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

NEXUS: Neural Energy Fields for Physically Consistent Contact-Rich 3D Object Dynamics

Physics-grounded video generation requires controllable 3D object dynamics that remain physically consistent under contact, deformation, and external forcing. Existing trajectory-based methods often model isolated physical effects, making it difficult to compose conservative and non-conservative dynamics in contact-rich 3D scenes. We present NEXUS, a neural energy-field framework for contact-rich 3D object dynamics. NEXUS represents each object as a structural graph and constructs dynamic object-object and object-environment contact graphs. Inspired by Hamiltonian Neural Networks, NEXUS formulates motion through scalar energy and dissipation terms rather than directly predicting states or accelerations. Conservative effects, including gravity and elastic deformation, are composed as additive energy terms, while non-conservative effects such as damping and impact-induced energy loss are modeled with learned Rayleigh-style dissipation. Forces are derived by differentiating the energy and dissipation functions and rolled out with a multi-substep semi-implicit integrator. Across controlled trajectory benchmarks, NEXUS improves long-horizon accuracy over representative learned and physics-structured dynamics baselines under varying mechanical properties and physical-effect compositions. We further show that NEXUS trajectories provide effective guidance for contact-rich video generation, improving physical plausibility while maintaining competitive visual quality.

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

Entity Binding Failures in Speech LLM Reasoning: Diagnosis and Chain-of-Thought Intervention

Speech Large Language Models (SLLMs) underperform their text counterparts on complex reasoning. We reveal that this gap is not a uniform cognitive deficit. Evaluating two architecturally diverse SLLMs, we show speech-to-text (S2T) matches or exceeds text-to-text (T2T) on spatial, syntactic, and factual tasks. Yet on logical tasks requiring entity tracking, S2T accuracy collapses to chance. We diagnose this as an entity binding failure: continuous speech features blur precise entity-property associations during implicit reasoning. To validate this diagnosis, we introduce Entity-Aware Chain-of-Thought (EA-CoT), a lightweight inference-time intervention forcing SLLMs to enumerate entities and bind them to claims before reasoning. EA-CoT bridges the gap, even when spoken names are misrecognized, yielding up to a 24.4 percentage-point accuracy gain. Ablations confirm the gains stem from explicit semantic binding, reframing the gap as an elicitation failure rather than a missing capability.

03.
arXiv (CS.CV) 2026-06-17

Do We Really Need Diffusion? A Fast U-Net for Paired Medical Image Translation

Magnetic resonance imaging-signal fat fraction (MRI-SFF) quantifies tissue fat and serves as an established biomarker for metabolic and musculoskeletal disorders. The acquisition requires, however, specialized MRI sequences, which are not available routinely. We investigate whether SFF can be estimated from widely available T2-weighted (T2w) MRI via image-to-image translation (I2I). We further compare a lightweight 4-level U-Net to a state-of-the-art Denoising Diffusion Probabilistic Model (DDPM) using a dataset of 230 048 paired 2D images (183 517 train, 23 621 val, 22 910 test) from the German National Cohort (NAKO). Both models clearly outperform the identity baseline (Pearson correlation r = 0.769, mean absolute error MAE = 0.070 +/- 0.054), which confirms that the models learn a non-trivial cross-modal mapping. Interestingly, the lightweight U-Net outperforms the DDPM in both correlation (r = 0.975 vs. 0.962) and error (MAE = 0.014 +/- 0.015 vs. 0.019 +/- 0.019), while reducing inference time by a factor of 208 (25.2 ms vs. 5 227.2 ms per image using 50 Denoising Diffusion Implicit Model (DDIM) steps). The strong clinical performance at substantially reduced computational cost enables real-time clinical use.

04.
bioRxiv (Bioinfo) 2026-06-19

Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket)

RNAs are important therapeutic targets, however identifying ligandable small-molecule binding pockets remains a major barrier to RNA-targeted drug discovery. Here, SMARTPocket, an atomic-level geometric deep learning framework for predicting RNA-small molecule binding pockets directly from three-dimensional structure is introduced. SMARTPocket represents RNA as full-atom point clouds and uses transfer learning from more than 110,000 protein binding interface structures to overcome the limited number of experimentally elucidated RNA-ligand complexes. Across four established single-chain benchmarks and three broader curated benchmarks, SMARTPocket consistently outperforms existing RNA pocket predictors and general biomolecular modeling approaches. The model generalizes to apo RNA structures when conformational changes are modest, identifies cryptic ligandable pockets, and recapitulates experimentally validated binding sites in the SARS-CoV-2 frameshifting element and an RNA aptamer evolved to bind small molecules. SMARTPocket-guided docking further improves near-native RNA-ligand pose recovery and computational efficiency compared with blind docking. These results establish SMARTPocket as a generalizable framework for structure-based identification of ligandable RNA pockets and for accelerating discovery of RNA-targeted small molecules.

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

Towards Next-Generation Healthcare: A Survey of Medical Embodied AI for Perception, Decision-Making, and Action

Foundation models have demonstrated impressive performance in enhancing healthcare efficiency across a wide range of medical applications. Nevertheless, their limited ability to perceive, understand, and interact with the physical world significantly constrains their effectiveness in real-world clinical workflows, where safety-critical decision-making and physical execution are tightly coupled. Recently, embodied artificial intelligence (AI) has emerged as a promising physical-interactive paradigm for intelligent healthcare, enabling agents to operate in complex medical environments. As research in this area rapidly expands, understanding how intelligent agents function as integrated, end-to-end systems in clinical environments becomes increasingly critical. However, existing surveys on medical embodied AI largely emphasize individual aspects or functional components, lacking a unified system-level organization of the field. To support and consolidate recent advances, we systematically survey the core components of medical embodied AI, with a particular emphasis on the coordinated integration of perception, decision-making, and action. We further review representative medical applications and relevant datasets, and we analyze the major challenges encountered in real-world clinical practice. Finally, we discuss key directions for future research in this rapidly evolving field. The associated project can be found at https://github.com/VMVLab/Medical_Embodied_AI_Paper_List.

07.
arXiv (CS.CL) 2026-06-15

Beyond Perplexity: UTF-8 Validity in Byte-aware Language Models

Byte-level tokenization enables language models to handle any Unicode input, but models can generate invalid UTF-8 sequences when encountering rare or unseen characters. We investigate the relationship between training scale and UTF-8 generation reliability with a 355M parameter model trained on 80B tokens from a balanced multilingual corpus of English, Japanese, Korean, and Chinese. We introduce multiple evaluation protocols that isolate UTF-8 structural validity from language modeling. UTF-8 validity convergence lags perplexity by a roughly a factor of two: perplexity stabilizes after 2.1B tokens, but UTF-8 validity requires 4.2B tokens. In context-free generation, rare characters achieve higher structural validity than common characters, suggesting over-specialization of frequent character representations. Through experiments, we observed that reliable UTF-8 generation is a distinct capability requiring evaluation beyond perplexity.

08.
arXiv (quant-ph) 2026-06-16

No Universal Purification in Quantum Mechanics

arXiv:2509.21111v2 Announce Type: replace Abstract: Many central tasks in fundamental physics and quantum information processing are possible only insofar as mixed quantum states can be made purer. In this work, we prove that the linearity and positivity of quantum mechanics impose general restrictions on quantum purification, unveiling a new fundamental principle of quantum information processing. We first establish that no quantum operation can transform a finite number of copies of an unknown quantum state or channel into an exactly pure output that depends non-trivially on the input, thereby ruling out an important form of universal purification in both static and dynamical settings. Building on this, we show that, upon relaxing the requirement of exact purity, one can establish quantitative sample-complexity lower bounds for approximate purification that hold for arbitrary physically allowed strategies, whose scaling matches the performance of purification-related tasks across several different areas of quantum information processing. Moreover, this lower bound leads to a generalized standard quantum limit for learning arbitrary functions of a quantum state, greatly extending earlier results based on quantum Fisher information and revealing a deep connection between purification and quantum learning. Extending this principle to other important settings, we establish, for the first time, an exponential sample-complexity lower bound for approximate pure dilation state preparation and a no-go theorem for approximate bosonic Gaussian state purification with passive Gaussian operations, establishing much more stringent limitations under practical operational constraints.

09.
arXiv (quant-ph) 2026-06-19

Optimal Shadow Estimation with Minimal Measurement Settings

arXiv:2606.20003v1 Announce Type: new Abstract: Shadow estimation is a powerful framework for predicting quantum properties from randomized measurements. While $3$-design protocols achieve optimal worst-case performance, the minimal number of measurement bases required for such optimality has remained open. Here we prove that $\Theta(d^2)$ measurement bases are both necessary and sufficient for worst-case optimal shadow estimation and construct an explicit basis family. In stark contrast, any state $2$-design already suffices for average-case optimality: the mean squared shadow norm of normalized observables is bounded by a universal constant, and we prove strong concentration for Haar-random states, yielding constant sample complexity for generic pure-state fidelity estimation. Easily implementable $2$-designs – from mutually unbiased bases, cyclic measurements, or shallow $\mathcal{O}(\log n)$-depth circuits – enable optimal average-case protocols with remarkably simple measurement strategies. Our results establish a fundamental complexity separation: worst-case estimation requires $\Theta(d^2)$ bases, whereas average-case performance requires only $\Theta(d)$ bases, with broad implications for quantum information theory and near-term experiments.

10.
arXiv (CS.CL) 2026-06-19

Thermodynamic Signatures of Reasoning: Free-Energy and Spectral-Form-Factor Diagnostics for Hallucination Detection in Large Language Models

Authors:

Hallucination detection in large language models (LLMs) is deployment-critical, and recent work shows that the spectrum of attention-derived graph Laplacians carries strong signal about reasoning quality. Prior spectral diagnostics, however, summarize the Laplacian spectrum by a handful of eigenvalues or hand-picked scalars, leaving most of its structure unused. We propose Free-Energy Signatures (Fes), a spectral descriptor that treats each layer's attention Laplacian as a Hamiltonian and extracts its thermodynamic potentials partition function, free energy, spectral entropy, heat capacity together with the random-matrix-theory (RMT) spectral form factor. We prove three results: (i)~Lipschitz stability of Fes under attention perturbation; (ii)~an expressiveness result showing that Fes enriches finite spectral summaries and approximates moment-derived spectral functionals under explicit regularity and grid-resolution assumptions; and (iii)~a finite-sample PAC bound on the AUROC of a training-free detector built from Fes. Empirically, across six open-weight LLMs and six benchmarks, a lightweight probe on Fes descriptors achieves the strongest aggregate AUROC among attention-spectral baselines, improving over LapEig by $+6.5$ AUROC points and over GoR-4 by $+2.4$ points on average, while requiring no update to the underlying LLM. In the fully unsupervised setting, an RMT-deviation score achieves mean AUROC $0.71$, providing a label-free but weaker detector. A complementary RMT analysis shows that correct generations exhibit more Wigner-Dyson like spectral statistics, whereas hallucinations exhibit more Poisson-like statistics. The anonymized code and config are provided in the supplementary material.

11.
arXiv (quant-ph) 2026-06-15

Multiple-time Quantum Imaginary Time Evolution

arXiv:2512.10875v2 Announce Type: replace Abstract: Quantum Imaginary-Time Evolution (QITE) is a powerful method for preparing ground states on quantum hardware. However, executing QITE has costly measurement budgets for general Hamiltonians. Both fidelity and computational cost are strongly dependent on the definition of suitable local domains and Hamiltonian partitions. In this work, we introduce the Multiple-Time QITE algorithm (MT-QITE). We show how using more than one imaginary time substantially improves the fidelity of the resulting ground state as well as the measurement overhead with respect to the previously published QITE algorithm, while preserving its deterministic character and its independence from ad hoc ansatze. Moreover, unlike QITE and other QITE-based algorithms, MT-QITE is parallelizable, and we show that even in Hamiltonians with non-local interactions, partitioning may entail a computational advantage.

12.
arXiv (CS.LG) 2026-06-18

Diffusion-Proof: Recipe for Formal Theorem Proving Beyond Auto-Regressive Generation

arXiv:2606.19315v1 Announce Type: new Abstract: Enhancing the formal math reasoning capabilities of Large Language Models (LLMs) has become a key focus in both mathematical and computer science communities in recent years. While significant progress has been made in using state-of-the-art Auto-Regressive (AR) LLMs for formal theorem proving, these models suffer from inherent limitations. Their next-token prediction generation methods may yield suboptimal performance due to the challenges of long-range coherence and the compounding of errors over long sequences. Recent advancements in diffusion LLMs (dLLMs), which generate text through iterative denoising of a multi-token block, offer a promising alternative. However, the application of dLLMs to formal mathematics, where maintaining long-range coherence is critical, remains largely understudied. To address the challenges above, we propose **Diffusion-Proof**, to the best of our knowledge, the first framework to train and apply dLLMs for formal theorem proving. Our frameworks contain training and inference methods for two models. The first one is *dLLM-Prover-7B*, which performs whole-proof writing with long-range coherent tactic usage. The second one is *dLLM-Corrector-7B*, which is a novel large block diffusion-based correction model. It leverages the in-filling capabilities of dLLMs to perform local proof correction using bi-directional information. Extensive experiments demonstrate that **Diffusion-Proof** relatively significantly outperforms the AR LLM baseline trained under the same dataset. **Diffusion-Proof** achieves an absolute improvement of **1.61%** on ProofNet-Test and **6.14%** on MiniF2F-Test benchmarks compare to the baseline. Notably, **Diffusion-Proof** successfully resolves one IMO problem that more advanced thinking model DeepSeek-Prover-V2-7B could not solve, showcasing the unique advantage of dLLMs in formal theorem proving.

13.
medRxiv (Medicine) 2026-06-18

MOSAIC: Methylation-Oriented Site Analysis and Information Classifier for Robust Epigenomic Classification of Acute Leukemia in Clinical Cohorts with Variable Tumor Purity

DNA methylation-based classification offers a rapid diagnostic complement to conventional molecular workflows in acute leukemia. Existing classifiers are trained on array-derived reference cohorts whose construction favors specimens with adequate tumor content, leaving clinically relevant low-purity specimens underrepresented and classifier robustness in this regime uncharacterized. On held-out low-purity specimens, existing classifiers were concordant with expert pathology in only 7 of 10 (MARLIN) and 5 of 10 (ALMA) cases, motivating a classifier built to maintain accuracy at low tumor purity. We developed MOSAIC (Methylation-Oriented Site Analysis and Information Classifier), a neural network classifier built to maintain accuracy across the full range of tumor purities encountered in clinical practice. MOSAIC is a neural network trained on publicly available array-based methylation data augmented with native methylation calls from Oxford Nanopore sequencing. MOSAIC was evaluated on low-purity specimens held out entirely from training. On these held-out low-blast leukemia specimens, all below 25% blasts and including a case at 1.4%, MOSAIC was concordant with expert pathology in every case, recovering the correct subtype where diluted disease signal would otherwise be mistaken for normal or unrelated tissue. Gradient-based saliency analysis showed that the network relies on a partially distinct set of discriminative CpG probes when classifying low-blast specimens. MOSAIC demonstrates that augmenting training with clinically representative clinical specimens yields methylation-based leukemia classification that maintains effectiveness under the variable tumor purity of real clinical cohorts.

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

LLM Parameters for Math Across Languages: Shared or Separate?

Large language models (LLMs) exhibit substantial cross-lingual variation in mathematical reasoning performance, but it remains unclear whether these differences reflect language-specific parameters or a shared mechanism that manifests differently by language. We present a cross-lingual mechanistic analysis of mathematical reasoning in LLMs, enabling us to localize and compare model parameters that support mathematical reasoning across languages. We find that the extracted math-associated parameters exhibit partial cross-lingual overlap, with the strongest overlap concentrated in intermediate model layers. We further observe that English consistently produces the largest set of math-relevant parameters, whereas lower-resource languages reveal smaller sets of relevant parameters. These results suggest that math-related behavior in multilingual LLMs is neither fully language-invariant nor fully language-specific, but instead exhibits partial cross-lingual parameter overlap with systematic language-dependent differences.

15.
arXiv (quant-ph) 2026-06-16

High-dimensional coherence to entanglement transduction under canonical noise

arXiv:2606.16695v1 Announce Type: new Abstract: We develop an analytical framework for coherence-to-entanglement conversion in bipartite high-dimensional quantum systems, so-called qunits. An arbitrary coherent input qunit is coupled to an incoherent ancilla through a generalized controlled-shift operation, producing a maximally correlated bipartite state. By analyzing the partial transpose of the output state, we establish an exact dimension-independent connection between the input coherence and the generated entanglement. We then study how this conversion is affected by three standard noise processes applied after the conversion step: phase damping, global depolarizing noise, and independent amplitude damping. The resulting expressions show that these channels degrade entanglement in qualitatively different ways. Phase damping leads to a uniform attenuation of the entanglement generated from coherence, depolarizing noise introduces pairwise thresholds associated with entanglement sudden death, and amplitude damping produces an asymmetric decay governed by relaxation toward the ground state. For maximally coherent inputs, the general results reduce to simple closed-form behavior, allowing direct comparison of the three noise mechanisms as the system dimension increases. In particular, global depolarizing noise exhibits a dimension-dependent sudden-death threshold, while amplitude damping leads to a smooth suppression in the maximally coherent case. These results provide useful analytical benchmarks for high-dimensional resource conversion and for assessing noisy entanglement generation in qudit-based quantum-information settings.

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

DeepMine-Mamba: Mitigating Information Dilution in Mamba-Based State Space Models for Document Image Binarization

Document image binarization aims to separate foreground text from degraded backgrounds while preserving thin, broken, and low-contrast strokes. Although deep learning methods have improved binarization performance, most existing approaches rely on convolutional, transformer-based, or generative architectures, while Mamba-based state space models remain largely unexplored for this task. In this work, we investigate Mamba-based feature propagation and observe that direct state-space propagation may dilute weak foreground cues during long-range modeling, especially faint ink traces, fragmented characters, and boundary-sensitive stroke details. To address this problem, we propose DeepMine-Mamba, a Mamba-based binarization framework equipped with a novel Anti-Dilution Gate that estimates propagation-induced feature changes and selectively restores stroke-sensitive local responses while suppressing unnecessary background enhancement. Experiments on DIBCO/H-DIBCO benchmarks under a strict leave-one-year-out protocol show that DeepMine-Mamba achieves competitive overall performance, with strong average FM and Fps across benchmark years. Ablation results further show that the Anti-Dilution Gate is the key component for mitigating propagation-induced foreground dilution and improving stroke preservation.

17.
Nature (Science) 2026-06-08

Fifty years since a simple equation described the chaos of biology

An exploration of chaos theory in population dynamics showed that unpredictable systems can often be modelled using surprisingly simple mathematics. An exploration of chaos theory in population dynamics showed that unpredictable systems can often be modelled using surprisingly simple mathematics.

18.
arXiv (CS.AI) 2026-06-16

From Tokens to Regions: CUDA-Sensitive Instruction Tuning for GPU Kernel Generation

arXiv:2606.16231v1 Announce Type: cross Abstract: High-performance CUDA kernels are essential for scalable AI systems, while Large Language Models (LLMs) still struggle to generate correct kernels due to strict and implicit execution constraints. Existing LLM-based approaches either rely on costly agentic or reinforcement-learning (RL) pipelines, or adopt supervised fine-tuning (SFT) objectives that fail to explicitly model CUDA sensitivity, namely code tokens or regions tightly coupled with execution constraints. In this work, we investigate CUDA sensitivity from the perspective of token confidence patterns, showing that CUDA sensitivity appears at both token and region levels, where most CUDA-sensitive tokens are predicted with high confidence, while a smaller low-confidence subset forms regions corresponding to execution-critical structures. These findings suggest that effective CUDA kernel generation should both leverage high-confidence CUDA-sensitive tokens and preserve low-confidence CUDA-sensitive regions. Building on these insights, we propose \underline{CUDA-\underline{Se}nsitive Instruction \underline{T}uning (CuSeT)}, a low-cost post-training method within a simple SFT framework. CuSeT follows the principle of ``from tokens to regions'' by combining adaptive token-level masking with region-aware sample reweighting. Experiments show that CuSeT consistently improves functional correctness across multiple model families and scales, outperforming standard SFT and advanced SFT variants, while achieving competitive performance against frontier CUDA kernel generation models with substantially lower inference cost.

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

SpikF-GO: Spiking Fourier Graph Operators for Multivariate Time Series Forecasting

arXiv:2606.13901v1 Announce Type: new Abstract: Spiking Neural Networks (SNNs) have emerged as an energy-efficient alternative to conventional neural networks, demonstrating strong performance in computer vision and robotics. More recently, SNNs have been applied to time series forecasting (TSF), with methods exploring spiking temporal backbones, spike-compatible positional encodings, Fourier-domain processing, and redesigned neuron dynamics. However, existing SNN forecasting approaches process variables independently, lacking explicit mechanisms for modeling inter-variable dependencies. This is a critical limitation in multivariate settings, where cross-variable correlations carry substantial predictive information. We propose Spiking Fourier Graph Operators (SpikF-GO), which addresses this gap by combining a hypervariate graph formulation in which every scalar observation becomes a graph node with spike-driven spectral processing. SpikF-GO introduces a Hard Concrete frequency gate for learnable sparse frequency selection and a Complex LIF gate that applies independent spiking neurons to real and imaginary Fourier components, preserving binary, event-driven computation throughout the spectral domain. We further present a variant incorporating Central Pattern Generator-based positional encodings for stronger long-range temporal modeling. Evaluated on eight benchmarks under a unified experimental protocol, SpikF-GO achieves the best average rank among all SNN methods and outperforms its ANN counterpart, FourierGNN, at reduced energy cost. SpikF-GO maintains competitive accuracy even at substantially smaller embedding dimensions, thereby achieving significant energy reductions. To our knowledge, this is among the first works to bring graph-based multivariate modeling into the spiking domain for TSF and the first to provide a unified comparison across SNN forecasting architectures under a common experimental protocol.

20.
bioRxiv (Bioinfo) 2026-06-19

Nickel-Driven Dynamics of Urease in Sporosarcina pasteurii: Integrated Computational and Experimental Insights

Urease is a nickel-dependent enzyme that plays an important role in urea hydrolysis and in a process named as microbial-induced calcium carbonate precipitation (MICP), which is widely used in sustainable environmental biotechnology. Despite its ecological importance, urease powers Biogrout (biocementation), a promising green technology for soil stabilization and infrastructure repair. Yet, the relationship between nickel availability, enzyme activation, and bacterial fitness remains poorly understood. In this study, we reveal a striking dual effect of nickel on Sporosarcina pasteurii: while high Ni2+ concentrations strongly inhibit growth (IC50 {approx} 637.7 {micro}M), they simultaneously boost specific urease activity up to six-fold. This uncoupling between biomass and enzymatic efficiency highlights a previously overlooked adaptive strategy under metal stress. Using structural bioinformatics and molecular docking, we show that Ure1–the catalytic subunit–exhibits the strongest nickel affinity (-4.3 kcal{middle dot}mol-1), supported by highly conserved active-site residues, whereas accessory proteins UreE and UreG display moderate and weak binding, consistent with their roles in metal delivery and GTP-dependent maturation. In addition, microscopic observations confirmed that calcium carbonate precipitation was most pronounced at intermediate nickel concentrations (approximately 400-1000 {micro}M), whereas higher concentrations ([≥]1000-1300 {micro}M) led to reduced mineral formation due to loss viable cells. Taken together, these results indicates that nickel availability controls both urease activation and bacterial fitness, and that an optimal balance is required to maximize biomenerilization efficiency in environmental applications, particularly in biocementation technology.

21.
arXiv (CS.AI) 2026-06-11

TAPIOCA: Why Task- Aware Pruning Improves OOD model Capability

arXiv:2605.14738v3 Announce Type: replace-cross Abstract: Recent work has promoted task-aware layer pruning as a way to improve model performance on particular tasks, as shown by TALE. In this paper, we investigate when such improvements occur and why. We show first that, across controlled polynomial regression tasks and large language models, such pruning yields no benefit on in-distribution (ID) data but consistently improves out-of-distribution (OOD) accuracy. We further show empirically that OOD inputs induce layerwise norm and pairwise-distance profiles that deviate from the corresponding ID profiles. This leads to a geometric explanation of task-aware pruning: each task induces a task-adapted geometry, characterized empirically by the representation profiles observed on ID inputs. OOD inputs can introduce a distorted version of the task-adapted geometry. Task-aware pruning identifies layers that create or amplify this distortion; by removing them, it shifts OOD representational norms and pairwise distances toward those observed on the adapted distribution. This realigns OOD inputs with the model's task-adapted geometry and improves performance. We provide causal evidence through controlled distribution shifts and residual-scaling interventions, and demonstrate consistent behavior across model scales.

22.
arXiv (quant-ph) 2026-06-19

Applications of quantum annealing to magnetic dipole hyperfine structure constants: First results beyond energies for atoms

arXiv:2606.20166v1 Announce Type: new Abstract: We report the first results of the magnetic dipole hyperfine structure (HFS) constants of neutral $\mathrm{Li}$, Li-like $\mathrm{Be}$, neutral $\mathrm{Na}$, and Na-like $\mathrm{Mg}$ using a modified version of the Quantum Annealer Eigensolver (QAE) algorithm on D-Wave's quantum hardware. The results are benchmarked against relativistic configuration interaction with multiconfiguration Dirac Hartree-Fock (MCDHF) calculations using the General-purpose Relativistic Atomic Structure Package (GRASP), and simulated annealing. In our modified QAE, a zooming-and-sigma-annealing approach with a floating-point encoding scheme is adopted to estimate the ground-state eigenvalue and eigenvector of the relativistic Dirac-Coulomb Hamiltonian matrices ($H_{\mathrm{DC}}$) constructed from 11 or fewer configuration state functions (CSFs). For calculations with extended correlation orbital sets, we applied a CSF truncation scheme, retaining only CSFs (up to 12) that make significant contributions to the ground-state wavefunction. Our modified QAE precision is kept limited to three decimal places (up to 10 qubits). Hardware demonstrations on the D-Wave quantum processing unit (QPU) yielded results that were completely consistent with GRASP (at the chosen precision) in determining the magnetic dipole HFS constants, with accuracy varying across systems and $H_{\mathrm{DC}}$ matrix dimensions.

23.
arXiv (CS.AI) 2026-06-12

Select and Improve: Understanding the Mechanics of Post-Training for Reasoning

arXiv:2606.13125v1 Announce Type: cross Abstract: Reinforcement learning has rapidly emerged as a key component in the training of reasoning and coding models, yet it remains poorly understood from a mechanistic perspective. We study how and through what underlying processes capabilities are acquired or enhanced via reinforcement learning post-training. Our analysis, based on controlled math reasoning experiments with Qwen-2.5-1.5B, reveals two core mechanisms: strategy selection and strategy improvement. Our results highlight the role of SFT data and reinforcement learning data in activating these mechanisms, in particular showing how supervising the model on diverse reasoning strategies can enable strategy selection and how increasing difficulty in reinforcement learning data can enable strategy improvement. Taken together, our results provide mechanistic insight into RL training and suggest practical interventions to continue scaling reasoning capabilities.

25.
PLOS Computational Biology 2026-06-08

Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings

by Julia Pilarski, Tanja Stadler, Sophie Seidel Multicellular organisms develop from a single cell by repeated rounds of cell division, differentiation, and death, which can be represented as a single-cell phylogenetic tree. Genetic lineage tracing allows us to investigate this development by tracking the ancestry of individual cells as populations grow and change over time. However, accurate reconstruction of the cell phylogeny and quantification of the corresponding phylodynamic parameters – cell division, differentiation, and death rates – from this tracking data remains challenging and needs to be systematically evaluated. We perform simulations and assess, using the Bayesian framework, the joint inference of time-scaled cell phylogenies and phylodynamic parameters from CRISPR lineage recordings with random or sequential edits. Principally, we characterize the inference improvements as the recorder capacity increases. We observe more accurate phylogenetic reconstruction from sequential compared to random recordings, but no substantial improvement in phylodynamic inference when using the additional information contained in the order of edits. Overall, we find that CRISPR lineage recordings carry a strong signal on the rates of cell division when appropriate models are used. However, we detect biases in the inferred rates of cell division and death under phylodynamic model misspecification, i.e., when fitting classic memoryless birth-death processes to synchronous cell divisions. Moreover, for scenarios when cells differentiate into distinct types, we demonstrate that Bayesian phylodynamic analysis of sparse end-point measurements can resolve these cell differentiation trajectories by lineage and time. Under prototypical dynamics, we recover cell type-specific division and death rates, and cell type transition rates in over 80% of simulations. Overall, this simulation study explores how much information on cellular development can be extracted from state-of-the-art genetic lineage tracing data using phylogenetic and phylodynamic methodology.