapley Additive exPlanations (SHAP), Permutation Feature Importance (PFI), and Variable Importance in Projection scores (VIP) were not designed for the physical continuity and high collinearity of spectral data, and their variable-level outputs require post-hoc aggregation to recover zone-level information. This study introduces the Spectral Model eXplainer (SMX), a post-hoc, global, model-agnostic XAI framework that explains spectral classifiers through expert-informed spectral zones. SMX summarizes each zone via PCA, defines quantile-based logical predicates, estimates predicate relevance with perturbation in stochastic subsamples, and aggregates bag-wise rankings in a directed weighted graph summarized by Local Reaching Centrality. A key component is threshold spectrum reconstruction, which back-projects predicate boundaries to the original spectral domain in natural measurement units, enabling direct visual comparison with measured spectra. The method was evaluated on eight real spectral datasets (six based on X-ray Fluorescence–XRF and two based on Gamma-ray Spectrometry) and one synthetic benchmark with known gr

This paper introduces an extension of generalised filtering for online applications. Generalised filtering refers to data assimilation schemes that jointly infer latent states, learn unknown model parameters, and estimate uncertainty in an integrated framework – e.g., estimate state and observation noise – at the same time (i.e., triple estimation). This framework appears across disciplines under different names, including variational Kalman-Bucy filtering in engineering, generalised predictive coding in neuroscience, and Dynamic Expectation Maximisation (DEM) in time-series analysis. Here, we specialise DEM for “online” data assimilation, through a separation of temporal scales. We describe the variational principles and procedures that allow one to assimilate data in a way that allows for a slow updating of parameters and precisions, which contextualise fast Bayesian belief updating about the dynamic hidden states. Using numerical studies, we demonstrate the validity of online DEM (ODEM) using a non-linear – and potentially chaotic – generative model, to show that the ODEM scheme can track the latent states of the generative process, even when its functional form differs fundamentally from the dynamics of the generative model. Framed from a neuro-mimetic predictive coding perspective, ODEM offers a biologically inspired solution to online inference, learning, and uncertainty estimation in dynamic environments.

Estimating free energy differences quantifies thermodynamic preferences in molecular interactions, which is central to chemistry and drug discovery. Despite fruitful progress, existing methods still face key limitations: classical computational approaches remain prohibitively expensive due to their reliance on extensive molecular dynamics simulations, while deep learning-based methods are constrained by either less-expressive generative models or input dimensions tied to a specific system, resulting in negligible generalization. To address these challenges, we propose CARD, a generative framework that employs a novel radix-based decomposition to bijectively convert 3D coordinates into mixed discrete-continuous sequences, enabling coarse-to-fine autoregressive modeling with enhanced expressiveness. Notably, the model corresponds to a distribution with zero free energy, serving as a proposal for absolute free energy computation of arbitrary systems without relying on alchemical pathways. Experiments across diverse tasks demonstrate that CARD matches the accuracy of classical computational methods on unseen systems with diverse topologies, while achieving an approximately 40-fold speedup in inference.

Scientific peer review increasingly struggles to assess reproducibility at the scale and complexity of modern research output. Evaluating reproducibility requires reconstructing experimental dependencies, methodological choices, data flows, and result-generating procedures, which often exceeds what human reviewers can provide. Agentic Reproducibility Assessment (ARA) formalizes reproducibility assessment as a structured reasoning task over scientific documents. Given a paper, ARA extracts a directed workflow graph linking sources, methods, experiments, and outputs, then evaluates its reconstructability using structural and content-based scores for reproducibility assessments. Experiments on 213 ReScience C articles - the largest cross-domain benchmark of human-validated computational reproducibility studies considered to date - demonstrate ARA's generalizability and consistent workflow reconstruction and assessment across LLMs, model temperatures, and scientific domains. ARA achieves ~61% accuracy on three benchmarks, and the highest accuracy reported on ReproBench (60.71% vs. 36.84%) and GoldStandardDB (61.68% vs. 43.56%), highlighting its potential to complement human review at scale and enabling next-generation peer review. Code and Data available: https://github.com/AndresLaverdeMarin/agentic_reproducibility_assessment.

Near-infrared (NIR and Vis-NIR) spectroscopy is widely used for rapid, non-destructive analysis in food, agriculture, pharmaceuticals, process analytical technology, and bioprocess monitoring. Nevertheless, deep-learning studies in NIR chemometrics often reach conflicting conclusions about convolutional neural network (CNN) design, including kernel size, depth, preprocessing, model complexity, and transfer robustness. This review argues that many apparent contradictions reflect incomplete experimental conditioning rather than incompatible findings. CNN performance depends on interactions among spectral physics, dataset regime, acquisition protocol, validation design, and deployment conditions. We organize the literature around three moderators. First, NIR signals are indirect, highly collinear, and shaped by broad overlapping bands, scattering, temperature, and matrix effects. Second, CNN design should be interpreted through receptive-field reasoning: kernel size, depth, dilation, and multi-scale branches determine the wavelength span available to the model, whereas the effective receptive field indicates which parts are actually used. Third, validation design can behave as a hidden hyperparameter because random splits may reward architectures that exploit shared batch, instrument, season, or process-run structure instead of transferable chemical information. We therefore propose a conditional design framework in which preprocessing, architecture, hyperparameter optimization, transfer evaluation, interpretability, and reproducibility are treated as coupled components. Rather than seeking a universally optimal CNN, the framework aims to support physics-aware, shift-aware, and reproducible model comparison in NIR chemometrics.

Direct Preference Optimization (DPO) improves relative preference by increasing the margin between chosen and rejected responses, but this objective does not specify how probability mass should be redistributed to achieve that margin. Consequently, preference separation can improve even as probability mass collapses away from both preferred and unrelated responses, a phenomenon associated with the squeezing effect. We show that this pathology is localized: continued negative updates become destructive when rejected responses enter low-probability valleys, where further suppression induces harmful redistribution through the coupled softmax geometry. We introduce Gradient-Gated Preference Optimization (Gate-DPO), which uses the current probability geometry of each rejected response to selectively attenuate its contribution, limiting excessive rejected suppression while delaying preference-loss saturation. Gate-DPO is objective-agnostic and composes with existing preference methods. Across four architectures, two preference datasets, and multiple objectives, gating consistently reduces squeezing and improves chosen-response likelihood, while exhibiting robust reductions in rejected-response collapse across architectures and objectives. Mass-dynamics analysis further shows that large preference margins can conceal substantial suppression of unrelated responses, while gating achieves healthier redistribution. Together, our results show that preference margin alone is insufficient to characterize optimization health and that selectively controlling probability dynamics provides a simple, general mechanism for stabilizing preference optimization.

Reproducing an empirical NLP study used to take weeks. Given the released data and a modern agentic-research harness, we redo every experiment of a recent ACL\,2026 study on personal-style post-editing of LLM drafts – and add three new ones – with the human investigator acting only as a reviewer-in-the-loop. We reproduce all seven preregistered hypotheses and recover the paper's headline correlation between perceived self-similarity and embedding-measured self-similarity to three decimal places ($r{=}{+}0.244$, $p{<}10^{-8}$, $n{=}648$). Under a leakage-free held-out protocol, GPT-5.5 and Claude\,Opus\,4.7 close $71$–$75\,\%$ of the style gap to the same-author ceiling on $324$ paired tasks, against $24\,\%$ for the human post-edit, and beat the human post-edit on $\sim$$80\,\%$ of tasks. We then frame the same data as an AI-text detection arms race. A leave-authors-out linear SVM on LUAR-MUD embeddings reaches AUC $0.93$–$1.00$ across approaches; six diagnostics show that GPT-5.5 detection is mostly a length confound while Opus detection is a genuine stylistic signature. Given $T{=}20$ feedback iterations against the frozen detector, an Opus agent flips two of five held-out test mimics to the human half-space and shrinks every margin by an order of magnitude. With moderate effort against a known detector, a frontier LLM can already efficiently lower its own AI-detection probability. All code, $648$ mimic drafts, trained detectors, diagnostics, and adversarial trajectories are released.

The lack of analytical models describing diffusion time dependence at intermediate time scales in complex tissue microstructure limits accurate quantification of extracellular diffusivity and tissue microstructure. Cell membrane water permeability modulates the signal in complex ways and is often disregarded in tumor microstructure models. We introduce TRACED-X, a Monte Carlo-based model that incorporates diffusion time dependence and membrane permeability in cell distributions to quantify pathologically-relevant properties in solid tumors. Monte Carlo simulations of water diffusion in semipermeable spheres were used to train neural network regressors for parameter estimation. A separate neural network was trained to predict the extracellular effective diffusivity, enabling the estimation of extracellular space tortuosity. Diffusion data from eight mixed-grade glioma patients were fitted with TRACED-X and analyzed in conjunction with clinical images. Simulation results demonstrate improved parameter estimation compared to comparator models. TRACED-X enabled the simultaneous in vivo quantification of intracellular volume fraction, cell size distribution, intrinsic extracellular diffusivity, tortuosity, and membrane permeability in glioma patients. Parameter maps show coherence with radiological findings and expected tumor phenotypes. TRACED-X permits the rapid estimate of unique biophysical properties in solid tumors, such as intrinsic extracellular diffusivity, tortuosity, and membrane permeability, in addition to cell microstructure. TRACED-X maps show promise in identifying heterogenous tumor subregions before and after treatment. Neural network implementations of diffusion time-dependence and tortuosity showed behavior consistent with coarse-graining and effective medium theory, respectively. Future work will explore the clinical utility of TRACED-X parameters in additional patients.

We consider selective classification with abstention in the fixed-pool (or transductive) setting, where the unlabeled pool is given beforehand and only a subset of points can be queried for labels. Our main insight is to view selective prediction through agreement: given queried labels and Lipschitz margin constraints in an embedding space, the version space of Lipschitz-consistent classification heads is well defined. We obtain upper and lower Lipschitz margin bounds that define, for each pool point, a set of certified valid labels containing the prediction of every head in the version space. The model therefore predicts only when the label is forced (i.e., all consistent heads agree), and abstains otherwise. We also propose a monotone submodular geometric proxy for budgeted querying, and show that a greedy algorithm retains the standard approximation factor.