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01.
Nature (Science) 2026-06-17

The EU needs to back its ambition to end animal testing with cash

作者: 未知作者

The European Union has declared that it wants to stop using animals in chemical safety testing. Its goal will need a timeline and a serious funding commitment. The European Union has declared that it wants to stop using animals in chemical safety testing. Its goal will need a timeline and a serious funding commitment.

02.
arXiv (CS.AI) 2026-06-11

APPO: Agentic Procedural Policy Optimization

arXiv:2606.12384v1 Announce Type: cross Abstract: Recent advances in agentic Reinforcement Learning (RL) have substantially improved the multi-turn tool-use capabilities of large language model agents. However, most existing methods assign credit over coarse heuristic units, such as tool-call boundaries or fixed workflows, making it difficult to identify which intermediate decisions influence downstream outcomes. In this work, we study agentic RL from two perspectives: where to branch and how to assign credit after branching. Our pilot analysis shows that influential decision points are broadly distributed throughout the generated sequence rather than concentrated at tool calls, while token entropy alone does not reliably reflect their impact on final outcomes. Motivated by these observations, we propose Agentic Procedural Policy Optimization (APPO), which shifts branching and credit assignment from coarse interaction units to fine-grained decision points in the sequence. APPO selects branching locations using a Branching Score that combines token uncertainty with policy-induced likelihood gains of subsequent continuations, enabling more targeted exploration while filtering out spurious high-entropy positions. It further introduces procedure-level advantage scaling to better distribute credit across branched rollouts. Experiments on 13 benchmarks show that APPO consistently improves strong agentic RL baselines by nearly 4 points, while keeping efficient tool-calls and maintaining behavior interpretability.

03.
arXiv (CS.CL) 2026-06-19

EndoCoT: Scaling Endogenous Chain-of-Thought Reasoning in Diffusion Models

Recently, Multimodal Large Language Models (MLLMs) have been widely integrated into diffusion frameworks primarily as text encoders to tackle complex tasks such as spatial reasoning. However, this paradigm suffers from two critical limitations: (i) MLLMs text encoder exhibits insufficient reasoning depth. Single-step encoding fails to activate the Chain-of-Thought process, which is essential for MLLMs to provide accurate guidance for complex tasks. (ii) The guidance remains invariant during the decoding process. Invariant guidance during decoding prevents DiT from progressively decomposing complex instructions into actionable denoising steps, even with correct MLLM encodings. To this end, we propose Endogenous Chain-of-Thought (EndoCoT), a novel framework that first activates MLLMs' reasoning potential by iteratively refining latent thought states through an iterative thought guidance module, and then bridges these states to the DiT's denoising process. Second, a terminal thought grounding module is applied to ensure the reasoning trajectory remains grounded in textual supervision by aligning the final state with ground-truth answers. With these two components, the MLLM text encoder delivers meticulously reasoned guidance, enabling the DiT to execute it progressively and ultimately solve complex tasks in a step-by-step manner. Extensive evaluations across diverse benchmarks (e.g., Maze, TSP, VSP, and Sudoku) achieve an average accuracy of 92.1%, outperforming the strongest baseline by 8.3 percentage points. The code and dataset are publicly available at https://internlm.github.io/EndoCoT/.

04.
arXiv (CS.CL) 2026-06-11

RLCSD: Reinforcement Learning with Contrastive On-Policy Self-Distillation

On-policy self-distillation (OPSD) provides dense, token-level supervision for reasoning models by aligning a model's own distribution with the distribution it produces under privileged context, typically a verified solution. However, we show that the learning signal drawn from this distributional gap concentrates on style tokens rather than task-bearing ones, as the hinted model tends to produce more direct, shorter outputs. We term this pathology privilege-induced style drift, which destabilizes training or causes response length to shrink. To address this, we propose RLCSD (Reinforcement Learning with Contrastive on-policy Self-Distillation), which mitigates this drift by contrasting the teacher-student gap under a correct hint against that under a wrong hint, suppressing the style shift that conditioning on a hint tends to induce regardless of correctness, and yielding a signal that is more concentrated on task-bearing tokens. Experiments on Qwen3 (1.7B/4B/8B) and Olmo-3-7B-Think across mathematical and logical reasoning show that RLCSD consistently outperforms GRPO and prior OPSD methods. We further show that the contrastive principle is general: it plugs into existing OPSD methods to improve them, and its underlying insight extends to the broader cross-model on-policy distillation setting.

05.
arXiv (CS.AI) 2026-06-11

Are LLMs Bad at Moral Reasoning?

arXiv:2606.11635v1 Announce Type: cross Abstract: For highly capable AI systems to operate safely in dynamic, open-ended environments, they must be able to identify, understand, and respond to moral reasons for action, and constrain their behaviour accordingly. A growing body of research aims to evaluate this capacity – moral competence – in today's most capable AI systems, recently reaching broadly pessimistic conclusions. One of the most ambitious such papers collects gold-standard human-authored rubrics for evaluating moral reasoning in 1,000 cases, and benchmarks frontier AI models against those rubrics, with underwhelming results. In this paper, we argue that the MoReBench dataset can be redeployed to give a much more optimistic picture of LLMs' moral reasoning (an essential part of moral competence). We show that if, instead of scoring LLMs' responses to these cases against these rubrics, we instead give the LLMs the same task given to humans – to generate scoring rubrics for the moral analysis of particular cases – the rubrics they generate are both better calibrated to the human rubrics than their open-ended responses, and, where they differ, plausibly reflect nothing more than the vast dimensionality of most moral problems, as well as highlighting some human departures from the "rubric for creating rubrics". Taking these points into consideration, the MoReBench dataset suggests that LLMs are significantly more capable at moral reasoning than was previously believed.

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

NaturalFlow: Reducing Disruptive Pauses for Natural Speech Flow in Simultaneous Speech-to-Speech Translation

Simultaneous speech-to-speech translation aims to enable near-real-time communication by minimizing latency, offering a compelling, real-time alternative to the high latency of consecutive translation. However, the excessive pursuit of low latency often results in fragmented chunk-wise speech. Consequently, listeners are subjected to an unnatural acoustic flow punctuated by frequent pauses, which could increase their cognitive load. To bridge this gap, we introduce a fluency-aware optimization framework designed to discover the sweet spot between the low-latency benefits of simultaneous translation and the natural flow of consecutive translation. Our framework minimizes inter-chunk silences by leveraging model-internal signals, including linguistic diversity and induced temporal variability in speech durations. Experiments on short- and long-form benchmarks show that our framework produces natural speech flow while maintaining competitive latency and translation quality.

07.
arXiv (CS.LG) 2026-06-18

Adaptive Speech-to-Spike Encoding for Spiking Neural Networks

arXiv:2606.19039v1 Announce Type: cross Abstract: The mismatch between continuous acoustic signals and discrete event-driven processing remains a fundamental bottleneck for neuromorphic speech processing. Current systems typically rely on fixed spike encoders, forcing downstream Spiking Neural Networks (SNNs) to compensate for non-adaptive input representations. To address this, we present a learnable residual speech-to-spike encoder jointly trained end-to-end with a Recurrent Leaky Integrate-and-Fire (R-LIF) backbone. We validate this approach on the Google Speech Commands v2 (GSC-v2) benchmark, achieving up to 94.97% accuracy. Notably, the learned encoder remains highly parameter-efficient with a compact 35k-parameter variant that reaches 89.8%, matching or exceeding prior baselines that require an order of magnitude more parameters. Our encoder-focused analysis, including linear probing and gradient-residual inspection, indicates that the encoder does not target faithful signal reconstruction but instead learns task-aligned spike representations that enhance class separability. Finally, we benchmark bio-inspired, hardware-friendly credit assignment by comparing Direct Feedback Alignment (DFA) with surrogate-gradient BPTT under identical architectures and training conditions. We find that DFA reaches 91.5% accuracy, quantifying the performance trade-off of bio-inspired learning rules for modern neuromorphic audio.

08.
arXiv (CS.CV) 2026-06-17

Phys4D: Fine-Grained Physics-Consistent 4D Modeling from Video Diffusion

Recent video diffusion models have achieved impressive capabilities as large-scale generative world models. However, these models often struggle with fine-grained physical consistency, exhibiting physically implausible dynamics over time. In this work, we present Phys4D, a pipeline for learning physics-consistent 4D world representations from video diffusion models. Phys4D adopts a three-stage training paradigm that progressively lifts appearance-driven video diffusion models into physics-consistent 4D world representations. We first bootstrap robust geometry and motion representations through large-scale pseudo-supervised pretraining, establishing a foundation for 4D scene modeling. We then perform physics-grounded supervised fine-tuning using simulation-generated data, enforcing temporally consistent 4D dynamics. Finally, we apply simulation-grounded reinforcement learning to correct residual physical violations that are difficult to capture through explicit supervision. To evaluate fine-grained physical consistency beyond appearance-based metrics, we introduce a set of 4D world consistency evaluation that probe geometric coherence, motion stability, and long-horizon physical plausibility. Experimental results demonstrate that Phys4D substantially improves fine-grained spatiotemporal and physical consistency compared to appearance-driven baselines, while maintaining strong generative performance. Our project page is available at https://sensational-brioche-7657e7.netlify.app/

09.
medRxiv (Medicine) 2026-06-10

Longitudinal brain structural changes during clozapine treatment: associations with neuroreceptor architecture and clinical response

In treatment-resistant schizophrenia, clozapine treatment has been associated with longitudinal reductions in subcortical volumes, ventricular enlargement, and widespread cortical thinning. However, it is unknown how these structural changes relate to clozapines pharmacological profile and clinical efficacy. We combined five longitudinal datasets with MRI acquired before and on average 5 months after clozapine initiation in 143 individuals to quantify brain structural changes and their association with normative maps relating to neuroreceptor architecture and physiological systems, and improvement in symptom severity. Clozapine treatment was associated with grey matter volume reductions across multiple subcortical regions (including the amygdala, hippocampus, thalamus, caudate, putamen and nucleus accumbens), increases in pallidal volume, ventricular enlargement, and widespread cortical thinning. Cortical regions showing the greatest magnitude of thinning corresponded to areas with higher normative densities of serotonergic 5-HT1A, 5-HT2A and 5-HT4 receptors. Changes in subcortical volume or cortical thickness during clozapine treatment were not associated with changes in total or positive symptom severity. In addition, baseline subcortical volume, cortical thickness, or gyrification prior to starting clozapine did not predict subsequent symptom improvement. Cortical thinning may partly reflect clozapines activity at serotonergic receptors, which have been implicated in cortical network stabilisation and neuroplasticity, however structural remodelling during clozapine treatment may reflect a process independent from its clinical efficacy in improving core symptoms of psychosis.

10.
arXiv (CS.LG) 2026-06-12

A Stationary (and Therefore Compatible) Representation is All You Need

arXiv:2606.12488v1 Announce Type: new Abstract: Learning compatible representations aims to learn feature representations that can be used interchangeably over time whenever a model undergoes updates. In this paper, we demonstrate that stationary representations learned by d-Simplex fixed classifiers imply compatibility as in its formal definition. This result establishes a foundation for future works and can be directly exploited in practical learning scenarios. We address the challenge of learning compatibility using $d$-Simplex fixed classifiers when the model is sequentially fine-tuned. Learning according to a d-Simplex fixed classifier with the cross-entropy loss aligns feature distributions at the first-order statistics. Consequently, it may not fully capture higher-order dependencies in the representation between model updates. To address this issue, we demonstrate that training the model using a $d$-Simplex fixed classifier through a convex combination of the cross-entropy loss and a contrastive loss not only captures higher-order dependencies, but is also equivalent to learning with the cross-entropy under the compatibility constraints. We confirm our findings with extensive experiments also considering a new scenario where a pre-trained model is sequentially fine-tuned and occasionally replaced with an improved model. We show that stationary representations enable uninterrupted retrieval services (without reprocessing gallery images) while improving performance during model updates and replacements, achieving state-of-the-art. Code at https://github.com/miccunifi/iamcl2r.

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

HairLRM: Strand-based Hair Modeling via Large Reconstruction Models

The fundamental limitation of traditional strand-based modeling is not simply data scarcity, but the ill-posedness of inferring complex 3D fields from 2D imagery without structural constraints. This unconstrained regression leads to catastrophic failures in resolving both global occlusion (e.g., in ponytails) and local directionality (e.g., in curls), resulting in over-smoothed, plausible-but-incorrect geometries. To resolve this, we integrate the strong geometric priors of Large Reconstruction Models (LRMs) into the strand generation pipeline. Using the LRM mesh as a structural anchor, we employ a novel Dual Orientation AutoEncoder to lift coarse geometry into high-fidelity strands. By resolving vector field singularities through latent-space optimization and surface-guided refinement, our method effectively disentangles complex topological structures, setting a new benchmark for robustness and accuracy in hair reconstruction.

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

PhononBench:A Large-Scale Phonon-Based Benchmark for Dynamical Stability in Crystal Generation

arXiv:2512.21227v3 Announce Type: replace-cross Abstract: In recent years, generative artificial intelligence has made significant advances in the design of crystalline materials, giving rise to approaches based on graph neural networks, diffusion models, and large language models. Existing evaluations commonly follow the stability-uniqueness-novelty (S.U.N.) framework, where stability is primarily assessed using thermodynamic criteria, which do not fully capture the dynamical stability essential for a material's practical existence. Dynamical stability is a key determinant of whether a material can be synthesized and persist, with phonon spectrum calculations serving as the standard for its evaluation. However, the high computational cost of such calculations has prevented large-scale assessment of dynamical stability in generated crystals. In this work, we introduce PhononBench, the first large-scale benchmark for dynamical stability in AI-generated crystals. Leveraging the recently developed MatterSim interatomic potential, which achieves density-functional-theory (DFT)-level accuracy in phonon predictions across more than 10,000 materials, PhononBench enables efficient phonon calculations and dynamical-stability analysis for 133,838 crystal structures generated by 7 leading crystal generation models. PhononBench reveals a widespread limitation of current generative models: unless otherwise specified, all reported dynamical-stability metrics are evaluated at a phonon-frequency threshold of -0.1 THz, with the average dynamical-stability rate across all generated structures being only 32.15%, and the top-performing model, MatterGen, reaching just 45.05%.In addition, we identify 32,995 crystal structures that are phonon-stable across the entire Brillouin zone under a strict threshold of -0.001 THz. In addition, a web-based service is accessible at http://phononbench.cn/, enabling minute-level ultra-fast phonon predictions.

13.
bioRxiv (Bioinfo) 2026-06-20

The recount3 Python package for programmatic access to uniformly processed RNA-seq data

The recount3 online resource provides tens of thousands of uniformly processed RNA-seq samples across human and mouse from major sequencing repositories like the Sequence Read Archive. While access to these datasets has traditionally been centered in the R/Bioconductor ecosystem, the growing prominence of Python in bioinformatics and machine learning necessitates native, efficient tooling for Python users. Therefore, we present the recount3 Python package with robust application programming interface (API) and command-line interface (CLI) for discovering, downloading, and materializing recount3 resources. The software orchestrates uniform resource locator (URL) resolution, persistent on-disk caching, and the automatic parsing of data into analysis-ready data structures, including Pandas DataFrames and BiocPy RangedSummarizedExperiment objects. The recount3 Python package drastically lowers the barrier to entry for large-scale utilization of RNA-seq data in Python-based computational pipelines, bridging the gap between massive public transcriptomic data and modern machine learning ecosystems.

14.
arXiv (math.PR) 2026-06-16

Purely unrectifiable sets, fractal percolation and graphs of functions

arXiv:2606.15745v1 Announce Type: cross Abstract: This paper contains a survey of some of the results of the author related to unrectifiablity and is an extended version of the author's talk given at the Second Winter School Geometric Measure Theory Rectifiability vs. Pure Unrectifiability in Hanghzou, China. These results include irregular/purely unrectifiable $1$-sets on the graphs of continuous functions like the Takagi, the Weierstrass-Cellerier and the typical (in the sense of Baire) continuous function. It is also discussed that there exists $ {\alpha}_{0}\alpha_0$. The background of the $1$-unrectifiability is discussed in more detail.

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

Forecasting Future Behavior as a Learning Task

arXiv:2606.11445v1 Announce Type: new Abstract: Trust in an AI system is often anchored by explanations of how it works, which one then uses to forecast its behavior on new inputs. For large reasoning models (LRMs), this conventional route is particularly difficult to follow: explanation methods for single token generations do not naturally generalize to long trajectories, and the trajectories themselves are often not faithful when read as natural language. We propose an alternative that bypasses the explanation step: treat behavior forecasting as a learnable task and train Behavior Forecasters that operates on a single reasoning trajectory to make the same forecasts one would typically seek from an explanation. The forecaster's training data is obtained by querying the LRM with no human annotation, and its inference is done in a single forward pass. We instantiate this approach on two tasks: how likely the LRM is to repeat its answer on re-runs, and how removing parts of the input changes its answer. We evaluate this approach on both tasks across three diverse reasoning datasets and find that trained Behavior Forecasters are more accurate than GPT-5.4 and Claude Opus-4.6 reading the same trajectories as naive readers, at a small fraction of their inference cost. We find that fine-tuning the backbone end-to-end and initializing it from the target LRM are each necessary for strong performance. These results show that the reasoning trajectory carries information about the LRM's future behavior that goes beyond what naive reading conveys.

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

Learning Earthquake Wave Arrival Time Picking from Labels with Inaccuracies

arXiv:2606.15377v1 Announce Type: cross Abstract: Inaccurately labeled training data, or "label noise", poses a significant threat to the integrity of supervised machine learning models. This corruption directly degrades performance by teaching the model erroneous mappings between features and labels, which leads to poor generalization and reduced accuracy on properly labeled validation and test data. Current seismological applications mainly rely on large-scale training sets or data augmentation to reduce the label-noise impact, which can be labor-intensive and costly. Here, we introduce a Label Noise-Contrastive Robust Learning (LaNCoR) approach that can effectively handle noisy labels in seismic signal processing tasks, without requiring large-scale training datasets. In this approach, the input waveform feature and label representation distributions are aligned in the feature space to correct mislabeling and reduce its impact on the training process. We present LaNCoR's performance on the task of P-phase arrival-time picking of real microseismic data using two baseline models and training approaches. Our results indicate that LaNCoR can improve performance by up to 28.8% across performance metrics. This approach holds great promise for model training in seismology and geosciences.

17.
arXiv (quant-ph) 2026-06-15

Spin mixing induced dynamics of spinor solitons in $F=1$ Bose Einstein condensates

arXiv:2606.14231v1 Announce Type: cross Abstract: We explore soliton interactions in a homogeneous spinor $F=1$ Bose Einstein Condensate (BEC) in the presence of a magnetic field, focusing on dark bright dark and bright dark bright configurations. We investigate how these interactions depend on the phase differences among bright solitons and their influence during the dynamics. Our findings align with prior non spinor results, i.e., repulsion among in phase bright solitons and attraction among out of phase pairs in self repulsive atomic BECs. The potential bright soliton attraction, added to the short range repulsion of dark dark soliton interactions, can lead to bound states. However, we find that these bound states break in the presence of spinor interactions due to the particle exchange dynamics between the hyperfine states of the components. Additonally, we develop an effective classical model to describe the soliton dynamics, using a Lagrangian approach. The accuracy of the model is tested by comparing it against numerical simulations. Our results suggest that the proposed model captures the essential features of soliton behavior in the presence of spin interactions, and provides congruent soliton trajectories and interspecies particle exchange dynamics in most of the cases.

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

Generating Natural and Expressive Robot Gestures through Iterative Reinforcement Learning with Human Feedback using LLMs

arXiv:2606.18747v1 Announce Type: cross Abstract: Expressive gestures are essential for natural and effective communication, complementing speech when verbal cues alone are insufficient (e.g., pointing). For social robots such as the humanoid Pepper, producing natural and expressive movements is critical for improving human-robot interaction (HRI) and long-term acceptance. However, generating gestures remains challenging due to reliance on expert-authored animations, resulting in rigid behaviors that are impractical for dynamic and diverse environments. Alternatively, machine learning approaches often struggle to capture perceived naturalness, becoming increasingly challenging with more degrees of freedom. Consequently, producing expressive robot gestures requires a system that can adapt to the environment while adhering to social norms and physical constraints. Recent advances in large language models (LLMs) enable dynamic code generation, offering new opportunities for runtime gesture synthesis from natural language. In this paper, we integrate ChatGPT into the humanoid robot Pepper to generate co-speech gestures aligned with conversational output. While this baseline enables flexible gesture generation, the resulting motions are often perceived as stiff and unnatural. To address this limitation, we introduce an iterative reinforcement learning with human feedback (RLHF) system that finetunes gesture generation based on user evaluations, leveraging an iterative user study to compare Pepper's generated gestures. Our results show that RLHF improved the LLM's co-speech generative capabilities, producing more expressive, relevant and fluid movements.

19.
arXiv (CS.LG) 2026-06-12

Generalized Schrödinger Bridge on Graphs

arXiv:2602.04675v2 Announce Type: replace Abstract: Transportation on graphs is a fundamental challenge across many domains, where decisions must respect topological and operational constraints. Despite the need for actionable policies, existing graph-transport methods lack this expressivity. They rely on restrictive assumptions, fail to generalize across sparse topologies, and scale poorly with graph size and time horizon. To address these issues, we introduce Generalized Schrödinger Bridge on Graphs (GSBoG), a novel scalable data-driven framework for learning executable controlled continuous-time Markov chain (CTMC) policies on arbitrary graphs under state cost augmented dynamics. Notably, GSBoG learns trajectory-level policies, avoiding dense global solvers and thereby enhancing scalability. This is achieved via a likelihood optimization approach, satisfying the endpoint marginals, while simultaneously optimizing intermediate behavior under state-dependent running costs. Extensive experimentation on challenging real-world graph topologies shows that GSBoG reliably learns accurate, topology-respecting policies while optimizing application-specific intermediate state costs, highlighting its broad applicability and paving new avenues for cost-aware dynamical transport on general graphs.

20.
arXiv (CS.LG) 2026-06-18

Anti-causal domain generalization: Leveraging unlabeled data

arXiv:2602.17187v2 Announce Type: replace-cross Abstract: The problem of domain generalization concerns learning predictive models that are robust to distribution shifts when deployed in new, previously unseen environments. Existing methods typically require labeled data from multiple training environments, limiting their applicability when labeled data are scarce. In this work, we study domain generalization in an anti-causal setting, where the outcome causes the observed covariates. Under this structure, environment perturbations that affect the covariates do not propagate to the outcome, which motivates regularizing the model's sensitivity to these perturbations. Crucially, estimating these perturbation directions does not require labels, enabling us to leverage unlabeled data from multiple environments. We propose two methods that penalize the model's sensitivity to variations in the mean and covariance of the covariates across environments, respectively, and prove that these methods have worst-case optimality guarantees under certain classes of environments. Finally, we demonstrate the empirical performance of our approach on a controlled physical system and a physiological signal dataset.

21.
arXiv (CS.LG) 2026-06-19

Multi-Modal Contrastive Learning for Implicit Earth Embeddings via Location Tying

arXiv:2606.20167v1 Announce Type: new Abstract: Spatial prediction tasks are often limited by a lack of high-quality labelled ground-truth observations. To overcome this challenge, self-supervised pre-training is a possible solution, with contrastive learning dominant for location encoders. Those approaches usually align geographic coordinates with just one additional modality. We propose two multimodal contrastive learning architectures: Multimodal Embedding via Location Tying (MELT) and Sequential Alternating Location Training (SALT). These architectures expand this framework beyond two modalities by utilising unpaired geospatial data. Both methods are technically viable and match the performance of the strongest two-modality baseline (SATCLIP) across four downstream tasks. However, increasing the number of modalities does not consistently improve performance, suggesting that the chosen location encoder is the main limitation - the contrastive objective reaches its peak early, regardless of modality diversity or pre-training volume. MELT provides more stable training than SALT and presents a stronger foundation for future scaling.

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

libhmm: A Modern C++20 Library for Hidden Markov Models with Correct MLE Emission M-Steps

作者:

arXiv:2605.29208v2 Announce Type: replace-cross Abstract: We describe libhmm, a C++20 library for Hidden Markov Model parameter estimation, sequence decoding, and model selection. libhmm addresses two gaps in existing software: the absence of a well-maintained, zero-dependency C++ HMM library suitable for embedding in production systems, and the widespread use of method-of-moments (MOM) approximations in the emission distribution M-step of the Baum-Welch algorithm. The library implements correct maximum likelihood estimators for sixteen scalar emission distributions, including an ECME algorithm for the location-scale Student-t distribution, Newton-Raphson maximization for Gamma, Beta, Weibull, and Negative Binomial distributions, and the von Mises distribution for circular data. All forward-backward and Viterbi calculations operate in full log-space. SIMD acceleration is provided for AVX-512, AVX2, SSE2, and ARM NEON via compile-time dispatch with scalar fallback. Version 4 adds multivariate observation support via the BasicHmm template, with three multivariate emission families (diagonal Gaussian, full-covariance Gaussian, and independent components) each with correct weighted MLE M-steps. Python bindings are available via the companion package pylibhmm. We compare libhmm against established C and C++ HMM libraries and against published R reference packages on seven real-data benchmarks, and discuss the architectural tradeoffs made in the design.

23.
arXiv (quant-ph) 2026-06-19

QPU-scale randomized benchmarking via Bell-pair injection

arXiv:2606.20123v1 Announce Type: new Abstract: Mirror randomized benchmarking (MRB) is an established technique that provides a global error metric at the scale of a whole QPU. To expand upon this we introduce Mirror Quantum Awesomeness (MQA), a hybrid protocol that adds a structured entangling layer to MRB circuits. This enables per-edge correlation dynamics to be tracked via mutual information while preserving the MRB infidelity estimate. The resulting analysis of the injected entangled pairs locates a critical circuit depth, beyond which rudimentary error mitigation techniques can be expected to fail. A topological variant, Topological MQA, supplies a second critical depth via a decoder based on the surface-code decoding problem. Both are validated in simulation and demonstrated on the 156-qubit \texttt{ibm\_fez} and \texttt{ibm\_kingston} processors, where MQA closely agrees with MRB on the entanglement infidelity and the critical depth for \texttt{ibm\_fez} is found to be $\sim 50$.

24.
PLOS Computational Biology 2026-06-17

Combining machine learning and iterative experiments to keep pace with emerging viral variants of concern

by Thomas Sheffield, Ryan C. Bruneau, Stephen Won, Kenneth L. Sale, Brooke Harmon, Le Thanh Mai Pham Modeling and predicting viral mutations before they emerge plays a crucial role in pandemic preparedness, enabling the early identification of emerging variants of concern (VOCs) and guiding timely updates to vaccines, diagnostic tests, and therapeutic strategies. However, existing machine learning models and large-scale experiments lose their predictive power as viral variants evolve further from the original strains in sequence space. Here, we present a scalable framework that integrates random forest and neural network machine learning models with targeted high-throughput experimentation to anticipate and evaluate emerging SARS-CoV-2 receptor-binding domain (RBD) variants. Using public datasets, we trained predictive models for binding to human Angiotensin-converting enzyme 2 (ACE2), RBD expression, and antibody escape, and refined these models through iterative integration of experimental data focused on over 200 variants derived from wild-type (WT) and Omicron strains. Through an indirect transfer learning approach, our machine learning models achieved high accuracy having correlation coefficients of up to 0.79 for antibody binding. The models were also generalizable across diverse antibody types including heavy-chain-only antibodies (HCAbs) by encoding complementarity-determining regions (CDRs) as input features. This dynamic approach enables rapid assessment of emerging variants, facilities prioritization of the therapeutic strategies, and supports a proactive, data-driven response to evolving viral threats.

25.
arXiv (CS.AI) 2026-06-16

TNODEV: Toolbox for Neural ODE Verification

arXiv:2606.16567v1 Announce Type: new Abstract: Neural ordinary differential equations (neural ODE) have started to appear in safety critical settings such as continuous-time controllers for cyber-physical systems and classifiers integrated into automated decision pipelines, raising the question of whether their behavior can be formally verified. Existing tools dedicated to neural ODE provide only a single reachability call without iterative input set refinement, limiting the precision of their verdicts to whatever one reachability call can deliver. We present TNODEV, the first sound formal verifier for neural ODE that integrates a falsification checker, a fast interval-based reachability backend based on continuous-time mixed monotonicity, a verification and refinement loop with three input-set splitting heuristics, and a parallel scheduler in a single end-to-end pipeline. TNODEV supports safe-set inclusion verification on pure neural ODE, neural ODE in closed loop with a neural network controller and general neural ODE (GNODE), with the safe set specified either as an interval or as the half-space intersection induced by a target classification label. We evaluate TNODEV on a range of benchmarks across safe-set inclusion and classification-robustness properties, including a direct reachability comparison against NNV~2.0 and CORA and a verification comparison against NNV2.0 on MNIST general neural ODE classifiers.