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01.
arXiv (quant-ph) 2026-06-12

The Pound-Drever-Hall Method for Superconducting-Qubit Readout

arXiv:2512.03138v3 Announce Type: replace Abstract: Scaling quantum computers to large sizes requires the implementation of many parallel qubit readouts. Here we present an ultrastable superconducting-qubit readout method using the multi-tone self-phase-referenced Pound-Drever-Hall (PDH) technique, originally developed for use with optical cavities. In this work, we benchmark PDH readout of a single transmon qubit, using room-temperature heterodyne detection of all tones to reconstruct the PDH signal. We demonstrate that PDH qubit readout is insensitive to microwave phase drift, displaying $0.73^\circ$ phase stability over 2 hours, and capable of single-shot readout in the presence of phase errors exceeding the phase shift induced by the qubit state. We show that the PDH sideband tones do not cause unwanted measurement-induced state transitions for a transmon qubit, leading to a potential signal enhancement of at least $14$~dB.

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

Latent space mapping of interpretable structural coordinates from stochastic single-molecule signals

arXiv:2606.16950v1 Announce Type: cross Abstract: Nanopores are versatile single-molecular sensors, but their utility is fundamentally constrained by stochastic translocation dynamics warping any encoded information. We resolve it by shifting from time-domain analysis to a learned latent-space mapping via a contrastive encoder trained exclusively on simulated signals from a physics-informed model. This encoder maps solid-state nanopore signals of engineered DNA barcodes into an interpretable molecular coordinate system. The learned representation is responsive to structural barcode parameters while remaining invariant to acquisition conditions and translocation conformation, allowing data pooling across devices. Molecule identification requires a single pass through the encoder, reducing computational cost by three orders of magnitude relative to alignment-based methods. We experimentally validate through mixture quantification, rare-variant detection, consensus barcode reconstruction, and real-time signal acquisition. This shift from temporal analysis to mapping structural coordinates into a latent space changes the paradigm behind analyzing stochastic sensor signals by linking classification to interpretable encoded molecular information.

03.
arXiv (quant-ph) 2026-06-17

Tunneling Dynamics and Time Delay in Electron Transport through Time-Dependent Barriers with Finite-Bandwidth Reservoirs

arXiv:2507.20649v2 Announce Type: replace-cross Abstract: We study a model system consisting of a tunneling barrier driven by an external harmonic field and coupled to two leads with finite bandwidth. Avoiding Floquet expansions, we derive simple expressions for the time-dependent tunneling current in the adiabatic regime. Our approach relates the barrier modulation to a measurable time delay in the steady-state periodic current. It provides a physically consistent definition of the tunneling time inside the barrier by subtracting the time delay associated with the leads from the total time delay. We find that the tunneling time always vanishes for wide/high barriers. Remarkably, the time delay persists even when the barrier becomes static, i.e., in the limit where the modulation frequency vanishes. This indicates that the time delay obtained through the introduction of an external periodic perturbation actually reflects an intrinsic property of the tunneling dynamics, rather than an effect of the external drive or of a particular system. We apply our results to the analysis of tunneling times in optical experiments and find good agreement with the experimental data.

04.
medRxiv (Medicine) 2026-06-12

Estimating the effectiveness of syndromic screening at airports for Bundibugyo ebolavirus disease

We used a stochastic simulation model to estimate the effectiveness of combined exit and entry airport screening for Bundibugyo ebolavirus disease (BVD), using natural-history parameters from a Bayesian re-analysis of the 2012 Isiro outbreak. For a 12-hour international flight from DRC or Uganda at 86% screening sensitivity, we estimate 65% of infected travellers would arrive undetected (95% CrI: 38 - 76%). The main driver of this outcome is the relative duration of the the incubation period (approximately 7.7 days) and the onset-to-severe-disease interval (approximately 4 days): most infected travellers board before symptom onset and are undetectable by any syndromic screen, whilst those who are symptomatic progress rapidly to illness severe enough to preclude travel. This is compounded during active epidemic growth, when recently exposed (and therefore pre-symptomatic) cases are overrepresented among travellers. Syndromic airport screening offers limited protection against BVD spread via air travel, and should be complemented by outbreak control at source and strengthened clinical surveillance in receiving countries with high travel connectivity to affected areas.

05.
medRxiv (Medicine) 2026-06-16

Utilising Artificial Intelligence to Identify Ventricular Tachycardia Ablation Targets in Sinus Rhythm

Background and Aims: Machine learning has shown potential in predicting ablation targets for ventricular tachycardia (VT) in an animal model. This study progresses to externally validating deep learning approaches for human data. Methods: The development and external validation dataset included 21 and 13 patients, respectively, with structural VT undergoing catheter ablation. In the development datasets, electrophysiological studies were conducted using the AdvisorTM HD grid (EnsiteTM X), while both CARTO and Ensite Precision were used in the validation dataset. In each patient, VT ablation targets were defined as mapping points within 8 mm of VT isthmuses. Three advanced machine learning models were trained using cardiac mapping data acquired in both omnipolar and unipolar configurations during sinus rhythm and ventricular pacing. Discrimination was evaluated using nested leave-one-out cross-validation at patient level. Results: Overall, graph convolutional networks (GCNs), which integrate intracardiac signal waveforms with three-dimensional electroanatomical geometries, achieved the highest performance, with optimal results obtained from unipolar electrograms acquired in sinus rhythm (median AUC 0.793, sensitivity 83.6%, specificity 69.0%). This may be partly explained by the inclusion of repolarization dynamics in unipolar electrograms and the higher point density of sinus rhythm maps. Comparable performance was observed in the external dataset. Conclusion: This study demonstrates that graph convolutional networks applied to sinus rhythm EGM waveforms collected during substrate mapping can localise critical components of VT re-entry circuits. This approach has potential to provide fast and accurate ablation guidance without the need to induce and map VT, improving safety and efficacy of VT catheter ablation.

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

Toward Preference-aligned Large Language Models via Residual-based Model Steering

Preference alignment is a critical step in making Large Language Models (LLMs) useful and aligned with (human) preferences. Existing approaches such as Reinforcement Learning from Human Feedback or Direct Preference Optimization typically require curated data and expensive optimization over billions of parameters, and eventually lead to persistent task-specific models. In this work, we introduce Preference alignment of Large Language Models via Residual Steering (PaLRS), a training-free method that exploits preference signals encoded in the residual streams of LLMs. From as few as one hundred preference pairs, PaLRS extracts lightweight, plug-and-play steering vectors that can be applied at inference time to push models toward preferred behaviors. We evaluate PaLRS on various small-to-medium-scale open-source LLMs, showing that PaLRS-aligned models achieve consistent gains on mathematical reasoning and code generation benchmarks while preserving baseline general-purpose performance. Moreover, when compared to models aligned with DPO and SimPO, they perform better with great time-savings. Our findings highlight that PaLRS offers an effective, much more efficient and flexible alternative to standard preference optimization pipelines, offering a training-free, plug-and-play mechanism for alignment with minimal data.

07.
arXiv (CS.LG) 2026-06-12

An Empirical Study on Predictive Maintenance for Component X in Heavy-Duty Scania Trucks

arXiv:2606.12486v1 Announce Type: new Abstract: Condition-based Predictive Maintenance (PdM) for truck fleets has gained momentum in recent years. This maintenance strategy aims to minimize unplanned downtimes and reduce costs by monitoring the health status of vehicles and taking proactive action based on their condition. However, the implementation of condition-based PdM systems is challenging due to the large volume of data generated by the trucks, the inherent complexity of detecting failures through sensor data and the difficulties in finding cost-effective trade-offs in the solution's implementation. In this paper, we define and validate a condition-based PdM methodology built on the assumption that the wear-and-tear state of the monitored component can be represented as a monotonically non-decreasing time series. It involves selecting only the most recent observations from the time series and transforming them into a tabular format for classification using machine learning (ML) models designed for tabular data. Our results indicate that the proposed methodology reduces costs on the Scania Component X dataset compared to current state-of-the-art (SOTA) approaches, while also simplifying the modeling process through AutoML.

08.
arXiv (CS.LG) 2026-06-11

Anatomy of Post-Training: Using Interpretability to Characterize Data and Shape the Learning Signal

arXiv:2606.12360v1 Announce Type: new Abstract: Language-model post-training is the main stage at which model behavior is shaped, yet it still largely involves optimization of scalar rewards that summarize diverse desiderata. This abstraction gives practitioners little visibility into what their data actually teaches models, allowing spurious correlations to be learned by a model and inducing undesirable behaviors such as over-stylization and sycophancy. To address this problem, we ask: can we inspect a preference dataset before optimization and decide, at the level of concepts, which behaviors a model should be allowed to learn? Motivated by this, we introduce a data-centric post-training pipeline that uses interpretability protocols to develop statistical hypotheses for the latent concepts separating preferred from dispreferred generations, making them explicit for fine-grained user feedback. Building on this view, we unify several interpretability-based training protocols as ways of shaping rewards via feature or data interventions. Empirically, we show that our pipeline diagnoses undesirable signals in existing preference data, mitigates off-target learning, and can also help amplify or shape desired properties such as safeguards and model personality. More broadly, our results suggest that interpretability can turn post-training from optimizing opaque proxy rewards into a process of auditing and sculpting the learning signal itself.

09.
bioRxiv (Bioinfo) 2026-06-10

Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins

Motivation: Spurious protein sequences, resulting from gene prediction errors, theoretically should not yield folded structures. AlphaFold2 was previously shown to predict short spurious sequences with high pLDDT scores and was therefore unlikely to distinguish between real proteins and spurious proteins which are usually short. We evaluate whether newer structure prediction methods (ESMFold and AlphaFold3) similarly predict short sequences with high pLDDT or if they better discriminate between spurious and real proteins. Results: All three structure prediction methods (ESMFold, AlphaFold2, and AlphaFold3) predict short spurious sequences from AntiFam with unexpectedly high pLDDT scores, however the discrimination between spurious and real proteins improves beyond 100 amino acids. By analysing sequences with disparate pTM and pLDDT scores, we identified two likely spurious shadow ORFs in Swiss-Prot and one potentially non-spurious AntiFam entry. Using the structure prediction scores, we developed a Gaussian Process Model and evaluated its performance on AlphaFold DB, identifying potential spurious proteins at scale. While limited on its own, this model can increase confidence in spurious protein identification when combined with other methods.

10.
arXiv (CS.CV) 2026-06-17

TivTok: Broadcasting Time-Invariant Tokens for Scalable Video Tokenization

Video tokenization is fundamental to scalable video generation, as the number of tokens directly determines the computational cost and the length of videos that can be modeled. Existing tokenizers mainly improve scalability by compressing videos into fewer tokens, but they often continue to represent persistent content, such as static backgrounds and consistent object appearances, repeatedly across frames and chunks. In this paper, we propose TivTok (Time-Invariant Tokenizer), a reuse-aware video tokenizer that makes persistent information reusable across time. TivTok represents a clip with Time-Invariant (TIV) tokens that encode information shared across frames and Time-Variant (TV) tokens that encode frame-specific residuals. To obtain this factorization, we introduce Scope-Induced Factorization (SIF), which assigns different attention scopes to the two token groups: TIV tokens attend to the full clip, whereas each TV token only accesses its corresponding frame together with the TIV tokens. In the decoder, Invariant Broadcasting (IB) reuses the same TIV tokens across frames and chunks for parallel reconstruction and long-video tokenization. Experiments show that TivTok achieves an rFVD of 12.65 on the standard $16{\times}256{\times}256$ benchmark and improves compression efficiency by 2.91$\times$ for 128-frame videos compared with the evaluated baselines, while using only 1.1\% of the tokens required by downsample-based tokenizers in our evaluation.

11.
arXiv (math.PR) 2026-06-19

Establishing an $\Omega(\sqrt{d})$ complexity lower bound for PDMP samplers and how to break it: a sub-$\sqrt{d}$ algorithm for Gaussian-tailed targets

arXiv:2606.19909v1 Announce Type: cross Abstract: Despite the theoretical appeal of their non-reversibility, to date, no Piecewise Deterministic Markov Process (PDMP) samplers have been developed that scale better than $\mathcal{O}(\sqrt{d})$ in computational complexity with respect to the target dimension $d$. We prove that this is a fundamental limitation by establishing an $\Omega(\sqrt{d})$ lower bound on the algorithmic complexity of PDMP samplers in a standard setup. By relaxing the assumption that the target density must remain invariant at all continuous times, we then demonstrate how to bypass this barrier. Specifically, we introduce a novel PDMP sampling scheme and show that it achieves an empirical complexity of $\mathcal{O}(d^\alpha)$, where $\alpha \in [0.2, 0.3]$ for Gaussian-tailed targets. In addition, this PDMP scheme is locally adaptive in both trajectory length and distance between velocity updates.

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

Multi-Head Attention-Based Feature Extractor Integration with Soft Actor-Critic for Porosity Prediction and Process Parameter Optimization in Additive Manufacturing

arXiv:2606.20087v1 Announce Type: new Abstract: Additive manufacturing process optimization requires precise parameter control to minimize defects such as porosity. Traditional reinforcement learning (RL) approaches using discrete action spaces suffer from slow convergence and susceptibility to local optima, limiting their effectiveness for high-precision manufacturing tasks. This study addresses these limitations by employing a continuous action space combined with a novel architecture that integrates a multi-head attention mechanism with the Soft Actor-Critic (SAC) algorithm. The attention-based feature extractor enhances the agent's ability to capture subtle variations in low-dimensional input features, enabling more effective exploration-exploitation balance for navigating value spaces with local minima. We validate our approach on porosity prediction and process parameter optimization in laser powder bed fusion, demonstrating faster convergence and higher final reward values compared to standard RL methods including DQN, PPO, TD3, and vanilla SAC. The proposed methodology achieves a convergence value of 322.79 within 14 episodes, outperforming existing approaches while maintaining stability throughout training.

13.
arXiv (CS.CV) 2026-06-19

Gaussian Process Prior Variational Autoencoder for Endoscopic Videos

Endoscopic video analysis is essential for gastrointestinal diagnosis and computer-assisted interventions, but video sequences are routinely degraded by specular reflections, motion artifacts, and missing frames. These transient corruptions can distract clinicians, reduce image interpretability, and disrupt downstream tasks such as 3D reconstruction and navigation. Effective restoration therefore requires methods that exploit temporal continuity rather than treating frames in isolation. We introduce a Gaussian Process Prior Variational Autoencoder (GPVAE) framework for endoscopic video restoration that replaces the standard factorized latent prior with a temporal Gaussian process prior, enabling interpolation of missing frames with uncertainty-aware reconstruction. The framework combines endoscopy-specific encoders, including a convolutional EndoVAE backbone and pretrained Vision Transformer encoders from GastroNet-5M, with two scalable GP approximations: Hierarchical Prior Approximation (HPA) and Sparse Precision Approximation (SPA). Specular reflections are handled using a DUCKNet-based masking pipeline that excludes corrupted pixels from the reconstruction objective. On the C3VDv2 colonoscopy dataset, the best GPVAE variants reduced image reconstruction RMSE by 21.9\% on average, and by up to 26.1\%, relative to matched VAE baselines. Downstream trajectory RMSE was reduced by 12.7\% on average across classical visual odometry and a pretrained PoseNet, at an average increase of 27.3\% in training time per epoch. Finally, the GP posterior provides per-frame uncertainty estimates that reflect temporal support and offer a confidence signal for restored frames.

14.
arXiv (CS.CL) 2026-06-12

TAB-PO: Preference Optimization with a Token-Level Adaptive Barrier for Token-Critical Structured Generation

Direct Preference Optimization (DPO) is an effective and widely adopted approach for offline alignment but is poorly matched to ontology-driven structured prediction, where preferred and rejected JSON objects often differ in only a few schema-defining tokens. In this low-edit-distance regime, sequence-level DPO spreads gradient mass across non-critical serialization tokens (gradient dilution) and can reduce likelihood on rare, under-confident preferred schema tokens (token erosion). To address these limitations, we first develop a confusion-aware preference-construction strategy that augments expert-curated ambiguity patterns with empirical structured-error modes estimated from validation-set SFT predictions, synthesizing minimally perturbed, schema-valid negatives that focus preference learning on realistic ontology-level decision errors. We then introduce Token-Adaptive Barrier Preference Optimization (TAB-PO), a post-SFT objective for token-critical structured generation. TAB-PO adds a confidence-gated token-level barrier that applies supervised anchoring to under-confident schema tokens. On the public SciERC scientific information extraction task, evaluated with Llama/Qwen models from 1.5B to 70B, TAB-PO improves ontology-critical semantic-label and relational-linking metrics over SFT by 11.59% on average, wins 100% of comparisons against the strongest token-level and sequence-level DPO variants on these metrics, and surpasses leading frontier models by 14.71%, while delivering strong gains in textual grounding.

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

Can Deep Neural Networks Improve Compression of Very Large Scientific Data?

arXiv:2606.14353v1 Announce Type: new Abstract: Error-bounded lossy compression is a fundamental technique for managing the rapidly growing volumes of scientific data produced by modern simulations and observational instruments. Most state-of-the-art-compressors follow a prediction-residual paradigm, where compression effectiveness depends on the quality of the predictor: more accurate predictions generate smaller residuals that are easier to compress. This observation raises a question: can modern machine learning models serve as superior predictors for scientific data compression? Answering this question directly is challenging because developing compression-specific ML predictors requires substantial resources. Instead, we leverage the climate domain where highly accurate pretrained weather forecasting foundation models already exist, making them an ideal testbed. We present a framework that integrates spatial and temporal deep learning models into a conventional error-bounded compression pipeline. The framework supports auto-regressive forecasting models and avoids error accumulation. Using ERA5 climate data as a representative large-scale scientific dataset, we evaluate three distinct ML predictors: a VAEformer-based codec (CRA5), a graph neural network forecaster (GraphCast), and a vision-transformer forecaster (Aurora), against the state-of-the-art compressor SZ3.1 under identical quantization and entropy-coding backends. Our evaluation over approximately 1.7 TB of data reveals a surprising result: although ML predictors generate more accurate predictions and can improve reconstruction quality by up to 91% while achieving up to 9.6x higher compression ratios for highly predictable variables, they do not improve overall dataset-level compression ratio. We show that prediction accuracy alone is insufficient: the spatial structure of the resulting residuals plays a decisive role in entropy coding efficiency.

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

Detecting Hate and Inflammatory Content in Bengali Memes: A New Multimodal Dataset and Co-Attention Framework

Internet memes have become a dominant form of expression on social media, including within the Bengali speaking community. While often humorous, memes can also be exploited to spread offensive, harmful, and inflammatory content targeting individuals and groups. Detecting this type of content is exceptionally challenging due to its satirical, subtle, and culturally specific nature. This problem is magnified for low-resource languages like Bengali, as existing research predominantly focuses on high-resource languages. To address this critical research gap, we introduce Bn-HIB (Bangla Hate Inflammatory Benign), a novel dataset containing 3,247 manually annotated Bengali memes categorized as Benign, Hate, or Inflammatory. Significantly, Bn- HIB is the first dataset to distinguish inflammatory content from direct hate speech in Bengali memes. Furthermore, we propose the MCFM (Multi-Modal Co-Attention Fusion Model), a simple yet effective architecture that mutually analyses both the visual and textual elements of a meme. MCFM employs a co-attention mechanism to identify and fuse the most critical features from each modality, leading to a more accurate classification. Our experiments show that MCFM significantly outperforms several state-of-the-art models on the Bn-HIB dataset, demonstrating its effectiveness in this nuanced task. To facilitate reproducibility and future research, the Bn-HIB dataset has been made publicly available through Mendeley Data. Warning: This work contains material that may be disturbing to some audience members. Viewer discretion is advised

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

Human genetic evidence is associated with drug approval across therapeutic areas: an observational analysis of 26,278 target-disease pairs with temporal validation and feature ablation

Genetic evidence is enriched among approved drug targets: in an observational analysis of 26,278 target-disease pairs from Open Targets and ChEMBL, targets with any genetic association had a 3.25-fold higher approval rate than those without (OR = 3.25, 95% CI 2.79-3.79, p = 1.91e-42). A target-level analysis accounting for non-independence of pairs sharing the same gene gave OR = 2.79 (bootstrap 95% CI 2.22-3.53); the oncology pair-level OR of 6.72 attenuates to 2.71 at the target level, illustrating how non-independence inflates area-specific estimates. The enrichment replicated in post-2015 approvals (OR = 3.51, p = 1.72e-8). Feature ablation across six evidence types revealed that literature mining alone accounts for most classifier performance (AUPRC = 0.099 versus 0.109 for all features), consistent with temporal leakage from post-approval publications. Excluding literature, remaining evidence types retain above-baseline signal (AUPRC = 0.084, 1.63x baseline). Sensitivity analyses bracket the pair-level OR between 3.25 and 4.93. Genetic evidence alone yields only a 1.0-percentage-point absolute AUPRC gain and the best model has poor calibration; the classifier has limited practical predictive value. We catalogue 1,433 genetically supported Phase 1/2 pairs as a hypothesis-generating resource. All findings are observational.

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

Learning Robust Pair Confidence for Multimodal Emotion-Cause Pair Extraction

Multimodal emotion-cause pair extraction (MECPE) requires reliable pair confidence over candidate pairs. Existing pair scorers commonly use pair-level cross entropy over valid candidates, which treats links mostly independently. This leaves the relative confidence geometry among competing causes under-constrained, allowing gold pairs to stay close to hard negatives or rely on incidental non-gold context. We study this vulnerability as pair-confidence brittleness and propose RPCL (Robust Pair Confidence Learning), a training-only framework for pair-confidence learning. RPCL encourages pair confidence to be both discriminative and stable: gold pairs are separated from row-wise hard negatives through a confidence-difference margin constraint, and clean pair predictions are aligned with predictions from a corrupted view where non-gold contextual utterance representations are partially corrupted. The original clean pair scorer and decoding pipeline are used unchanged at inference time. On ECF, MECAD, and MEC4, RPCL improves the three-seed mean Pair F1 over a matched base model by 2.58 to 2.83 percentage points in the full text-audio-video setting, and improves mean Pair AUPRC on all three datasets. Diagnostic analysis further shows larger gold-negative confidence gaps and lower margin-violation severity. These results suggest that explicitly shaping pair confidence is an effective training strategy for MECPE.

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

How LLMs Fail and Generalize in RTL Coding for Hardware Design?

Translating sequential programming priors into the parallel temporal logic of hardware design remains a crucial bottleneck for large language models(LLM). To investigate this, we introduce a new error taxonomy grounded in problem solvability, inspired by cognitive theory. Our taxonomy categorizes failures into syntactic, semantic, solvable functional, and unsolvable functional types. Evaluations reveal a strict empirical ceiling on the VerilogEval benchmark, as frontier models plateau at a 90.8% initial pass rate. These plateaus are defined by unsolvable functional errors, exposing persistent knowledge gaps immune to test time compute scaling. Furthermore, we expose a striking surface convergence gap: optimization readily eliminates syntax errors but concurrently exacerbates deeper functional failures. Our findings demonstrate that alignment techniques merely teach models to compile. While repeated sampling strategies can patch solvable errors, register-transfer level(RTL) coding capacity remains strictly bounded by pretraining knowledge. Addressing challenges in the current LLM based hardware generation pipeline requires more studies in model reasoning rather than alignment interventions.

20.
arXiv (CS.LG) 2026-06-16

Probing Dec-POMDP Reasoning in Cooperative MARL

arXiv:2602.20804v2 Announce Type: replace Abstract: Cooperative multi-agent reinforcement learning (MARL) is typically framed as a decentralised partially observable Markov decision process (Dec-POMDP), a setting whose hardness stems from two key challenges: partial observability and decentralised coordination. Genuinely solving such tasks requires Dec-POMDP reasoning, where agents use history to infer hidden states and coordinate based on local information. Yet it remains unclear whether popular benchmarks actually demand this reasoning or permit success via simpler strategies. We introduce a diagnostic suite combining statistically grounded performance comparisons and information-theoretic probes to audit the behavioural complexity of baseline policies (IPPO and MAPPO) across 37 scenarios spanning MPE, SMAX, Overcooked, Hanabi, and MaBrax. Our diagnostics reveal that success on these benchmarks rarely requires genuine Dec-POMDP reasoning. Reactive policies match the performance of memory-based agents in over half the scenarios, and emergent coordination frequently relies on brittle, synchronous action coupling rather than robust temporal influence. These findings suggest that some widely used benchmarks may not adequately test core Dec-POMDP assumptions under current training paradigms, potentially leading to over-optimistic assessments of progress. We release our diagnostic tooling to support more rigorous environment design and evaluation in cooperative MARL.

21.
bioRxiv (Bioinfo) 2026-06-10

Promera: a unified model for biomolecular structure prediction, filtering, and design

Generative models have become staple tools for modeling and designing biomolecular structures. However, although these tools have improved in structural prediction accuracy, their ability to filter designed binders—an essential use case—remains insufficient; whereas design methods have focused more on unconstrained binder generation rather than capabilities enabled by controllable design. We introduce Promera, a unified generative model that combines all-atom structure prediction with improved filtering and controllable design. We find that Promera's confidence metrics are more accurate for filtering binders from non-binders for both miniproteins and nanobodies, while its co-folding performance surpasses popular open-source models (OpenFold3-p2, Boltz-2) on therapeutically relevant categories. As a design model, Promera generates binders by predicting masked protein sequences with optional epitope, paratope, and template constraints. Remarkably, our nanobody designs match the in silico success rates from backprop-based techniques (mBER) when evaluated under co-folding confidence filters. We further provide two in silico demonstrations of the the versatile capabilities of our design method: epitope targeting of the Andes hantavirus glycoprotein with VHHs and active state stabilization of the beta-2 andrenergic GPCR. We conclude by proposing a scaling law for co-folding models, suggesting a path for further performance improvement.

22.
arXiv (CS.LG) 2026-06-12

Differentiable Thermodynamic Phase-Equilibria for Machine Learning

arXiv:2603.11249v3 Announce Type: replace Abstract: Accurate prediction of phase equilibria remains a central challenge in chemical engineering. Physics-consistent machine learning methods that incorporate thermodynamic structure into neural networks have recently shown strong performance for activity-coefficient modeling. However, extending such approaches to equilibrium data arising from an extremum principle, such as liquid-liquid equilibria, remains difficult. Here we present DISCOMAX, a differentiable algorithm for phase-equilibrium calculation that guarantees thermodynamic consistency at both training and inference, only subject to a user-specified discretization. The method combines discrete enumeration of feasible phase states with masked softmax aggregation in the backward pass, with the propagation of the true equilibrium state in the forward pass, using a straight-through gradient estimator to enable physics-consistent end-to-end learning of neural \gls{gE}-models. We show that this approach bears analogy to statistical thermodynamics, and we evaluate it on binary liquid-liquid equilibrium data where it outperforms existing surrogate-based methods, while offering a general framework for learning from different kinds of equilibrium data.

23.
arXiv (CS.AI) 2026-06-19

Tri-Info: Generalizable, Interpretable Failure Prediction for VLA Models via Information Theory

arXiv:2606.19998v1 Announce Type: cross Abstract: Vision-Language-Action (VLA) models are increasingly deployed across diverse tasks, yet they remain black boxes whose physical interactions can cause irreversible harm, making generalizable and interpretable failure detection essential. We observe that successful and failed rollouts carry systematically different information-theoretic signatures. Building on this, we formalize VLA control as a closed-loop information pipeline and derive the Triple Information-theoretic (Tri-Info) signals that capture whether actions remain diverse, temporally consistent, and coupled to state transitions. Across six VLA models and three benchmark environments, Tri-Info matches the strongest baselines in-domain. Moreover, Tri-Info transfers across architectures, environments, and the sim-to-real gap without retraining, reaching 83\% accuracy on real-world tasks where prior detectors collapse to chance. This establishes Tri-Info as a simple yet powerful method that not only detects failures with strong cross-domain generalization, but also delivers interpretable diagnostics of the underlying failure modes.

24.
arXiv (CS.CV) 2026-06-19

LEAP: Layer-skipping Efficiency via Adaptive Progression for Vision Transformer Distillation

Vision Foundation Models (VFMs) with Vision Transformer (ViT) backbones, such as DINOv2, have become essential for downstream tasks like object recognition and semantic segmentation. The immense computational requirements of backbones often necessitate distillation into smaller architectures for edge deployment. Feature-based knowledge distillation (KD) often suffers from the teacher-student gap; the student struggles to imitate teacher's complex feature map due to its limited capacity. To mitigate this bottleneck, we propose LEAP: Layer-skipping Efficiency via Adaptive Progression, a training curriculum for ViT feature-based knowledge distillation. By utilizing the teacher's intermediate feature maps as a sequence of progressively more difficult targets, our curriculum allows the student to build a foundational representation before tackling higher-level abstractions. Our results demonstrate that this paradigm significantly accelerates convergence through adaptive difficulty selection across various student model sizes and dataset scales. With our curriculum, the LEAP-distilled ViT-S achieves 90.1% accuracy on ImageNet-100, a +12.24% improvement compared with baseline. On ImageNet-1K, LEAP achieves +3.84% and +7.75% improvement for the instance retrieval task on the Oxford and Paris datasets, respectively. Furthermore, the curriculum enables 25.1% savings in training FLOPs and 21% savings in training time on ImageNet-100 by implementing early-stopping for teacher inference during the initial stages of training. Code is available at https://github.com/KevinZ0217/LEAP

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

ThousandWorlds: A benchmark for climate emulation of potentially habitable exoplanets

arXiv:2606.18338v1 Announce Type: new Abstract: The search for life beyond Earth will depend on detecting faint signatures in the atmospheres of potentially habitable exoplanets. Interpreting those signatures requires understanding the host planet's climate: the same molecule may signal life on one planet and abiotic chemistry on another. Global climate models (GCMs) provide this understanding, but individual runs can require up to millions of core-hours and substantial domain expert time. Machine-learning emulators could remove this bottleneck, but progress has been limited by the absence of a curated, multi-model exoclimate dataset. We introduce ThousandWorlds, an ML-ready benchmark for exoclimate emulation and for the broader regime of low-data, multi-simulator, parameter-to-field regression. The dataset contains approximately 1800 simulations from five GCMs, mapping eight planet parameters to 3D atmospheric fields including temperature, humidity, winds, clouds, and radiation. Three nested subsets define progressively harder challenges: single-simulator regression, multi-simulator regression with complete observations, and multi-simulator regression with structured missingness. We propose two evaluation protocols: one for ranking methods, and one that measures performance relative to the disagreement between GCMs themselves. We evaluate seven baselines spanning simple methods, deep learning, and Gaussian processes. GP-based methods perform best, suggesting that ThousandWorlds exposes a regime where off-the-shelf deep learning does not yet succeed. Data: https://doi.org/10.57967/hf/8695. Code: https://github.com/edstevenson/ThousandWorlds.