Near-critical Ornstein–Zernike theory for the planar random-cluster model
arXiv:2510.13648v3 Announce Type: replace Abstract: We develop an Ornstein–Zernike theory for the two-dimensional random-cluster model with $1 \leq q
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arXiv:2510.13648v3 Announce Type: replace Abstract: We develop an Ornstein–Zernike theory for the two-dimensional random-cluster model with $1 \leq q
Stepwise group-based RL is an attractive way to train long-horizon LLM agents without a learned critic: it reuses multiple sampled rollouts to estimate local advantages. Its weakness is less visible but more fundamental: every group-relative estimator assumes that the steps it compares are equivalent for credit assignment. We show that current agentic variants violate this assumption through a state-action credit mismatch. The observation-hash partition is overly fine on the state side, creating singleton groups with zero step-level signal, while a single within-group mean is too coarse on the action side, mixing state-value estimation with action-specific credit. We introduce BiPACE (Bisimulation-Guided Policy Optimization with Action Counterfactual Estimation), a drop-in advantage estimator that fixes both sides without adding a critic, auxiliary loss, or extra rollouts. BiGPO clusters steps by cosine distance in the actor's own hidden-state geometry, an empirical policy-induced proxy for bisimulation that substantially lowers the singleton rate left by observation hashing. PACE then recenters returns within each behavioral cluster using action-conditioned peer baselines; its Q-style instance estimates a local Q(s,a)-V(s) nonparametrically. On ALFWorld/Qwen2.5-7B, BiPACE_Q raises overall validation success from GiGPO's 90.8 to $97.1\pm0.9$ over three seeds, and crosses the 95% threshold on every seed, which GiGPO never does within the same budget. On Qwen2.5-1.5B it reaches $93.5\pm1.2$ versus GiGPO's 86.7, and on WebShop and TextCraft it improves over GRPO and GiGPO at both model scales. The measured BiPACE-specific overhead is 11.3% of a single training-step wall time. Yet it changes the estimator's comparison unit from surface identity to approximate behavioral equivalence plus action-side counterfactuals. The code is available at https://github.com/TianxiangZhao/BiPACE.
Online web agents often augment a base actor with memory, workflow, or skill modules. These modules can improve performance, but they also consume test-time tokens, a cost rarely reported alongside the actor's inference cost. We study online augmentation, where this overhead is paid on every task, and re-evaluate its benefits under a fixed total inference budget. We compare AWM, ASI, and ReasoningBank with a token-matched vanilla baseline that uses the same budget for additional actor steps. Across three WebArena domains and three models, Gemini 3 Flash, GPT-5.4-mini, and Qwen 3.6-27B, the vanilla baseline matches or surpasses all three augmentation methods in aggregate success rate while often using fewer total tokens. We observe a similar trend on WorkArena-L1 with Qwen 3.6-27B, indicating that the effect extends to enterprise knowledge-work tasks. Our results suggest that skills and workflow memory can be useful in specific domains, but their apparent gains often vanish against a budget-matched actor. We further show that run-to-run variance materially affects outcomes and should be reported as a core evaluation criterion for online web agents.
Diffusion-based text-to-speech (TTS) models have achieved significant improvements in speech quality. However, modeling sharp prosodic transitions and rapid pitch variations in expressive speech remains challenging. Existing diffusion-based TTS decoders commonly utilize periodic nonlinearities such as Snake activation function to capture harmonic structures, but this activation funcation provides limited adaptability when modeling abrupt amplitude and frequency variations. In this paper, we investigate the role of oscillatory inductive bias in diffusion-based TTS decoders and introduce an adaptive oscillatory nonlinearity that enables controllable periodic modulation while maintaining signal stability through a linear bypass component. We refer the resulting TTS system as OscillaTTS. Experiments on the LJSpeech and Emotional Speech Dataset show consistent improvements across objective and subjective evaluations, indicating improved modeling of expressive prosodic dynamics.
Speech-to-speech translation (S2ST) systems have achieved impressive progress in semantic accuracy and speech naturalness. However, the cross-lingual transfer of lexical stress, a vital cue for emphasis and speaker intent, remains heavily underexplored, compounded by a lack of reliable automatic evaluation metrics for tonal languages like Chinese. We investigate English-to-Chinese S2ST stress transfer by constructing a stress-annotated Chinese dataset and an XLS-R-based Mandarin stress detector. Integrating this with the English EmphAssess system, we propose a novel objective metric for cross-lingual stress evaluation. Furthermore, we fine-tune CosyVoice3 to build a stress-aware S2ST system. Experiments demonstrate that our proposed S2ST architecture significantly outperforms existing systems in stress translation capability while maintaining competitive translation quality. Furthermore, our evaluation metric exhibits a strong correlation with human subjective judgments.
arXiv:2606.15716v1 Announce Type: new Abstract: Mixture-of-Experts (MoE) language models reduce per-token computation through sparse expert activation, yet deployment still requires storing the full expert pool, making one-shot expert pruning a practical approach for reducing memory usage. Although effective, existing criteria are largely heuristic, and no single criterion is universally optimal. Thus, establishing a principle for selecting pruning criteria suited to different deployment objectives remains an important yet largely underexplored problem in one-shot expert pruning. To this end, we introduce a unified formulation for one-shot MoE expert pruning organized around three factors: routing frequency, gate weighting, and activation strength. The formulation yields a criteria selection principle: task-agnostic pruning should favor routed-token-averaged, gate-free activation-based criteria, whereas task-specific pruning can benefit from retaining routing-frequency and gate-weight information. Beyond this principle, the formulation also provides a systematic view of existing heuristic criteria and gives rise to two new task-agnostic criteria, Mean Activation Norm (MAN) and Mean Squared Activation Norm (MSAN). Across four representative MoE models and 16 diverse benchmarks, MAN and MSAN are consistently strong in the task-agnostic setting, obtain the top-two average ranks, and improve average performance by up to 8.8 points over the strongest baseline.
The Voynich Manuscript (VMS) exhibits a script of uncertain origin whose grapheme sequences have resisted linguistic analysis. We present a systematic analysis of its grapheme sequences, revealing two complementary structural layers: a character-level right-to-left optimization in word-internal sequences and a left-to-right dependency at word boundaries, a directional dissociation not observed in any of our four comparison languages (English, French, Hebrew, Arabic). We further evaluate two classes of structured generator against a four-signature joint criterion: a parametric slot-based generator and a Cardan grille implementing Rugg's (2004) gibberish hypothesis. Across their full tested parameter spaces, neither class reproduces all four signatures simultaneously. While these results do not rule out generator classes we have not tested, they provide the first quantitative benchmarks against which any future generative or cryptanalytic model of the VMS can be evaluated, and they suggest that the VMS exhibits cipher-like structural constraints that are difficult to reproduce from simple positional or frequency-based mechanisms alone.
arXiv:2606.14517v1 Announce Type: cross Abstract: LLM-based guardrails have emerged as a highly effective defense against prompt injection and jailbreak attacks in autonomous agents. However, we reveal that the very reasoning and task-following capabilities enabling this protection introduce a novel vulnerability: attackers can inject crafted data to trap the guardrail in extended reasoning loops, effectuating a systematic denial-of-service (DoS) attack. To systematically expose this threat, we design a beam-search optimization framework that crafts natural-language payloads to maximize guardrail reasoning length, utilizing an LLM proposer guided by a strategy bank. Based on the observation of guardrail's schema-following nature, we also provide another attack framework driven by mechanism-aware structural mutations with less computational load. The attack efficacy is systematically evaluated in two parts. First, in standalone evaluations, the attack generalizes across diverse guardrail architectures, safety templates, and agent benchmarks. Payloads optimized on a single open-source surrogate successfully transfer to eight leading model backbones (e.g., Claude, GPT, Gemini, DeepSeek, and Qwen), achieving a 13–63$\times$ token amplification. Second, in end-to-end real-world agent deployments (web, desktop, code, and multi-agent systems), the attack reveals up to a 148$\times$ latency amplification. We show that a single poisoned document can saturate shared guardrail infrastructures, effectively starving co-located agents and paralyzing the entire system. By uncovering this availability flaw, our work underscores the urgent need to develop cost-bounded, reasoning-robust guardrails.
arXiv:2606.12445v1 Announce Type: new Abstract: Exact distance computation for quantum LDPC (QLDPC) codes plays a central role in validating candidate fault-tolerant quantum-code constructions, yet the computational structure of this problem remains poorly understood. Despite substantial recent progress in QLDPC design, it remains unclear which algorithmic principles govern the practical scalability of exact distance computation and which classes of exact solvers are best suited to this task. To address these questions, we conduct a systematic study of SAT- and MaxSAT-based formulations for exact QLDPC distance computation across representative codes. We further compare these formulations against several established exact-distance approaches in order to better understand the algorithmic landscape of exact QLDPC distance computation. Our study challenges and refines several prevailing intuitions about exact QLDPC distance computation. First, despite the XOR-rich structure of QLDPC parity checks, practical scalability appears to be governed more by the handling of cardinality constraints and optimization bounds than by parity reasoning alone. Accordingly, XOR-aware reasoning does not provide a systematic advantage across our benchmark suite. Second, Brouwer-Zimmermann-style search, long regarded as the benchmark paradigm for exact distance computation in sparse classical codes, no longer maintains its traditional scalability advantage in the QLDPC setting. This finding challenges the expectation that techniques successful for sparse classical codes remain dominant for QLDPC codes. Third, substantial qualitative differences arise even among MaxSAT solvers themselves. Branch-and-bound MaxSAT significantly outperforms unsat-core-based MaxSAT on challenging benchmarks, demonstrating that solver architecture and optimization strategy play a decisive role in practical scalability.
arXiv:2304.14445v2 Announce Type: replace Abstract: Major players in the global aerospace industry are shifting their focus toward achieving net carbon-neutral operations by 2050. A considerable portion of the overall carbon emission reduction is expected to come from new aircraft technologies, such as flight path optimization. In pursuing these sustainability objectives, we delve into the capacity of quantum computing to tackle computational challenges associated with flight path optimization, an essential operation within the aerospace engineering domain with important ecological and economic considerations. In recent years, the quantum computing field has made significant strides, paving the way for improved performance over classical algorithms. In order to effectively apply quantum algorithms in real-world scenarios, it is crucial to thoroughly examine and tackle the intrinsic overheads and constraints that exist in the present implementations of these algorithms. Our study delves into the application of quantum computers in flight path optimization problems and introduces a customizable modular framework designed to accommodate specific simulation requirements. We examine the running time of a hybrid quantum-classical algorithm across various quantum architectures and their simulations on CPUs and GPUs. A temporal comparison between the conventional classical algorithm and its quantum-improved counterpart indicates that achieving the theoretical speedup in practice may necessitate further innovation. We present our results from running the quantum algorithms on IBM hardware and discuss potential approaches to accelerate the incorporation of quantum algorithms within the problem domain.
Traffic scene understanding requires models to reason beyond object recognition, including lane topology, multi-view geometry, temporal evolution, and signal-phase semantics. However, existing traffic-oriented multimodal benchmarks largely emphasize passive visual recognition or isolated video understanding, offering limited support for evaluating structure-aware traffic reasoning under controlled conditions. We introduce OmniTraffic, a controllable generation pipeline and benchmark for spatio-temporal traffic reasoning. Built around 12 real-world intersections reconstructed into editable 3D traffic environments and complemented by surveillance footage from two countries, OmniTraffic supports both controlled and natural-condition evaluation. It defines a three-level task hierarchy spanning scene perception, multi-view and temporal reasoning, and decision support. Using structured traffic metadata, OmniTraffic generates synchronized multi-view VQA samples covering vehicle states, lane functions, view–BEV correspondence, temporal dynamics, and signal-phase analysis, resulting in 8M VQA samples and a 3K human-verified test set. Evaluation of eleven frontier MLLMs reveals a large human–model gap, with the most pronounced failures in topology-grounded and spatio-temporal reasoning tasks. Fine-tuning a lightweight MLLM on simulated OmniTraffic data further improves performance on real-world traffic scenes, demonstrating the value of simulation-generated supervision for traffic-specific multimodal reasoning. Beyond a fixed dataset, OmniTraffic provides an extensible pipeline with configurable intersections, camera views, traffic demands, signal phases, visual conditions, and rare events.
arXiv:2604.08389v2 Announce Type: replace Abstract: This work is inspired by a remark of de Gennes about polyelectrolytes, which are charged polymers. A common model for a polymer is a self-avoiding or self-repelling random walk or Brownian motion. For polyelectrolytes, the repelling potential is the Coulomb potential arising from pairs of charged particles. We show that in the continuous case of Brownian motion in three dimensions, the spread of the polymer, in particular the the radius of gyration of a polyelectrolyte of length $T$ grows linearly with $T$, up to logarithmic corrections.
Segmenting the Circle of Willis (CoW) from Magnetic Resonance Angiography (MRA) is challenging due to complex topology and thin vascular structures that are prone to fragmentation. Standard Convolutional Neural Networks (CNNs) often fail to capture these topological constraints, resulting in "broken vessel" artifacts. To address this, we propose the Anatomically Conditioned Recurrent Refinement U-Net (AC2RUNet). Our architecture decouples segmentation into two streams: a Static Stream that extracts invariant anatomical features and a lightweight Dynamic Stream that iteratively refines topological errors over time. We further introduce a dynamic curriculum learning strategy that transitions from high-recall geometric supervision to topology-aware constraints. Validated on the TopCoW dataset, AC2RUNet substantially reduces Hausdorff Distance (4.72 mm vs 9.17 mm) and Betti number errors (0.19 vs 0.40), improving topological connectivity over the nnU-Net baseline while maintaining comparable volumetric Dice.
In intelligent video surveillance, cameras record image sequences during day and night. Commonly, this demands different sensors. To achieve a better performance it is not unusual to combine them. We focus on the case that a long-wave infrared camera records continuously and in addition to this, another camera records in the visible spectral range during daytime and an intelligent algorithm supervises the picked up imagery. More accurate, our task is multispectral CNN-based object detection. At first glance, images originating from the visible spectral range differ between thermal infrared ones in the presence of color and distinct texture information on the one hand and in not containing information about thermal radiation that emits from objects on the other hand. Although color can provide valuable information for classification tasks, effects such as varying illumination and specialties of different sensors still represent significant problems. Anyway, obtaining sufficient and practical thermal infrared datasets for training a deep neural network poses still a challenge. That is the reason why training with the help of data from the visible spectral range could be advantageous, particularly if the data, which has to be evaluated contains both visible and infrared data. However, there is no clear evidence of how strongly variations in thermal radiation, shape, or color information influence classification accuracy. To gain deeper insight into how Convolutional Neural Networks make decisions and what they learn from different sensor input data, we investigate the suitability and robustness of different augmentation techniques...
arXiv:2606.13604v1 Announce Type: new Abstract: Dispatch in three-sided marketplaces provides a natural setting for reinforcement learning from world feedback: decisions are evaluated by delayed operational outcomes such as delivery speed, courier utilization, and merchant congestion. We present a deployed reinforcement learning system at DoorDash that adapts dispatch objective weights in a large-scale food-delivery marketplace using delayed signals. Rather than replacing the combinatorial assignment optimizer, a store-level policy learned from logged marketplace data selects a discrete multiplier that shifts the dispatch optimizer's tradeoff between delivery quality and batching efficiency. This interface enables offline policy learning under noisy, delayed, and coupled feedback while preserving production feasibility constraints and operational safeguards. We train a shared value function using centralized offline data and decentralized store-level execution, with Double Q-learning targets and a conservative regularizer to reduce out-of-distribution value overestimation. In a production switchback experiment, the offline-trained policy increases batching and reduces courier-side time costs without degrading customer-facing delivery quality. Results illustrate how world feedback from a live economic and logistics system can be used to safely adapt decision policies online.
arXiv:2510.11228v2 Announce Type: replace Abstract: The present paper is devoted to the study of mean-field backward stochastic differential equations (MFBSDEs) with double mean reflections whose generators are not Lipschitz continuous. With the help of the Skorokhod problem and some a priori estimates for MFBSDEs, we establish the existence and uniqueness results for doubly mean reflected MFBSDEs.
Continual Test-time adaptation (CTTA) continuously adapts the deployed model on every incoming batch of data. While achieving optimal accuracy, existing CTTA approaches present poor real-world applicability on resource-constrained edge devices, due to the substantial memory overhead and energy consumption. In this work, we first introduce a novel paradigm – on-demand TTA – which triggers adaptation only when a significant domain shift is detected. Then, we present OD-TTA, an on-demand TTA framework for accurate and efficient adaptation on edge devices. OD-TTA comprises three innovative techniques: 1) a lightweight domain shift detection mechanism to activate TTA only when it is needed, drastically reducing the overall computation overhead, 2) a source domain selection module that chooses an appropriate source model for adaptation, ensuring high and robust accuracy, 3) a decoupled Batch Normalization (BN) update scheme to enable memory-efficient adaptation with small batch sizes. Extensive experiments show that OD-TTA achieves comparable and even better performance while reducing the energy and computation overhead remarkably, making TTA a practical reality.
Omni-modal large language models (OLLMs) aim to unify multimodal understanding and generation, yet extending them to jointly produce speech and 3D facial animation remains largely unexplored despite its importance for natural human-computer interaction. A key challenge is the mismatch between the discrete semantic reasoning of LLMs and the dense temporal dynamics required for 3D facial motion. We propose Expressive Omni (Ex-Omni), an open-source model that augments OLLMs with native speech-accompanied 3D facial animation. Ex-Omni decouples semantic reasoning from temporal generation through a blendshape-aware speech unit generator and a blendshape decoder, where speech units provide temporal scaffolding and hidden speech representations carry facially relevant cues. We further introduce a unified token-as-query gated fusion (TQGF) mechanism for controlled semantic injection, as well as InstructS2SF-1200K, a dataset consisting of 1200K samples for pre-training. Extensive experiments show that Ex-Omni maintains competitive speech understanding and generation ability while achieving better audio-visual synchronization and lower face-generation latency than cascaded pipelines.
arXiv:2606.19060v1 Announce Type: cross Abstract: We study the vorticity formulation of the 3D Navier-Stokes equation driven by transport noise in a periodic channel with Navier-slip boundary conditions. We consider both non-degenerate transport noise and degenerate tangential transport noise. For any prescribed $T>0$ and $\epsilon>0$, we prove that, by choosing the noise intensity sufficiently large and concentrating the noise on sufficiently high modes, the solution exists up to $T$ with probability at least $1-\epsilon$. A main contribution of this work is to identify and analyze the interaction between enhanced dissipation induced by transport noise and physical boundary effects. The no-flux condition breaks the isotropy of the noise and changes the scaling limit of the Itô-Stratonovich corrector. In the non-degenerate case, a boundary feedback term appears in the limiting effective operator; in the degenerate case, the limiting operator is a nonlocal anisotropic tangential dissipation. The proof is based on a combination of a boundary correction operator, a Meyers-type estimate, a scaling-limit analysis of the Itô-Stratonovich corrector, and resolvent estimates for the deterministic limiting equations.
Objective. Figure copy and recall tests are sensitive measures of visuoconstruction and visual episodic memory, but their clinical is constrained by labor-intensive manual scoring. We developed and validated an automated, element-level scoring pipeline using Vertex AI object detection for the tablet-based figure copy and recall tasks in the California Cognitive Assessment Battery (CCAB). The automated scoring pipeline duplicated the scoring procedures used by expert manual raters. Methods. A normative sample of 2,011 community-dwelling adults aged 18-90 completed figure copy and delayed recall trials at baseline, with subsamples retested at 1 day and at 6, 18, and 30 months. Participants completed the drawings with their index finger on a tablet computer with finger position digitized to analyze the speed and timing of individual drawing strokes A convolutional object-detection model trained on the Vertex AI AutoML Vision platform identified each of twelve canonical figure elements in rendered drawings. Separate element presence and location scores were computed after homographically warping drawings onto a canonical template to produce trial-level Element, Location, and Total scores. To compare Vertex and human scores, Vertex AI and expert human raters independently scored 1500 randomly selected drawings to evaluate inter-rater agreement, including a common subset of 100 drawings scored by Vertex AI and all raters. Results. Total scores were virtually indistinguishable (r = 0.966) from human-human agreement (mean r = 0.971) as were Element presence scores (mean r = 0.959 vs. r = 0.963). Location-score agreement (r = 0.951) was slightly below the human-human mean (r = 0.972) due to pixel-level analysis by Vertex AI that was impossible for human raters. The Vertex pipeline showed no preferential advantage for the single expert rater who categorized Elements during training. Automated scores showed strong demographic gradients, age effects on Recall (r = -0.32) were approximately twice those in Copy conditions (r = -0.16). A Memory Cost score (Recall - Copy) showed a monotonic age-related decline from +0.40 z in the youngest subjects to -0.54 z in the oldest. Kinetic analysis revealed that drawing speed and efficiency showed significant age-related changes. Overnight test-retest reliability was high (Recall r = 0.72) and the Recall trial showed a large overnight learning effect ({Delta} = +1.18) that continued with repeated tests up to 30 months ({Delta} = +0.75).
arXiv:2606.11731v1 Announce Type: new Abstract: We study the dynamics of quantum correlations in the hydrogen hyperfine spin system subject to Markovian phase noise. Treating the electron and proton spin degrees of freedom as an open two-qubit system governed by an isotropic hyperfine Hamiltonian and local dephasing, we obtain the exact time-dependent density matrix and derive analytical expressions for the full X-state family. We compute concurrence($C$), trace-distance measurement-induced nonlocality (Trace MIN–$\mathcal{N}_1$), and average steering coherence (ASC) in closed form and establish their strict ordering $ C(t)\leq \mathcal{N}_1(t)\leq \mathrm{ASC}(t) $ at all times. Entanglement is identified as the most fragile resource, undergoing sudden death at a finite time. Trace MIN exhibits dephasing-immune freezing for states with nonzero population imbalance, while ASC is the most robust quantity, persisting longest in every scenario studied.We additionally demonstrate that the dephased thermal hyperfine state serves as a resource for quantum teleportation, deriving a closed-form expression for the average fidelity and establishing that the teleportation advantage window coincides exactly with the entanglement survival interval, $\mathcal{F}_A > 2/3 \Longleftrightarrow \mathcal{C} > 0$, for the full X-state family with maximally mixed marginals. We identify four distinct dynamical regimes and map all three correlation measures onto directly measurable Pauli spin correlators, enabling experimental reconstruction of the full hierarchy without full state tomography.
arXiv:2606.20151v1 Announce Type: cross Abstract: This work proposes a hybrid ANN-SNN pipeline that effectively leverages the rich embeddings of pretrained artificial neural networks (ANNs) to enable high-performance spiking neural networks (SNNs). The architecture couples a pretrained EfficientNet encoder with a CoLaNET spiking classifier. We convert the encoder's activations into spike trains via rate-coding and train the subsequent SNN classifier using local, biologically inspired learning rules, bypassing end-to-end gradient propagation. This approach achieves 99.09% accuracy on a 64-class ImageNet benchmark, demonstrating performance on par with conventional deep networks. The work presents a biologically plausible and efficient framework for adapting powerful pretrained encoders to downstream spiking neural network tasks.
Mendelian randomization (MR) is a powerful approach for causal inference, however, its reliability is frequently compromised by unadjusted covariates and unmeasured confounders, such as unmeasured pleiotropy and sample structure. To address these challenges, we introduce MRMU, a novel paradigm for the MR framework. Unlike traditional single-variable or multivariable MR methods, MRMU selects instrumental variables only from the exposure of interest and estimates one exposure effect at a time, while jointly accounting for measured covariates and unmeasured confounders. This design improves the reliability of MR analyses. In simulations and real data, MRMU achieved better type I error control, higher statistical power, and more accurate effect estimation than existing MR methods. Applying to coronary artery disease (CAD), MRMU identified robust cardiometabolic risk factors, including LDL-C, APOB, systolic blood pressure, body mass index, and smoking initiation, with consistent evidence across multiple CAD datasets. In contrast, traits such as HDL-C, height, and educational attainment, which were found to be significant by existing MR methods, were no longer supported by MRMU. MRMU further supported blood pressure-related traits, rather than lipid traits, as the more relevant pathway linking urate to CAD. Finally, by integrating large-scale plasma proteomics data, MRMU identified candidate CAD drug targets beyond established HMGCR- and PCSK9-related pathways, highlighting its utility for therapeutic target prioritization.
De novo protein binder design has been dominated by structure-based pipelines that require known three-dimensional target conformations and consume substantial compute and generation time per design, limiting their throughput and accessibility for routine large-scale binder exploration. Sequence-only generative models promise a faster and lighter alternative, yet existing systems remain uniformly dense and frequently reintroduce structural computation at inference, undermining the core advantages they were intended to deliver. Across the broader language modelling community, transformers have meanwhile transitioned from fully dense designs to sparse Mixture-of-Experts architectures that decouple capacity from per-token compute, a shift that has yet to reach sequence-only protein binder generation. We present MoE-Bind, an autoregressive protein binder generator that, for the first time in this domain, combines Multi-head Latent Attention with a sparse Mixture-of-Experts feed-forward network and is evaluated under two independent structure predictors, Boltz-2 and AlphaFold2-Multimer. Despite activating less than half the per-token parameters of compute-matched dense baselines, MoE-Bind matches or exceeds them on full-length receptor-conditioned binder generation on a leakage-free Docking Benchmark 5.0 evaluation, transfers without peptide-specific training to short-peptide design, and reduces training and inference compute by a large margin. Routing analysis on generated binders reveals interpretable expert specialization at both the individual amino acid and biochemical group level, a structured expert-token alignment not previously reported for natural-language MoE models. These results show that sparse architectural design, rather than scale, can deliver fast, structure-free, and interpretable protein binder generation.
arXiv:2606.08956v2 Announce Type: replace Abstract: Scientists have historically relied on mathematical models based on differential equations to relate system inputs – forces, fluxes, or heat sources – to outputs, such as displacement, velocity, concentration, and temperature. These models rely on deep domain knowledge to determine the form of the governing differential equation, which is then calibrated with data by solving an inverse problem. In recent years, the field of Scientific Machine Learning has introduced a variety of alternative modeling strategies for physical systems. A method called Sparse Identification of Nonlinear Dynamics learns the governing equation as a sparse linear combination of terms in a user-defined library. Neural Ordinary Differential Equations construct the governing equation by taking in the state and its derivatives at the input layer of a neural network. Entirely foregoing the modeling framework of differential equations, neural operators directly learn a non-linear mapping between the system inputs and outputs. From inverse problems to neural operators, all of these modeling strategies can be conceptualized as data-driven machinery to predict a system's response over a range of inputs. It is then natural to wonder how exactly these various strategies relate to each other, and whether they can be neatly taxonomized. Drawing from the philosophical literature on scientific models, we argue that many model types have a common structure, differing only in the assumed model class of the input-output relation they define. Connecting to philosophical ideas on mechanism, and arguing that data from physical systems arises from solutions to parsimonious differential equations, we propose that only certain models are capable of mechanism discovery, and thus generalization. Our analysis is intended to unite apparently disparate modeling strategies and provide insight into their appropriate use cases.