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01.
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.

02.
arXiv (CS.CL) 2026-06-25

How Pragmatics Shape Articulation: A Computational Case Study in STEM ASL Discourse

Most state-of-the-art sign language models are trained on interpreter or isolated vocabulary data, which overlooks the variability that characterizes natural dialogue. However, human communication dynamically adapts to contexts and interlocutors through spatiotemporal changes and articulation style. This specifically manifests itself in educational settings, where novel vocabularies are used by teachers, and students. To address this gap, we collect a motion capture dataset of American Sign Language (ASL) STEM (Science, Technology, Engineering, and Mathematics) dialogue that enables quantitative comparison between dyadic interactive signing, solo signed lecture, and interpreted articles. Using continuous kinematic features, we disentangle dialogue-specific entrainment from individual effort reduction and show spatiotemporal changes across repeated mentions of STEM terms. On average, dialogue signs are 24.6%-44.6% shorter in duration than the isolated signs, and show significant reductions absent in monologue contexts. Finally, we evaluate sign embedding models on their ability to recognize STEM signs and approximate how entrained the participants become over time. Our study bridges linguistic analysis and computational modeling to understand how pragmatics shape sign articulation and its representation in sign language technologies.

03.
arXiv (CS.AI) 2026-06-24

Reentrant value fields as delayed coupled reaction-diffusion systems on finite graphs

arXiv:2605.03940v4 Announce Type: cross Abstract: We describe a dynamical system in which a symbolic field is coupled to a geometric field via a bipartite Hilbert-Schmidt kernel. The system is fully described by a retarded functional differential equation (RFDE) on the history space, subject to Lipschitz and small gain conditions. We show that the RFDE is well-posed under constant input and that it admits a compact global attractor. The principal subsystem $(H_L, X_R, P)$, which is comprised of the two primary fields as well as an executive field, is shown to be globally stable independent of delay, provided that the interfield coupling satisfies $C_{\mathcal{K}}^2

04.
bioRxiv (Bioinfo) 2026-06-15

RepGene: Toward a Unified Gene Representation Space Robust to Missing Biological Views

Genes can be described through multiple heterogeneous biological views, including genomic sequence, transcript sequence, protein sequence, textual knowledge, and single-cell expression context, yet existing gene embeddings remain largely modality-specific and difficult to compare or reuse when many views are unavailable. We study a narrower but practically important question: whether pretrained embeddings from these distinct sources can be organized into a shared gene representation interface that remains usable under severe missing-modality conditions. To investigate this question, we introduce RepGene, a lightweight single-branch framework that combines modality adapters, a shared encoder, presence-aware fusion, and self-supervised cross-view objectives to map five biological views into one latent space. Our goal is not to claim a new multimodal learning principle or to establish superiority over all simpler fusion strategies, but to provide an initial technical instantiation for testing whether such a shared interface is feasible in a fixed-feature setting. Under a two-stage protocol in which RepGene is trained self-supervised on frozen upstream embeddings and evaluated by downstream linear probing, we find preliminary evidence that the learned representation is broadly competitive in the full-modality setting and remains informative when only partial modality subsets are observed at inference time. The strongest signal in our study is robustness under missing views: average performance changes are often limited when one modality is removed, and even single-view inference remains non-trivial in the evaluated benchmark regime.These results do not resolve unified biological representation learning, and they should be interpreted in light of incomplete simple-fusion baselines, limited architectural ablation, benchmark dependence, and possible upstream feature exposure. We therefore position RepGene as a feasibility study and a starting point for stronger comparisons, broader benchmarks, and leakage-aware validation.

05.
arXiv (CS.AI) 2026-06-19

Advancing DialNav through Automatic Embodied Dialog Augmentation

arXiv:2606.19948v1 Announce Type: new Abstract: For embodied agents capable of physical interaction, the capability to create and understand dialog is crucial to ensure both safety and effectiveness. While DialNav[han2025dialnav] provides a framework for holistic evaluation of the dialog–execution loop in photorealistic indoor navigation, its performance remains limited by a critical scarcity of training data (2K episodes). To address this, we propose an automatic generation pipeline, and construct the RAINbow dataset, a large-scale training dataset with 238K episodes for DialNav. Our pipeline converts existing VLN datasets into multi-turn dialog and creates cost-efficient and high-quality dataset. Then, we introduce two additional complementary advances to unlock the data's full potential: (1) Dual-Strategy Training, a navigation training scheme to align the navigation training with the dynamic dialog-navigation loop, and (2) a localization model that leverages VLN knowledge. By combining these complementary solutions, our model substantially outperforms the baseline in success rate on both Val Seen (58.24, +89\%) and Val Unseen (29.05, +100\%) splits, establishing a new state of the art.

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

CTS-MoE: Implicit Terrain Adaptation via Mixture-of-Experts for Perceptive Locomotion

arXiv:2606.19633v1 Announce Type: cross Abstract: Perceptive legged locomotion over discontinuous terrain (e.g., stairs, gaps, and obstacles) requires adaptive behavior, as a single conservative gait cannot produce the anticipatory maneuvers needed for abrupt topology changes. Cast as multi-task reinforcement learning, this problem introduces a tension between sharing and separation. Tasks use a common locomotion base but have conflicting rewards, so a policy must share behavior while avoiding value interference. Prior work addresses only one side, with monolithic policies sacrificing specialization and hierarchical sub-policies sacrificing generalization across transitions and unseen terrain. We propose CTS-MoE, which combines a dense mixture-of-experts actor with perception-based gating to compose shared behaviors and a multi-critic with task-specific value heads to prevent interference. The model is trained end-to-end in a single-stage concurrent teacher-student setup that handles partial observability and avoids sequential distillation, with task labels used only during training. At deployment, routing depends solely on perception, allowing terrain adaptation without a high-level selector or terrain classifier. Experiments on a Unitree Go1 in simulation and on hardware across seen and unseen terrains show task-aware specialization, with lower tracking error and higher success rates than monolithic baselines. Project Website: https://cts-moe.github.io/ .

07.
arXiv (quant-ph) 2026-06-25

Distillation of supersinglet states

arXiv:2509.20962v2 Announce Type: replace Abstract: We introduce an entanglement distillation (purification) protocol for supersinglet states composed of N qubits. The supersinglet state we target is a total spin zero state with zero spin variance, and has a fully entangled structure involving all qubits. In our distillation protocol, three copies of an initial spin zero state are measured in the local total spin basis such that a higher fidelity supersinglet state is generated upon postselection. The initial state can be prepared using conventional Bell state distillation methods distributed in a way to target the supersinglet symmetries. The protocol uses only local operations and classical communications, and is suitable for long-distance applications such as quantum clock synchronization and cryptography, and avoids a high dimensional Schur transform such that it can be used for tasks such as quantum metrology.

08.
arXiv (CS.AI) 2026-06-18

ARIADNE: Agnostic Routing for Inference-time Adapter DyNamic sElection

arXiv:2606.19079v1 Announce Type: new Abstract: The increasing deployment of parameter-efficient fine-tuning (PEFT) has led to model ecosystems in which a single backbone is paired with many task-specialized adapters. In this setting, inference-time queries often arrive without task labels, requiring the system to automatically select the most appropriate adapter from a growing and heterogeneous adapter pool. Existing routing methods either depend on access to adapter internals, such as weight decompositions or gradient-based statistics, or require additional router training, which limits scalability and portability as new adapters are added. We introduce ARIADNE, a training-free, adapter-agnostic routing framework for dynamic adapter selection at inference time. ARIADNE represents each adapter through a set of centroids computed from embeddings of its training set, capturing the data distribution associated with that adapter. Given an unlabeled input, it selects an adapter by measuring proximity to these centroids in latent space. Because routing is performed entirely in the input embedding space, ARIADNE is compatible with arbitrary PEFT methods and requires no modification to the adapters or training procedures. Primarily evaluated with Llama 3.2 1B Instruct on 23 diverse NLP tasks, ARIADNE recovers 97.44% of the upper bound performance. Scaling to 44 tasks, it achieves 89.7% average selection accuracy, without additional training or access to adapter internals.

09.
arXiv (CS.CV) 2026-06-25

TTSA3R: Training-Free Temporal-Spatial Adaptive Persistent State for Streaming 3D Reconstruction

Streaming recurrent models enable efficient 3D reconstruction by maintaining persistent state representations. However, they suffer from catastrophic forgetting over long sequences due to balancing historical information with new observations. Recent methods alleviate this by deriving adaptive signals from the attention perspective, but they operate on single dimensions without considering temporal and spatial consistency. To this end, we propose a training-free framework termed TTSA3R that leverages both temporal state evolution and spatial observation quality for adaptive state updates in 3D reconstruction. In particular, we devise a Temporal Adaptive Update Module that regulates update magnitude by analyzing temporal state evolution patterns. Then, a Spatial Contextual Update Module is introduced to localize spatial regions that require updates through observation-state alignment and scene dynamics. These complementary signals are finally fused to determine the state updating strategies. Extensive experiments show that TTSA3R achieves competitive performance on standard short-sequence benchmarks and provides substantially stronger robustness on extended sequences. On NRGBD, as sequences extend from 50 to 250 frames, TTSA3R exhibits only a 1.33x error increase, compared with over 4x degradation for CUT3R. This highlights the practical value of temporal-spatial adaptive updates for long-term reconstruction stability. Our code is available at https://github.com/anonus2357/ttsa3r.

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

Who Pays the Price? Stakeholder-Centric Prompt Injection Benchmarking for Real-world Web Agents

arXiv:2606.13385v1 Announce Type: cross Abstract: Web agents driven by large language models (LLMs) are increasingly deployed in real-world environments, where they operate over untrusted web content and execute actions with direct consequences. This makes them vulnerable to prompt-injection attacks, in which seemingly benign content embeds adversarial instructions that manipulate agent behaviour. Existing security benchmarks adopt an attack-centric perspective, focusing on the technical feasibility of injections while overlooking the nuanced distribution of resulting harms. In practice, however, prompt-injection risk is victim-dependent: a single exploit can produce asymmetric consequences for different stakeholders, and the same attack pattern may exhibit substantially different effectiveness depending on whom it targets. To capture these properties, we introduce \sysname, a stakeholder-centric benchmark to systematically categorize and attribute harm in real-world web agent systems. It distinguishes between affected entities (e.g., user, seller, platform), decomposes the attacks into concrete objectives, and evaluates each case with complementary outcome- and process-level metrics. Our results reveal substantial and heterogeneous vulnerabilities: not a single attack objective is reliably resisted by current agents, and failures distribute across qualitatively distinct modes ranging from stealthy parasitism (attack succeeds without disrupting the user's delegated task) to misaligned disruption (task disrupted without attack success) and compounded failure (both adversarial objective and task integrity simultaneously violated). These patterns are missed by conventional evaluation, highlighting the need for stakeholder-aware assessment of LLM-based agents in real-world deployments. Benchmark is available at https://github.com/StakeBench/SBC.

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

IBAD: Interpretable Behavioral Anomaly Detection on Human Mobility Data

arXiv:2606.16023v1 Announce Type: new Abstract: Human mobility appears highly diverse, yet much of a person's daily mobility can be explained by a small set of recurring behavioral templates, such as commuting, school-centered activities, caregiving, nightlife, or errand patterns. We present \texttt{IBAD} (\underline{I}nterpretable \underline{B}ehavioral \underline{A}nomaly \underline{D}etection), a framework that learns interpretable daily mobility templates and represents each individual as a distribution over mixtures of these templates. Rather than focusing on specific locations, IBAD characterizes activities that individuals perform across locations. This approach first discovers global behavioral templates using Latent Dirichlet Allocation (LDA), then employs a hierarchical self-supervised model to learn normal behavior of individuals from their soft behavioral templates. We also introduce a splicing benchmark that creates controlled behavioral mismatches between an individual's historical profile and injected mobility patterns. Experiments on real-world and synthetic datasets show that daily behavior can be effectively decomposed into a small number of interpretable templates. Crucially, we show that the learned behavioral archetypes transfer across distinct geographic and demographic contexts. Furthermore, IBAD maintains a robust competitive performance across all settings. For reproducibility purposes, the code is accessible at ~\href{https://github.com/USC-InfoLab/IBAD}{https://github.com/USC-InfoLab/IBAD}.

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

SpectralDiT: Timestep-Conditioned Spectral Residual Correction for Flow-Matching DiTs

Authors:

We propose SpectralDiT, a lightweight modification to flow-matching Diffusion Transformers that adds timestep-conditioned spectral correction to the MLP residual branch. The module decomposes each residual update into low- and high-frequency components on the patch-token grid, then learns a zero-initialized additive gate so the model initially matches the baseline DiT. On CIFAR-10 pixel-space generation, SpectralDiT improves FID from 20.78 to 19.71 at patch size 1 and reduces the radial Fourier spectrum gap. Furthermore, we scale our method to latent diffusion on ImageNet-100. With 0.6% additional theoretical FLOPs and 1.36% additional parameters, SpectralDiT improves latent flow-matching, achieving an 8.7% relative FID reduction under classifier-free guidance (CFG 2.0). All reported results are averaged over five seeds. Ablations and gate visualizations on CIFAR-10 reveal stable block-specific spectral correction patterns.

13.
Nature (Science) 2026-06-17

Confined migration induces non-lethal DNA damage in developing neurons

Authors:

Migratory cells tend to have soft nuclei that deform and penetrate narrow spaces1,2. Extensive nuclear deformation during migration can cause nuclear-envelope rupture and DNA damage in cancer cells, which may contribute to malignant transformation during tumour progression3–6. However, the importance of DNA damage in physiological migration is less well understood. Here we demonstrate that the migration of neurons in developing cerebral and cerebellar cortices is accompanied by massive DNA double-stranded breaks (DSBs) due to mechanostress during passage through narrow interstitial spaces. In contrast to many other migratory cells, these DSBs occur without detectable nuclear envelope rupture. Confined migration increases topoisomerase-IIβ covalently bound DSBs, and these lesions are repaired through non-homologous end-joining during brain development without causing cell death. Genome sequencing revealed that DSBs tend to occur at transcriptionally inactive regions. The deletion of ligase IV at the onset of neuronal migration leads to persistent DSB accumulation in cerebellar neurons with moderate transcriptional changes in genes related to synaptic function, neuronal development and stress and immune responses. The mutant mouse develops mild motor deficits in later life, suggesting that the DNA damage generated during normal brain development poses a potential disease risk if left unrepaired. The migration of neurons in developing cerebral and cerebellar cortices is accompanied by massive DNA double-strand breaks due to mechanostress during passage through narrow interstitial spaces.

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

Contextualizing Biological Language Models across Modalities via Logit-Space Contrastive Alignment

arXiv:2606.18703v1 Announce Type: new Abstract: Pretrained biological language models expose per-token probability distributions through masked-token prediction, providing the likelihood interface central to sequence design, variant scoring, and mechanistic interpretation. Yet these distributions are learned from broad unlabeled corpora and are not naturally conditioned on task-specific biological contexts such as interaction partners, cellular environments, or therapeutic interventions. Existing contextual matching methods often distort this interface through pooled embeddings, contrastive latent spaces, or task-specific prediction heads. We introduce LOGICA (Logit-space Contrastive Alignment), a framework for context-conditioned prediction that performs contrastive learning directly in output-logit space. Using gated cross-modal adapters compatible with each model's native token head, LOGICA preserves the pretrained likelihood interface and converts contextualized token log-likelihoods into matching scores. Alignment is defined through context-sensitive token probabilities rather than proximity in a shared embedding space, enabling learning from sparse paired data across models with distinct vocabularies, without a shared tokenizer or decoder. LOGICA is particularly effective for mutation-local variant ranking, where comparisons reduce to context-conditioned likelihoods of mutant tokens at perturbed sites. Across protein–ligand binding, TCR–peptide activity, and drug-conditioned resistance prediction, LOGICA improves over prior state-of-the-art methods, including matched latent-contrastive and conditional MLM baselines, while retaining a token-level interface for interpretation and generation. On held-out-gene single-mutation drug-resistance prediction, LOGICA improves AUC from near-random latent-space baselines of $\sim$0.55 to $\sim$0.65.

15.
arXiv (CS.AI) 2026-06-12

M*: A Modular, Extensible, Serving System for Multimodal Models

arXiv:2606.12688v1 Announce Type: cross Abstract: We are entering a new era of composite model architectures that integrate diverse components such as vision encoders, language backbones, diffusion and flow heads, audio codecs, action generators, and world-model predictors. Such architectures underpin a broad class of multimodal models, including unified multimodal models, omni models, speech-language models, vision-language-action policies, and world models. However, existing model serving frameworks were built on narrow assumptions about model structure, making them ill-suited to accommodate this new architectural diversity. Here we present M*, a universal serving system for efficient serving of composite AI models. M* represents models as dataflow graphs, processing requests spanning diverse modalities and tasks as traversals over these graphs. The core insight is a modular abstraction that supports arbitrary composition of model components, flexible placement onto a physical cluster, and model-agnostic optimizations within a distributed runtime. We call this abstraction the Walk Graph and show how it can concisely capture composite models from a broad range of families. We instantiate M* on representative models and find that it achieves, on average, 20% lower end-to-end latency than vLLM-Omni for text-to-image workloads on BAGEL, while delivering up to 2.9x lower real-time factor and 2.7x higher throughput for text-to-speech workloads on Qwen3-Omni. M* also outperforms the V-JEPA 2-AC rollout baseline for robotic planning by up to 12.5x. Thus, our work paves the road towards more efficient serving of complex models with minimal developer effort.

16.
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.

17.
arXiv (CS.CL) 2026-06-19

The Voice Behind the Words: Quantifying Intersectional Bias in SpeechLLMs

Speech Large Language Models (SpeechLLMs) process spoken input directly, retaining cues such as accent and perceived gender that were previously removed in cascaded pipelines. This introduces speaker identity dependent variation in responses. We present a large-scale intersectional evaluation of accent and gender bias in three SpeechLLMs using 2,880 controlled interactions across six English accents and two gender presentations, keeping linguistic content constant through voice cloning. Using pointwise LLM-judge ratings, pairwise comparisons, and Best-Worst Scaling with human validation, we detect recurring directional disparities. Eastern European-accented speech receives lower helpfulness scores, particularly for female-presenting voices. Responses remain polite but differ in helpfulness. While LLM judges capture the directional trend of these biases, human evaluators exhibit significantly higher sensitivity, showing stronger accent-level contrasts.

18.
arXiv (quant-ph) 2026-06-15

Dealing with locality in QAOA

arXiv:2606.14447v1 Announce Type: new Abstract: Shallow-depth QAOA on sparse, high-diameter MaxCut instances faces a locality bottleneck: at depth \(p\), local observables can depend only on a bounded neighborhood of the circuit interaction graph. We propose a transport-augmented QAOA that keeps the MaxCut cost Hamiltonian unchanged but enriches the mixer with optimized, unweighted shortcut couplings (scheduled \(XX+YY\)) to collapse the effective interaction-graph diameter. Using exact finite-depth support recursions, we relate optimal shortcut placement to bounded-diameter graph augmentation, and show in benchmarks that (unlike ma-QAOA) performance becomes effectively size-invariant once the diameter is reduced. For bipartite families (base diameter 4), reducing the interaction path to \(d=1\) raises the ensemble-averaged approximation ratio from 0.7378 (ma-QAOA) to 0.9767 at \(p=1\) (\(\sigma=0.0251\), nine system sizes); on random trees (base diameter 10), at \(p=2\) it improves from 0.9226 to 0.9997 (\(\sigma=0.0001\)).

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

Computing noise-canceling observables via Pauli propagation

arXiv:2606.20441v1 Announce Type: new Abstract: The pursuit of quantum advantage is driving the co-evolution of quantum processors and classical simulation methods. Despite advances in scale and quality, the accuracy of quantum simulation is ultimately limited by error rates and sampling overheads. Similarly, while classical simulation methods such as Pauli propagation have made remarkable progress, their accuracy is ultimately limited by the exponential growth of operator paths and the truncations needed to control memory and runtime. Here we show that these complementary limitations can be mitigated by embedding Pauli propagation within a hybrid error-mitigation framework that reduces quantum sampling overhead while achieving lower truncation errors with fewer classical resources than traditional Pauli propagation alone. In this framework, a target observable is classically propagated through noise-canceling inverse channels, producing a modified observable that is measured directly on a quantum processor. We prototype two implementations and benchmark their performance numerically on canonical models that challenge traditional Pauli propagation. We also perform experiments on a quantum processor using 56 superconducting qubits, revealing the tradeoffs of their respective truncation strategies. These results illustrate how classical and quantum resources can be orchestrated to extend observable estimation beyond the limits of either approach alone, providing a foundation for quantum-centric supercomputing and future demonstrations of quantum advantage.

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

RegMix-D: Dynamic Data Mixing via Proxy Training Trajectories

Data mixture selection is critical for Large Language Model pretraining. Existing methods such as RegMix select a single static mixture by fitting a regression model on small-scale proxy runs. We propose RegMix-D, a simple extension of RegMix to dynamic mixing. Our key observation is that proxy runs produce not only endpoint losses, but also full loss trajectories, which can be used to further improve data mixture. By training regression model on these trajectories, we can predict optimal mixtures at multiple training stages. RegMix-D supports two deployment modes: an offline variant that generates a complete mixture schedule before target training, and an online variant that adapts the mixture during training using observed loss. Experiments on 25B tokens of the Pile dataset with a 1B parameter target model show that RegMix-D consistently improves over RegMix and DoReMi across 13 downstream tasks while remaining proxy-efficient: it surpasses RegMix even with only 128 proxy models (25% of RegMix's proxy compute budget).

21.
arXiv (CS.CV) 2026-06-16

Through-Foliage Surface-Temperature Reconstruction for Early Wildfire Detection

We present a method to reconstruct surface temperatures through forest vegetation by combining signal processing and machine learning, enabling fully automated aerial wildfire monitoring with drones for early fire detection. Synthetic aperture (SA) sensing reduces canopy occlusion but introduces thermal blur. To overcome this, we train a visual state space model to recover subtle thermal signals of partially occluded soil and fire hotspots from blurred data. To address limited real-world training data, we generate realistic surface temperature simulations using a latent diffusion model, temperature augmentation, and procedural thermal forest modeling. On simulated datasets, our method reduces RMSE by 2-2.5 versus conventional thermal and uncorrected SA imaging; in field experiments on hotspots, RMSE improved by 12.8-fold and 2.6-fold, respectively. Our approach also generalizes to other thermal signals, including human signatures, capturing morphology and extent – critical where simple thresholding fails – while conventional imaging struggles with partial occlusion.

22.
bioRxiv (Bioinfo) 2026-06-23

Multi-Scale Machine Learning for Antibody-Antigen Binding Affinity Prediction Using Deep Mutational Scanning and Structural Features

Authors:

Predicting how mutations alter antibody-antigen binding affinity is essential for antibody engineering and vaccine design, yet current methods generalize poorly to unseen complexes. We present a multi-scale machine learning framework integrating 93 descriptors across four modalities: physicochemical, structural, ESM-2 protein language model, and solvent-accessible surface area (SASA)/{Delta}{Delta}G_fold features. Under leave-one-complex-out deep mutational scanning (LOCO-DMS) cross-validation on AbAgym (36,541 mutations, 68 experiments, 13 pathogens), gradient boosting achieved MCC = 0.206; a confidence-stratified ensemble reached MCC = 0.374 (83.5% accuracy, 25.5% coverage). No single modality exceeds the majority baseline alone; only multi-scale fusion succeeds. Boltzmann ceiling analysis shows 45.9% of mutations are near-neutral (|{Delta}{Delta}G| < k_BT), bounding theoretical maximum MCC at 0.473; our method achieves 79.1% of this limit. Five deep learning architectures benchmarked under LOCO-DMS showed self-attention matching gradient boosting (MCC = 0.200). Cross-pathogen transfer failed systematically (mean 46.7%), confirming universal binding predictors remain an open challenge.

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

LatentLens: Revealing Highly Interpretable Visual Tokens in LLMs

Transforming a large language model (LLM) into a vision-language model (VLM) can be achieved by mapping the visual tokens from a vision encoder into the embedding space of an LLM. Intriguingly, this mapping can be as simple as a shallow MLP transformation. To understand why LLMs can so readily process visual tokens, we need interpretability methods that reveal what is encoded in the visual token representations at every layer of LLM processing. In this work, we introduce LatentLens, a novel approach for mapping latent representations to descriptions in natural language. LatentLens encodes a large text corpus and stores contextualized token representations for each token in that corpus. Visual token representations are then compared to these contextualized representations and the top-nearest neighbor representations serve as descriptions of the visual token. We evaluate this method on 15 different VLMs, showing that commonly used methods, such as LogitLens, substantially underestimate the interpretability of visual tokens. With LatentLens instead, the majority of visual tokens are interpretable across all studied models and all layers. Qualitatively, we show that the descriptions produced by LatentLens are semantically meaningful and provide more fine-grained interpretations for humans compared to individual tokens. More broadly, our findings contribute new evidence on the alignment between vision and language representations and open up new directions for analyzing the latent representations of LLMs.

24.
arXiv (quant-ph) 2026-06-12

Schrödinger Symmetry in Spherically-symmetric Static Mini-superspaces with Matter Fields

arXiv:2512.13651v3 Announce Type: replace-cross Abstract: Schr\"{o}dinger symmetry has been shown to emerge in a ``fluid limit" from the full superspace to several mini-superspace models. To investigate one aspect of the robustness of this emergent symmetry, we consider two spherically-symmetric static mini-superspace models with matter fields at the classical level: (i) a Maxwell field with a cosmological constant and (ii) $n$ massless scalar fields. By developing a method based on canonical transformations, we demonstrate that for model (i), 3D Schrödinger symmetry emerges, and the solution is the (anti-)de Sitter Reissner-Nordström spacetime, and for model (ii), $(2+n)$D Schrödinger symmetry appears, and the solution is a generalized Janis-Newman-Winicour spacetime and its ``interior", a Kantowski-Sachs type closed universe. Furthermore, for the vacuum model, we find that 2D Schrödinger symmetry holds with different lapse functions and mini-superspace coordinates, suggesting the potential, yet unconfirmed, covariance of the symmetry. Finally, we propose a physical interpretation of the symmetry under the Hamiltonian constraint $H$: symmetry generators commuting with $H$ map a solution to another one, while those non-commuting with $H$ generate a new theory with the Schrödinger symmetry and the transformed configuration is a solution to the new theory. These results reinforce the robustness of the emergent Schrödinger symmetry and open new frontiers for exploring dynamics of matter and gravity.

25.
arXiv (math.PR) 2026-06-19

The central heat trace on large compact classical groups

arXiv:2511.08288v2 Announce Type: replace-cross Abstract: We study the large-$N$ asymptotics of the central trace of the heat kernel on compact classical groups. For every classical family $G_N\subset \mathrm{GL}_N(\C)$, we prove a full large-$N$ asymptotic expansion, using a highest weights/partitions correspondence adapted to the large-rank regime, under which the eigenvalues of the Laplace–Beltrami operator stabilize as observables in the algebra of shifted symmetric functions. Then, we prove a random surface representation of the trace in terms of ramified coverings of the torus. We provide two independent applications: an explicit large-rank counting law for the Casimir spectrum, with exponential Hardy–Ramanujan-type growth in contrast with the polynomial behavior of Weyl's law at fixed rank, and a rigorous probabilistic formulation of the Yang–Mills/Hurwitz duality on a two-dimensional torus initiated by Gross and Taylor, completing a previous work of the authors. We also extend this duality to a Yang–Mills/Gromov–Witten duality by expressing the coefficients of the central heat trace as explicit functionals of the generating function of Gromov–Witten invariants.