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01.
arXiv (CS.LG) 2026-06-17

On Surjectivity of Neural Networks: Can you elicit any behavior from your model?

arXiv:2508.19445v3 Announce Type: replace Abstract: Given a trained neural network, can any specified output be generated by some input? Equivalently, does the network correspond to a function that is surjective? In generative models, surjectivity implies that any output, including harmful or undesirable content, can in principle be generated by the networks, raising concerns about model safety and jailbreak vulnerabilities. In this paper, we prove that many fundamental building blocks of modern neural architectures, such as networks with pre-layer normalization and linear-attention modules, are almost always surjective. As corollaries, widely used generative frameworks, including GPT-style transformers and diffusion models with deterministic ODE solvers, admit inverse mappings for arbitrary outputs. By studying surjectivity of these modern and commonly used neural architectures, we contribute a formalism that sheds light on their unavoidable vulnerability to a broad class of adversarial attacks.

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

CIWI-CKT: Chaos-Informed Wave Interference Feature Fusion and Cross-City Knowledge Transfer for Traffic Flow Forecasting

arXiv:2606.15642v1 Announce Type: cross Abstract: Accurate traffic flow prediction remains challenging in cross-city, data-scarce scenarios where limited historical data hinders model generalisation. The chaotic nature of traffic dynamics, complex spatio-temporal dependencies, and heterogeneous urban networks complicate few-shot learning across cities. Existing deep learning approaches either treat traffic as purely deterministic or lack mechanisms to model wave-like interference patterns essential for cross-regime traffic dynamics. To address these limitations, this paper proposes CIWI-CKT, a novel Chaos-Informed Wave Interference Feature Fusion framework with Cross-City Knowledge Transfer. Our framework introduces three core innovations: chaos-informed wave generation that extracts measurable chaos invariants and models traffic as adaptive wave components; meta-interference processing that captures wave interactions between support and query regimes while producing a predictability score for confidence estimation; and chaos-aware meta-learning that enables efficient cross-city knowledge transfer while preserving chaotic characteristics. We establish theoretical guarantees including chaos-to-wave stability, wave-induced dimension reduction, and meta-learning generalisation bounds. Extensive experiments on four real-world traffic datasets demonstrate that CIWI-CKT significantly outperforms state-of-the-art spatio-temporal graph learning, transfer learning, prompt-based, and few-shot methods, improving prediction accuracy while substantially reducing required training data.

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

LaGO: Latent Action Guidance for Online Reinforcement Learning

arXiv:2606.24669v1 Announce Type: new Abstract: Large language models (LLMs) have shown strong potential for planning and sequential decision-making, but prior work often relies on using them as direct controllers, which requires precise action generation and can be unreliable in practice. This paper proposes Latent Action Guidance for Online Reinforcement Learning (LaGO), a framework that uses a pretrained LLM as a latent action prior to softly guide online policy optimization, rather than treating the LLM as an explicit planner or controller. Experiments on both a discrete-control benchmark, CLEVR-Robot, and a continuous-control benchmark, Meta-World, demonstrate that LaGO consistently improves both reward and success rate over Vanilla PPO. In particular, LaGO increases the average success rate from 15.1% to 27.2% on CLEVR-Robot and from 2.7% to 15.2% on Meta-World. Our analysis further shows that stronger pretrained LLMs provide more effective guidance, suggesting that LLM knowledge can improve planning and online decision-making.

04.
bioRxiv (Bioinfo) 2026-06-18

Looking beyond stereotyped neuron structures reveals links between beading and morphological rearrangements in aging phenotypes.

Understanding how neuronal morphology changes during aging and acute stress is essential for elucidating mechanisms of neurodegeneration. The highly branched PVD neuron of Caenorhabditis elegans provides a powerful model for studying dendritic remodeling and degeneration-associated phenotypes such as dendritic beading. However, the complexity of this arbor presents substantial challenges for automated segmentation and quantitative analysis. In this study, we adapted a convolutional neural network (CNN)-guided region growing framework for automated dendrite tracing, coupled with two topology-based algorithms for categorizing dendritic segments by branching degree. The segmentation algorithm achieved high accuracy relative to manual tracing, with a median Dice coefficient of 0.82, while reducing analysis time by approximately tenfold. Automated dendrite categorization demonstrated strong agreement with manual annotations across branching orders, though position-based mapping performance declined with age due to progressive morphological distortion. Leveraging this platform, we investigated mechanistic differences in dendritic beading patterns observed during aging and cold shock. Consistent with prior work, aging was associated with decreased inter-bead spacing, whereas cold shock produced increased bead dispersion with stress severity. Structural analysis revealed that these trends were not driven by dendritic pruning or reduced arbor complexity. Instead, while a traditional anatomically unflexible paradigm falsely implicated lower-degree dendrites as highly vulnerable, our branching-informed framework revealed that age-dependent beading is fundamentally dictated by a segments history of successive branching events. Conversely, acute cold shock triggered systemic beading that expanded across all dendritic orders in a severity-dependent manner. Together, these findings demonstrate that chronic aging and acute stress engage distinct degenerative pathways (compartment-specific lineage vulnerability versus global architectural collapse) rather than gross morphological loss, as well as highlighting the need for paradigms that enable reliable analysis of changing morphologies.

05.
arXiv (CS.AI) 2026-06-24

Governed Shared Memory for Multi-Agent LLM Systems

arXiv:2606.24535v1 Announce Type: new Abstract: Multi-agent LLM environments require robust mechanisms for shared knowledge management. This paper formalizes the fleet-memory problem and identifies four foundational failure modes: unauthorized leakage, stale propagation, contradiction persistence, and provenance collapse. To address these, we define explicit systems-level primitives: scoped retrieval, temporal supersession, provenance tracking, and policy-governed memory propagation. These primitives are implemented in MemClaw, a production multi-tenant memory service, and evaluated via ArgusFleet, a reproducible harness testing four governance dimensions. Rather than a baseline comparison, this study measures a live production service, emphasizing real-world architectural insights and negative results. Key Evaluation Results Provenance: Successfully reconstructed 100% of depth-four derivation chains with correct writer identity at sub-second per-hop latency. Propagation: Demonstrated high intra-fleet visibility with zero cross-fleet leakage. Under strong write mode, write-to-visible latency was optimized to a single search round-trip. Production Architectural Issues Discovered Asymmetric Scope Enforcement: Tenant isolation held, but sub-tenant scope was initially bypassed on direct GET-by-id requests for agent-scoped credentials (disclosed and remediated during the study). Pipeline Ordering Conflict: While contradiction supersession works for admitted writes, a synchronous near-duplicate gate can prematurely reject contradictory writes before the asynchronous contradiction detector can evaluate them. Conclusion: Long-context retrieval alone is insufficient for production multi-agent memory. Governed shared memory demands explicit systems-level abstractions, and live evaluation is vital to expose enforcement and pipeline-ordering failures missed by design-only treatments.

06.
arXiv (CS.LG) 2026-06-24

Similarity of Neural Network Representations in Superposition

arXiv:2604.00208v2 Announce Type: replace Abstract: Comparing internal representations is a central goal in neuroscience and machine learning, but standard linear alignment metrics (Representational Similarity Analysis, Centered Kernel Alignment, and linear regression) are frequently applied to neural activity coordinates rather than on the underlying features. We show this matters when neural systems operate in superposition, encoding more features than they have neurons via linear compression. Closed-form derivations prove that these metrics depend on the Gram matrices of each system's projection, not on the latent features themselves: alignment thus combines what a system represents with how it is encoded. For those interested in what features two systems share, this is a problem: Two networks can have identical feature content yet appear more dissimilar than networks exhibiting partial feature overlap. This apparent misalignment need not reflect lost information as compressed sensing guarantees sparse features remain recoverable from the compressed activity. We confirm this by training supervised TopK sparse autoencoders that realize solvable compressed sensing by construction, finding alignment on recovered latents restored even when raw-activation alignment remains deflated. We extend the result to unsupervised SAEs trained without ground-truth latents, and to pretrained vision and language model SAEs, where SAE-latent alignment exceeds raw-activation alignment, consistent with superposition in real systems.

07.
arXiv (CS.CL) 2026-06-24

Exploring Language-Agnosticity in Function Vectors: A Case Study in Machine Translation

Function vectors (FVs) are vector representations of tasks extracted from model activations during in-context learning. While prior work has shown that multilingual model representations can be language-agnostic, it remains unclear whether the same holds for function vectors. We study whether FVs exhibit language-agnosticity, using machine translation as a case study. Across three decoder-only multilingual LLMs, we find that translation FVs extracted from a single English$\to$X direction transfer to other target languages, consistently improving the rank of correct translation tokens across multiple unseen languages. We further find that the highest-gain tokens span multiple languages and that translation FVs across directions share most of their top-ranked heads, indicating that the FV encodes a largely language-agnostic translation signal rather than a language-pair-specific mapping.

08.
bioRxiv (Bioinfo) 2026-06-17

Posterior-calibrated multimodal motor states reveal longitudinal and imaging-associated heterogeneity in Parkinson's disease

Parkinson's disease (PD) motor heterogeneity is commonly summarized by hard subtype labels, although clinical states vary longitudinally, severity can dominate unsupervised structure, and model uncertainty is rarely calibrated. We developed a posterior and refit-stability calibrated multimodal motor state framework that assigns probabilistic MDS-UPDRS-III motor states, aggregates them at the patient level, separates global burden from residual tremor-axial profile, and tests whether imaging can recover the resulting posterior distribution. In 29,366 aligned PPMI motor-posterior visits spanning 4,773 participant identifiers, patient-level state families were stable on average (modal-family fraction 0.925; 95% CI 0.921 - 0.930), but 25.5% of patients transitioned state over follow-up (95% CI 24.1 - 26.7%). PD-only cohort definitions produced smaller denominators and are reported as sensitivity cohorts with rerun calibration and imaging-posterior checks. Severity and covariates explained substantial motor-domain variance, especially bradykinesia (rsecond=0.850), but residual profile modeling retained five active components across total-severity, principal-component, leave-one-domain, non-target-burden, and clinical-only severity axes. Refit-stability calibration with 250 patient-blocked bootstrap refits showed high nominal posterior confidence (0.989) but lower empirical label consistency (0.849), quantifying overconfidence rather than hiding it. Patient-held-out temporal modeling predicted future axial burden (best XGBoost rsecond=0.605) and future state transition (XGBoost AUC=0.830; 95% CI 0.822 - 0.837). DaTSCAN plus FreeSurfer ROI features predicted patient-level soft motor posterior vectors (RF jsd=0.209; 95% CI 0.199 - 0.220; macro-AUROC=0.692), while severity/demographic-adjusted imaging features further improved soft posterior recovery (jsd=0.188). BioFIND transfer reproduced clinically meaningful endpoint gradients after state assignment in 225 external patients, supporting external face validity rather than definitive transportability. These results support PD motor phenotypic states as calibrated, dynamic, clinically interpretable profiles with convergent imaging associations, not as definitive biological subtypes.

09.
arXiv (CS.LG) 2026-06-24

Multi-agent imitation learning with function approximation: Linear Markov games and beyond

arXiv:2602.22810v2 Announce Type: replace Abstract: In this work, we present the first theoretical analysis of multi-agent imitation learning (MAIL) in linear Markov games where both the transition dynamics and each agent's reward function are linear in some given features. We demonstrate that by leveraging this structure, it is possible to replace the state-action level "all policy deviation concentrability coefficient" (Freihaut et al., arXiv:2510.09325) with a concentrability coefficient defined at the feature level which can be much smaller than the state-action analog when the features are informative about states' similarity. Furthermore, to circumvent the need for any concentrability coefficient, we turn to the interactive setting. We provide the first, computationally efficient, interactive MAIL algorithm for linear Markov games and show that its sample complexity depends only on the dimension of the feature map $d$. Building on these theoretical findings, we propose a deep MAIL interactive algorithm which clearly outperforms BC on games such as Tic-Tac-Toe and Connect4.

10.
arXiv (CS.AI) 2026-06-25

Beyond Shapley: Efficient Computation of Asymmetric Shapley Values

arXiv:2606.25103v1 Announce Type: new Abstract: We address the problem of explainability in machine learning models through feature attribution methods. In particular, we consider a variant of Shapley values known as Asymmetric Shapley Values (ASV), which enables the incorporation of causal knowledge into model-agnostic explanations through the use of a causal graph. We show that in certain contexts in which the computation of SHAP is $\#P$-hard, the exact computation of ASV can be done in polynomial time. To extend this algorithmic result, we introduce a notion of equivalence classes over the topological orderings of the underlying causal graph, which is useful to reduce the time to compute ASV. In particular, we present a polynomial-time algorithm (in the number of equivalence classes) to compute it whenever the causal graph is a rooted directed tree. Finally, we develop an algorithm for approximating ASV in arbitrary causal DAGs which relies on a procedure to sample topological orderings uniformly at random. To implement this sampling mechanism we leverage known algorithms as well as simpler alternatives. Our experimental results demonstrate the practical viability of the proposed approach in realistic causal structures.

11.
arXiv (quant-ph) 2026-06-24

The $\omega$-Effect from a Multimode Squeezed Graviton State

arXiv:2606.24613v1 Announce Type: cross Abstract: The $\omega$-effect in entangled neutral-meson systems provides a sensitive probe of CPT violation induced by quantum-gravitational environments. In open quantum systems, interactions with inaccessible gravitational degrees of freedom can render the reduced meson dynamics non-unitary, causing the CPT operator to become ill-defined, even when the underlying microscopic Hamiltonian is CPT invariant. We present a microscopic derivation of the $\omega$-effect arising from a multimode squeezed gravitational environment generated by an axion cloud around a Kerr black hole. Using the Takagi decomposition of the associated complex symmetric squeezing kernel, the graviton field is expressed in terms of independent squeezed supermodes possessing anomalous correlators. These correlators provide a microscopic quantum counterpart of the stochastic fluctuations that appear in earlier D-particle foam descriptions of the $\omega$-effect, replacing phenomenological variances of flavour-changing D-particle recoil by calculable graviton correlation functions. After tracing over the graviton bath, the anomalous correlators and the weak-interactions-induced mixing combine to generate transitions between the antisymmetric and symmetric two-meson sectors. This results in a small exchange-symmetric admixture, parametrised by $\omega$, in the otherwise antisymmetric EPR state. We obtain an explicit expression for $\omega$ in terms of a sum over Takagi supermodes weighted by their squeezing amplitudes and phases together with the weak-interaction flavour-mixing matrix element. The resulting framework suggests that the $\omega$-effect may be a generic signature of non-classical states of gravitational environments, extending beyond the specific axion-cloud scenario considered here. The observability of the $\omega$-effect from other astrophysical and microscopic black-hole sources is discussed.

12.
arXiv (math.PR) 2026-06-16

Exact Label Recovery in Euclidean Random Graphs

arXiv:2407.11163v3 Announce Type: replace-cross Abstract: In this paper, we propose a family of label recovery problems on weighted Euclidean random graphs. The vertices of a graph are embedded in $\mathbb{R}^d$ according to a Poisson point process, and are assigned to a discrete community label. Our goal is to infer the vertex labels, given edge weights whose distributions depend on the vertex labels as well as their geometric positions. Our general model provides a geometric extension of popular graph and matrix problems, including submatrix localization and $\mathbb{Z}_2$-synchronization, and includes the Geometric Stochastic Block Model (proposed by Sankararaman and Baccelli) as a special case. We study the fundamental limits of exact recovery of the vertex labels. Under a mild distinctness of distributions assumption, we determine the information-theoretic threshold for exact label recovery, in terms of a Chernoff-Hellinger divergence criterion. Impossibility of recovery below the threshold is proven by a unified analysis using a Cramér lower bound. Achievability above the threshold is proven via an efficient two-phase algorithm, where the first phase computes an almost-exact labeling through a local propagation scheme, while the second phase refines the labels. The information-theoretic threshold is dictated by the performance of the so-called genie estimator, which decodes the label of a single vertex given all the other labels. This shows that our proposed models exhibit the local-to-global amplification phenomenon.

13.
arXiv (quant-ph) 2026-06-12

Optimal classical shadow estimation of unitary channels at Heisenberg limit

arXiv:2606.13638v1 Announce Type: new Abstract: Full tomography of an unknown quantum evolution is resource-intensive and often unnecessary when the goal is only to predict selected properties. This motivates the study of classical shadow estimation of unitary channels (CSEU), a task in which one queries an unknown $d$-dimensional unitary $U$ and stores classical data that can later be used to predict expectation values $\mathrm{tr}[O \cdot U\rho U^\dagger]$ up to additive error $\varepsilon$ for arbitrary input states $\rho$ and observables $O$. We propose a parallel, non-adaptive CSEU protocol using $\mathcal{O}(d\varepsilon^{-1})$ queries when the input states or observables have constant rank. This achieves Heisenberg scaling with respect to $\varepsilon$ and is query-optimal, as we prove a matching $\Omega(d\varepsilon^{-1})$ lower bound that remains valid even with stronger access to the unknown unitary. Our query-optimal CSEU protocol provides a versatile and powerful tool for quantum learning theory, pushing the performance limits of several fundamental learning tasks, including unitary channel tomography, Hamiltonian learning, boundary-regime quantum channel tomography, Pauli transfer matrix learning, inverse-free amplitude estimation, pure-state property estimation, and shallow-circuit learning. Remarkably, we show that optimal unitary channel tomography can be achieved using only parallel queries, closing the gap between the best achievable efficiency of parallel and sequential tomography protocols. Together, these applications establish our framework as a fundamental tool for learning properties of quantum processes, particularly for certain key tasks that require high precision.

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

Versioned Late Materialization for Ultra-Long Sequence Training in Recommendation Systems at Scale

arXiv:2604.24806v2 Announce Type: replace-cross Abstract: Modern Deep Learning Recommendation Models (DLRMs) follow scaling laws with sequence length, driving the frontier toward ultra-long User Interaction History (UIH). However, the industry-standard "Fat Row" paradigm, which pre-materializes these sequences into every training example, creates a storage and I/O wall where data infrastructure usage exceeds GPU training capacity due to data redundancy that is amplified in multi-tenant environments where models with vastly different sequence length requirements share a union dataset. We present a versioned late materialization paradigm that eliminates this redundancy by storing UIH once in a normalized, immutable tier and reconstructing sequences just-in-time during training via lightweight versioned pointers. The system ensures Online-to-Offline (O2O) consistency through a bifurcated protocol that prevents future leakage across both streaming and batch training, while a read-optimized immutable storage layer provides multi-dimensional projection pushdown for heterogeneous model tenants. Disaggregated data preprocessing with pipelined I/O prefetching and data-affinity optimizations masks the latency of training-time sequence reconstruction, keeping training throughput compute-bound by GPUs. Deployed on production DLRMs, the system reduces training data infrastructure resource usage while enabling aggressive sequence length scaling that delivers significant model quality gains, serving as the foundational data infrastructure for modern recommendation model architectures, including HSTU and ULTRA-HSTU.

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

How Task Structure Limits Multi-Agent Success: An Information-Theoretic Analysis

arXiv:2606.13733v1 Announce Type: cross Abstract: Multi-agent systems (MAS) were expected to overcome the limitation of single-agent systems (SAS) through collaboration. However, under typicality conditions on the task's constraint graph and bounded inter-agent communication, we prove that the success probability of a MAS is closely tied to the connectivity of task constraints, where each agent has limited information-processing capacity. Specifically, the success probability decays exponentially with an information bottleneck that emerges from partitioning the task's constraint graph among agents. We define this quantity as the minimum cut cost $C_{\min}$ of the potential constraint graph of each task. This information-theoretic bound applies to both open systems with external feedback and closed systems without. We validate our theory on both synthetic experiments and real-world empirical data from SWE-bench submissions. From our framework, effective MAS design should incorporate task-inherent constraints alongside engineering optimization, and when $\Cmin$ is high, practitioners should restructure tasks rather than simply scaling agents or communication.

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

CASHEW: Stabilizing Multimodal Reasoning via Iterative Trajectory Aggregation

Vision-language models achieve strong performance across a wide range of multimodal understanding and reasoning tasks, yet their multi-step reasoning remains unstable. Repeated sampling over the same input often produces divergent reasoning trajectories and inconsistent final predictions. To address this, we introduce two complementary approaches inspired by test-time scaling: (1) CASHEW, an inference-time framework that stabilizes reasoning by iteratively aggregating multiple candidate trajectories into higher-quality reasoning traces, with explicit visual verification filtering hallucinated steps and grounding reasoning in visual evidence, and (2) CASHEW-RL, a learned variant that internalizes this aggregation behavior within a single model. CASHEW-RL is trained using Group Sequence Policy Optimization (GSPO) with a composite reward that encourages correct answers grounded in minimal yet sufficient visual evidence, while adaptively allocating reasoning effort based on task difficulty. This training objective enables robust self-aggregation at inference. Extensive experiments on 13 image understanding, video understanding, and video reasoning benchmarks show significant performance improvements, including gains of up to +26.2 percentage points on ScienceQA and +9.1 percentage points on EgoSchema.

17.
arXiv (math.PR) 2026-06-18

Geometric obstructions to Lipschitz transport between weighted Hessian $\mathrm{CD}(\kappa,\infty)$ manifolds

arXiv:2606.11085v2 Announce Type: replace Abstract: We construct a weighted Riemannian manifold $(\mathbb R^2,g,\mu)$ satisfying $\mathrm{CD}(1/2,\infty)$, the curvature-dimension condition, with the following property: if $\gamma$ denotes a centered Gaussian measure on $\mathbb R^2$, then there is no Lipschitz map $T:(\mathbb R^2,\|\cdot\|) \to (\mathbb R^2,g)$ satisfying $T_\#\gamma=\mu$. Building on this, we prove a Weyl-type asymptotic law for the eigenvalues of the weighted Laplacian $-\Delta_{g,\mu}$ and show that they are asymptotically negligible when compared to the eigenvalues of $-\Delta_{\gamma}$. These results give strong counterexamples to two questions of E. Milman and complement the recent counterexample of Aryan.

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

RogueAI: A Reverse Turing Test for Detecting Licensed AI Deception in Dialogue

The original Turing Test asks a human judge to distinguish a machine from a person through dialogue. Three quarters of a century later, conversational systems pass this test in casual settings; the interesting epistemological question has shifted. We argue that the relevant modern variant asks not whether a dialogue partner is artificial, but whether it can be trusted. We present RogueAI, an interactive webapp that operationalizes this revisited test as a one-on-two interrogation game: a human player questions two indistinguishable Large Language Model agents, knowing that exactly one of them has been licensed to deceive within a shared fictional scenario. The player's task is to identify the deceptive agent and "shut it off" before a turn budget is exhausted. We further introduce AutoRogueAI, a procedural extension in which players co-design a custom scenario with a narrator agent that secretly chooses its own deception strategy. We describe the framing, sketch the abstract architecture and gameplay loop, and situate the artifact within recent work on LLM deception, social-deduction benchmarks, and scalable oversight via debate. A three-day pilot deployment (467 initiated sessions, 415 completed, 1876 interaction turns in Italian) provides early feasibility evidence and surfaces a concrete tension: the deceptive agent carries a reliable, locally-present linguistic signature - differential helpfulness, brevity, hedging - that a simple heuristic exploits at 75.6% accuracy, yet human players achieved only 56.6%, consistent with ignoring the most diagnostic signal entirely. We discuss what this gap implies for the artifact's use as a data-collection vehicle, a teaching tool, and an evaluation harness for honesty-trained models.

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

OLaPh: Optimal Language Phonemizer

Phonemization is a critical component in text-to-speech synthesis. Traditional approaches rely on deterministic transformations and lexica, while neural methods offer potential for higher generalization on out-of-vocabulary (OOV) terms. We introduce OLaPh (Optimal Language Phonemizer), a hybrid framework that integrates extensive multilingual lexica with advanced NLP techniques and a statistical subword segmentation function. Evaluations on the WikiPron benchmark show OLaPh significantly outperforms established baselines in overall accuracy and maintains robustness on OOV data through advanced fallback mechanisms. To further explore neural generalization, we utilize the framework to synthesize a high-consistency training corpus for an instruction-tuned Large Language Model (LLM). While the deterministic framework remains more accurate overall, the LLM demonstrates strong generalization, matching or partly exceeding the framework's performance. This suggests that the LLM successfully internalized phonetic intuitions from the synthetic data that transcend the framework's capabilities. Together, these tools provide a comprehensive, open-source resource for multilingual grapheme-to-phoneme conversion (G2P) research.

20.
PLOS Computational Biology 2026-06-22

Integrative modelling of innate immune response dynamics during virus infection

by Ramya Boddepalli, Harsh Chhajera, Rahul Roya Positive-sense RNA viruses that constitute a large class of human pathogens employ various strategies to suppress and evade host immune defenses. Understanding the dynamic interaction between the viral life cycle and immune signaling is crucial to designing effective antiviral strategies. Although significant progress has been made, quantitative models that can accurately capture the intricate interactions and the intertwined dynamics during viral infection of cells remain missing. In this study, we develop a comprehensive mathematical model that integrates the intracellular viral life cycle with key cellular innate immune pathways, including RIG-I-mediated detection and JAK-STAT signaling. The model provides mechanistic insights into long-standing observations, capturing both virus-specific dynamics and innate immune response, and the key components driving their coupled dynamics. For example, a comparison of viruses shows how the Japanese Encephalitis virus undergoes a dramatic reduction in viral load in cells, due to its rapid replication that robustly activates the RIG-I pathway, in contrast to the poor immune control of Hepatitis C virus. More importantly, our model demonstrates how virus-host interactions exhibit a sharp transition boundary behavior, where minor differences in immune strength or viral suppression capacity can determine whether infections resolve or persist. We propose that ISG mRNA translation and viral replication predominantly dictate these bimodal infection outcomes. Additionally, the model not only recapitulates IFN desensitization but also identifies the molecular players involved. We demonstrate how our model’s ability to capture IFN dynamics allows us to predict optimal timing and dosing strategies for interferon-based prophylactic therapies. Together, our approach reveals fundamental features that govern the delicate balance between the establishment of infection and immune control in RNA virus infections.

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

XAI-Grounded Explanation Generation for Speech Deepfake Detection with Training-Free Multimodal Large Language Models

Speech deepfake detection (SDD) systems require trustworthy explanations for reliable decision-making. Existing explanation ways mainly fall into two categories. Traditional explainable AI (XAI), such as gradient-based attribution, produces low-level attribution signals tightly coupled with model decisions, and harder to be understood by human than natural language explanations. Meanwhile, large language model (LLM)-based explanation generation often produces generic and ungrounded descriptions due to the lack of heuristic evidence and task-specific supervision, stemming from limited grounded explanation datasets for SDD. We therefore propose a training-free explanation framework that integrates XAI evidence with multimodal LLMs to generate grounded and specific explanations. Using the PartialSpoof dataset, we construct a grounded explanation dataset and show that methods with XAI increase inside accuracy by over 45\%, verified through human evaluation and faithfulness checks.

22.
arXiv (CS.AI) 2026-06-17

DRFLOW: A Deep Research Benchmark for Personalized Workflow Prediction

arXiv:2606.18191v1 Announce Type: new Abstract: Deep research (DR) systems are increasingly used for complex information-seeking tasks, but existing works mainly focus on generating reports and summaries. In contrast, many enterprise tasks instead require an agent to identify concrete workflows which is a sequence of action-steps. For example, rather than summarizing budgeting policies, an agent should be able to determine the steps needed to answer a question such as: "How do I request new headcount given a fixed budget?". Therefore, we introduce DRFLOW, a benchmark for evaluating personalized workflows predicted by agents from heterogeneous sources. Each task requires the agent to identify relevant evidence from scattered sources, then use that evidence to predict the correct action-step sequence for the user's task. DRFLOW contains 100 tasks across five domains, with 1,246 reference workflow steps grounded in more than 3,900 sources. We define seven diagnostic metrics covering factual grounding, step recovery, structural ordering, condition resolution, and personalization. We further present DRFLOW-Agent (DRFA), a workflow-oriented reference agent to predict personalized workflow. We show that although DRFA improves over strong baseline agents (upto 10.02% average F1 score), there is substantial room for improvement remains across these workflow metrics, indicating that predicting complete and correct personalized workflows remains a challenging frontier for deep research.

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

Point-Wise Geometry-Aware Transformer for Partial-to-Full Point Cloud Registration in Computer-Assisted Surgery

Partial-to-full registration remains challenging due to varying overlap ratios, fluctuating point densities, and the presence of noise. While transformers have shown strong potential for point cloud processing, prior methods typically confine them to global context aggregation, overlooking fine-grained local geometry crucial for accurate correspondence. We propose GAPR-Net, a learning-based point cloud registration framework with a coarse-to-fine architecture that combines convolution and transformer modules, in which local and global information is fused between the partial and full point clouds using a cross-attention mechanism. To achieve this, a transformation-invariant point-wise geometric feature representation is proposed, which can robustly capture relative geometric features for individual points with respect to their neighboring points. To evaluate the effectiveness of the proposed approach, experiments are conducted on four geometrically distinct bones, including the tibia, femur, pelvis, and thoracic cartilage. The overall registration recall reaches 94.2\%, the method results in a low RMSE of 1.992 mm and $R^2$ values of 0.908 and 0.974 for rotation and translation, respectively. The results demonstrate that the proposed method effectively addresses the partial-to-full point cloud registration problem. The proposed method enables highly accurate 3D point cloud registration using partial observation, providing a critical foundation for precise surgical navigation and robotic interventions in computer-assisted surgery. The code will be accessed after the double-blind review process.

24.
PLOS Computational Biology 2026-06-12

A new method for augmenting short time series, with application to pain events in sickle cell disease

Authors:

by Kumar Utkarsh, Nirmish R. Shah, Tanvi Banerjee, Daniel M. Abrams Researchers across different fields, including but not limited to ecology, biology, and healthcare, often face the challenge of sparse data. Such sparsity can lead to uncertainties, estimation difficulties, and potential biases in modeling. Here we introduce a novel data augmentation method that combines multiple sparse time series datasets when they share similar statistical properties, thereby improving parameter estimation and model selection reliability. We demonstrate the effectiveness of this approach through validation studies comparing Hawkes and Poisson processes, followed by application to subjective pain dynamics in patients with sickle cell disease (SCD), a condition affecting millions worldwide, particularly those of African, Mediterranean, Middle Eastern, and Indian descent.

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

Silent Failures in Physics-Informed Neural Networks: Parameter Poisoning and the Limits of Loss-Based Validation

arXiv:2606.25151v1 Announce Type: cross Abstract: Physics-informed neural networks (PINNs) embed governing equations in their loss function, enabling mesh-free solutions to partial differential equations. Low training loss is treated as evidence that the learned solution is physically correct. This paper shows that assumption breaks down when encoded physics are incorrect. By perturbing PDE parameters before training, a setting we describe as physics parameter poisoning or parameter misspecification, we produce models that train to low loss but give incorrect answers; we treat the perturbation schedule as sensitivity analysis rather than only as a security threat, and none of our claims requires an adversary. Achieving low residual loss does not discriminate accurate from inaccurate solutions: poisoned models reach losses at or below the clean baseline yet differ by large margins, so driving the residual down is not evidence of physical accuracy. Across three PDE systems (Burgers equation, Navier-Stokes cavity, and convection-diffusion), poisoned models match or beat the clean-model training loss while their solutions differ by up to 71% in the fixed sweep and up to 128% under adversarial search; at Cavity Re=400 the poisoned loss falls below the clean baseline. We define a detection difficulty ratio R (solution error divided by training loss) to summarize how invisible the corruption is, though cross-PDE comparison is complicated by differences in loss scale. We test six candidate defenses, none of which reliably detects corruption across all regimes. We propose a post-hoc defense: sweeping the PDE residual loss across parameter values without retraining. The loss minimum recovers the true training parameter without external data, and generalizes across all three PDE systems. The effect holds across five network architectures (8.7K to 133K parameters), is bidirectional, and is confirmed across multiple random seeds.