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01.
arXiv (CS.CV) 2026-06-16

Beer-Lambert Guided Representation Learning for Unsupervised Anomaly Detection in Sub-THz Food Inspection Images

Food manufacturing requires reliable inspection systems to detect foreign material contamination and maintain product safety. Sub-THz transmission imaging provides material-dependent attenuation characteristics that are useful for detecting low-density contaminants in food products. However, existing unsupervised anomaly detection methods mainly rely on RGB-pretrained visual representations, which may not adequately capture the transmission behavior of Sub-THz images. This paper proposes a Beer-Lambert guided representation learning framework for unsupervised anomaly detection in Sub-THz food inspection images. The proposed method introduces an attenuation decomposition module as an auxiliary regularization module that constrains student representations through attenuation reconstruction during training. In addition to the conventional one-class setting, we introduce a Leave-One-Food-Out protocol to evaluate generalization capability under unseen food categories. Experimental results on the Inline-Food-Inspection-THz dataset show that the proposed method improves overall anomaly detection performance over the baseline method.

02.
arXiv (CS.AI) 2026-06-15

Evidence-Gated LLM Priors for Multi-Objective Bayesian Optimization

arXiv:2606.01730v2 Announce Type: replace Abstract: Large language models (LLMs) are increasingly used as heuristic advisors for black-box optimization, yet their suggestions and self-reported confidence are not necessarily calibrated to downstream objective values. This issue becomes more pronounced in multi-objective Bayesian optimization, where different objectives may require different expert knowledge and where an LLM expert can be useful for one objective but misleading for another. We study how to use LLM-generated expert priors in discrete multi-objective Bayesian optimization without blindly trusting them. We propose an objective-wise reputation-market mechanism that treats each expert-objective pair as a falsifiable prior source. Expert weights are updated online from observed objective feedback, discounted over time, and gated by market-level trust. We then introduce a decoupled counterfactual gate that can use the LLM prior without confidence, use it with confidence, or abstain from the LLM prior entirely. Across controlled synthetic stress tests and three molecule optimization benchmarks with \qwenflash{}-generated expert priors, we find that dynamic objective-wise calibration improves robustness over fixed LLM priors. However, raw LLM confidence is not reliably beneficial: on ESOL, confidence is positively correlated with prediction error; on FreeSolv, confidence can help; and on Lipophilicity, ignoring confidence remains strongest. Our fixed three-arm counterfactual gate improves over the first counterfactual variant on ESOL and FreeSolv, while an attempted margin portfolio exposes a useful negative result: margin selection should be acquisition-aware rather than based only on one-step prior error.

03.
bioRxiv (Bioinfo) 2026-06-19

Morpho-FM: spatial molecular reconstruction from routine H&E histology using transcriptomic foundation-model priors

Routine haematoxylin and eosin (H&E) histology captures tissue architecture at clinical scale, but lacks a direct molecular readout of the transcriptional programmes that organise tumour epithelium, stroma, vasculature and immune compartments. Spatial transcriptomics provides this context, yet cost, workflow complexity and sparse sampling limit routine use. Most existing histology-to-expression models are trained de novo on small paired cohorts and therefore remain weakly constrained when extrapolating from sparse measurements to dense, tissue-wide molecular maps. Here we introduce Morpho-FM, a weakly supervised framework that predicts spatial gene expression from routine H&E whole-slide images by conditioning a pretrained single-cell transcriptomic foundation-model prior on local histological neighbourhoods. A lightweight morphology-to-transcriptome adapter maps cached whole-slide histology features into a transcriptomic decoder, enabling prediction at measured locations, dense full-section reconstruction, and re-aggregation to the original measurement support. Across harmonized prostate cancer benchmarks, Morpho-FM achieved the strongest overall performance among five representative methods, reaching mean per-gene Pearson correlations of 0.286 in rotating single-slide evaluation and 0.298 in multi-slide held-out validation. The framework reproduced this advantage across kidney cancer sections, achieved a mean correlation of 0.210 across 56 directed single-slide evaluations and retained measurable predictive signal after external transfer to clear-cell renal cell carcinoma sections. Controlled ablation analyses identified pretrained transcriptomic initialization as a reproducible source of performance gain exceeding that attributable to changes in the histology feature backbone. Beyond predictive accuracy benchmarks, Morpho-FM recovered ERBB2-enriched tumour compartments, boundary-associated molecular gradients, and annotation-aligned tissue domains across Xenium and HER2ST breast cancer datasets. Together, these results support transcriptomic foundation-model priors as an effective constraint for morphology-conditioned molecular decoding and demonstrate the potential of Morpho-FM to extend spatial transcriptomic insight across routine pathology sections.

04.
arXiv (CS.AI) 2026-06-16

User as Code: Executable Memory for Personalized Agents

作者:

arXiv:2606.16707v1 Announce Type: new Abstract: A personalized AI agent needs a user memory: a persistent model of who the user is, built across many conversations and consulted on each new one. Today this memory is almost always stored as unstructured text, a knowledge graph, or a flat store of facts, and consulted by retrieval – fetching the entries most similar to the current request. Such "bag-of-facts" memory recalls individual facts well, but because storing a fact and acting on it are separate steps, it struggles to resolve contradictions, aggregate over many records, or enforce rules. We argue that user memory should instead be executable. We introduce User as Code (UaC), a paradigm in which an agent's model of a user is a living software project: typed Python objects hold the user's state and ordinary Python functions encode the rules that govern it, so representing and reasoning about the user happen in one medium an interpreter can run. The enabling mechanism is a two-phase pipeline: an append-only log that never discards a fact, periodically checkpointed into typed code. This changes what memory can do. On standard long-term conversation benchmarks, UaC matches both a full-context upper bound and the strongest prior memory systems on recall (78.8% on LOCOMO). Its advantage emerges where representation matters most. On aggregate questions over a user's history – "how many international trips did I take last year?" – retrieval-based memory collapses (6-43%) while UaC stays near-perfect (99%), because the answer is a one-line computation over typed state rather than a search over text. And because its rules execute deterministically whenever the state changes, UaC can surface unsolicited, safety-critical alerts – such as a newly prescribed drug that conflicts with an allergy recorded months earlier – a capability query-driven memory cannot provide.

05.
medRxiv (Medicine) 2026-06-17

Investigating shared genetic overlap of immune-mediated inflammatory diseases and cardiometabolic diseases

Abstract Background: Immune-mediated inflammatory diseases (IMIDs) are associated with increased risk of cardiometabolic diseases. Investigating genetic overlap among these conditions can provide insights into their clinical management. Methods: Genetic correlation was assessed using linkage disequilibrium score regression (LDSC). Then, a meta-analysis was conducted using Association Analysis Based on SubSETs (ASSET) to pinpoint independent single nucleotide polymorphisms (SNPs) shared across the diseases. Each independent SNP was then used to define a genomic window (+/-500KB) for colocalisation analysis and Local Analysis of [co]Variant Association (LAVA) to offer multiple layers of regional pleiotropic evidence. Over-representation analysis was then run to identify enriched biological pathways, which then were used for drug target analysis. Results: The LDSC analysis showed a significant global genetic correlation for rheumatoid arthritis (RA) and cardiometabolic diseases including hypertension, coronary artery disease (CAD), heart failure (HF), stroke, atrial fibrillation (AF), and type two diabetes mellitus (T2DM) ranging from rg = 0.09 to 0.24. ASSET meta-analysis identified 164 independent SNPs shared across RA and the cardiometabolic diseases with P < 5 x 10- in the overall one-sided meta-analysis P-value, FDR < 0.05 in both individual GWASs, and TRUE phenotype matrix. Colocalisation analysis revealed multiple loci with strong evidence (Posterior probabilities [&ge;] 80) of single causal SNPs between the trait pairs. LAVA analysis was then used as an additional layer of confirmation for the findings generated by ASSET and colocalisation and thus several loci were highlighted. Over-representation analysis showed significant enriched immune-related pathways across RA-hypertension, RA-CAD, RA-AF, and RA-T2DM trait pairs. Drug target analysis highlighted several drugs which could be further tested for their effectiveness in RA and its common comorbidities. Conclusion: The findings revealed a shared genetic architecture and key immune-related biological pathways underlying RA and its associated cardiometabolic comorbidities. The identified genes and drugs provide opportunities for further therapeutic assessment which could improve clinical management strategies.

06.
bioRxiv (Bioinfo) 2026-06-19

OmniPath Metabo: chemical structures, interactions and mechanisms to study the metabolome

Mechanistic and functional analysis of omics data largely relies on the incorporation of prior knowledge; however, connecting metabolomics data and knowledge is a major methodological challenge. This is largely driven by the diverse prior knowledge being fragmented across many databases requiring the merging of different database records across chemical structures, identifiers, and varying levels of structural specificity. Hence, this limits mechanistic interpretation and functional characterisation of the metabolome. Here, we present OmniPath Metabo, a comprehensive, harmonized, metabolome-centric database covering metabolites, lipids, food-derived compounds, and small molecule drugs, along with their associated receptors, transporters, enzymes, reactions, allosteric regulators, and disease associations. OmniPath Metabo harmonizes attributes using controlled vocabularies and ontologies, structures and built-in cheminformatics to map identifiers and track ambiguity. OmniPath Metabo is built directly from 40+ original resources and is freely accessible via an interactive web app and API at metabo.omnipathdb.org. OmniPath Metabo enables dynamic, context-specific construction of subnetworks to serve dedicated purposes, such as cell-cell communication or integrated multi-omics metabolite-driven regulation, connecting reactions, allosteric regulation, metabolite-receptor and metabolite-transporter interactions. Combining it with the over 170 other resources in OmniPath, it can be used for integrated networks of signaling, gene regulation, and metabolism. We showcase the application of OmniPath Metabo by analysing publicly available metabolomics data of lung cancer cell lines and metabolic footprints to mutational patterns. In summary, OmniPath Metabo transforms fragmented resources into a harmonised prior knowledge framework for a mechanistic and functional analysis of the metabolome.

07.
arXiv (CS.AI) 2026-06-17

The Stanford EDGAR Filings Dataset: Reconstructing U.S. Corporate and Financial Disclosures into Layout-Faithful and Token-Efficient Pretraining Data

arXiv:2606.18192v1 Announce Type: new Abstract: As high-quality public web corpora become increasingly exhausted, clean long-context documents have become a scarce and expensive source of training data for large language models (LLMs). Existing long-context corpora are often proprietary and costly to acquire, synthetically generated, or concentrated in narrow domains such as programming. We introduce the Stanford EDGAR Filings Dataset (SEFD), an open reconstruction of SEC filings into layout-faithful MultiMarkdown for financial language modeling and evaluation. SEFD makes audited financial statements, risk disclosures, ownership reports, accounting notes, and market-moving event filings usable as long-context pretraining data and as a basis for financial reasoning, forecasting, compliance, and document understanding. The resulting corpus is token-efficient, model-ready, and has less than 0.1% overlap with Common Crawl-derived corpora. We release SEFD-v1, a 152B-token initial public snapshot, and provide corpus-level analyses of a larger 18.5M-filing archive estimated at 550B tokens. We further introduce two SEFD-derived benchmarks: EDGAR-Forecast, which evaluates filing-grounded numerical forecasting after model knowledge cutoffs, and EDGAR-OCR, which evaluates transcription of complex financial tables.

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

A T-API-Compliant ReAct Agentic Loop for Optical Networks: Generic vs. Domain-Specific Tool Abstractions

arXiv:2606.18000v1 Announce Type: cross Abstract: Optical networks need intent-driven, closed-loop agentic management, a key enabler for higher autonomy levels. We present the first T-API-compliant reasoning and act (ReAct) loop. We show that domain-specific composite tools achieve 90% oracle-validated correctness with threefold token savings compared to generic tools.

09.
arXiv (quant-ph) 2026-06-15

Correction scheme for molecular total energies from quantum phase estimation under limited qubit resources

arXiv:2603.02715v2 Announce Type: replace Abstract: We propose a practical method for accurately evaluating molecular total energies using a hybrid approach that integrates fault-tolerant quantum computers with classical computing. Our scheme consists of two complementary components: quantum dominant orbital selection (QDOS) and subspace dynamical correlation (SDC). QDOS extracts only the essential active orbitals from the complete active space (CAS) configuration interaction (CI) state on a quantum computer, yielding a compact active space suitable for classical CASCI calculations. SDC then evaluates dynamical-correlation corrections for the CASCI energy using this compact state, which remains tractable on classical machines. To demonstrate that the CAS energy obtained on a quantum computer can be post-corrected by SDC, we examine two frameworks: multireference perturbation theory and tailored coupled-cluster theory. Our scheme enables effective treatment of relatively large molecular systems by combining limited quantum and classical resources.

10.
arXiv (CS.AI) 2026-06-19

Movement Primitives in Robotics: A Comprehensive Survey

arXiv:2601.02379v2 Announce Type: replace-cross Abstract: Biological systems exhibit a continuous stream of movements, consisting of sequential segments, that allow them to perform complex tasks in a creative and versatile fashion. This observation has led researchers towards identifying elementary building blocks of motion known as movement primitives, which are well-suited for generating motor commands in autonomous systems, such as robots. In this survey, we provide an encyclopedic overview of movement primitive approaches and applications in chronological order. Concretely, we present movement primitive frameworks as a way of representing robotic control trajectories acquired through human demonstrations. Within the area of robotics, movement primitives can encode basic motions at the trajectory level, such as how a robot would grasp a cup or the sequence of motions necessary to toss a ball. Furthermore, movement primitives have been developed with the desirable analytical properties of a spring-damper system, probabilistic coupling of multiple demonstrations, using neural networks in high-dimensional systems, and more, to address difficult challenges in robotics. Although movement primitives have widespread application to a variety of fields, the goal of this survey is to inform practitioners on the use of these frameworks in the context of robotics. Specifically, we aim to (i) present a systematic review of major movement primitive frameworks and examine their strengths and weaknesses; (ii) highlight applications that have successfully made use of movement primitives; and (iii) examine open questions and discuss practical challenges when applying movement primitives in robotics.

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

Seeing What Matters: Perceptual Wrapper with Common Randomness for 3D Gaussian Splatting

While 3D Gaussian Splatting (3DGS) achieves impressive real-time rendering, it frequently struggles to synthesize high-frequency textures, a limitation heavily exacerbated in memory-constrained and rate-distortion-optimized (RDO) pipelines. To address this, we propose a versatile 2D perceptual wrapper that enhances the rendered outputs of existing 3DGS representations in a content- and view-dependent manner. Our method leverages a lightweight synthesis network conditioned on pseudo-random Gaussian noise to synthesize perceptually plausible textures. Supervised by Wasserstein Distortion, the network learns to match local feature statistics rather than strictly enforcing pixel-wise reconstruction fidelity, effectively mitigating the blurriness inherent in standard frameworks. We demonstrate the broad applicability of our plug-and-play approach across vanilla, memory-constrained, and RDO 3DGS methods. Comprehensive subjective and objective experiments confirm that our method significantly improves over existing baselines, yielding superior perceptual quality at sharply reduced file or model sizes.

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

TurnGuide: Enhancing Meaningful Full Duplex Spoken Interactions via Dynamic Turn-Level Text-Speech Interleaving

Full-Duplex Speech Language Models (FD-SLMs) are specialized foundation models designed to enable natural, real-time spoken interactions by modeling complex conversational turn-taking such as interruptions, backchannels, and overlapping speech. End-to-end (e2e) FD-SLMs leverage real-world double-channel conversational data to capture nuanced two-speaker dialogue patterns for human-like interactions, but their conversational abilities often degrade compared to pure-text conversation due to prolonged speech sequences and limited high-quality spoken dialogue data. Although interleaved text-speech generation could mitigate this degradation, integrating discrete text tokens into continuous double-channel audio streams could disrupt the precise time alignment required for fluid interaction. To address this, we propose TurnGuide, a novel text-speech interleaved generation approach for e2e FD-SLMs that dynamically segments assistant speech into dialogue turns and interleaves turn-level text and speech generation. This approach allows FD-SLMs to integrate the semantic intelligence of LLMs without compromising the natural acoustic flow. Extensive experiments show that TurnGuide not only significantly improves e2e FD-SLMs to produce semantically meaningful, coherent speech but also achieves state-of-the-art performance on various turn-taking events. Demos are available at https://dreamtheater123.github.io/TurnGuide-Demo/. Code is available at https://github.com/dreamtheater123/TurnGuide.

13.
arXiv (quant-ph) 2026-06-19

Quantum Computing Applications for Flight Trajectory Optimization

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.

14.
arXiv (CS.AI) 2026-06-11

The Power of Test-Time Training for Approximate Sampling

arXiv:2606.11437v1 Announce Type: cross Abstract: Efficiently sampling from a complex probability distribution is a fundamental problem which has become increasingly pertinent in recent years with the rise of generative AI, as sophisticated sampling procedures from LLMs have been proposed to solve challenging reasoning problems. The efficacy of such sampling algorithms is limited, however, by the relationship between the LLM and the particular sampling task at hand, which has motivated the framework of test-time training (TTT). TTT works by updating a model's weights in response to partial generations and reward feedback received at inference time, thus adapting to the particular problem. In this work, we propose a formalization for TTT as the problem of producing a sample from a given probability measure $\mu^\star$ belonging to a known class ${F}$ of distributions, given an oracle $\hat \mu$ which yields approximate density estimates for $\mu^\star$. This is closely related to the problem of reducing sampling to approximate counting studied in seminal works of Jerrum, Valiant & Vazirani (1986) and Jerrum & Sinclair (1989): namely, when ${F}$ is the class of all distributions, it coincides exactly with the aforementioned counting-to-sampling reduction. In this paper, we first show a quadratic lower bound on the query complexity of sampling from $\mu^\star$ given query access to $\hat \mu$ (for sufficiently large classes ${F}$), thus showing that the random walk approach proposed by Jerrum & Sinclair (1989) and refined by Hayes & Sinclair (2010), is optimal. This answers an open question posed by Hayes & Sinclair. We then show that this lower bound can be circumvented if the size of ${F}$ is bounded appropriately. As we discuss, this latter result can be viewed as an abstraction of TTT, and thus represents a starting point for the development of a principled theoretical framework for TTT.

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

ViPER: Vision-based Packing-Aware Encoder for Robust Malware Detection

Visualization-based malware detection maps raw binary bytes to grayscale images and applies learned visual classifiers, providing an evasion-resistant and disassembly-free alternative to conventional analysis pipelines. However, executable packing remains a critical failure mode: packed binaries produce high-entropy images that obscure the structural patterns these models rely on. Because packing is also prevalent in benign software (e.g., for compression or copy protection), packing state alone is not a reliable indicator of maliciousness, and existing approaches do not address this challenge within a unified supervised framework. We present ViPER, a Vision-based Packing-Aware Encoder for Robust malware detection. ViPER builds on a LoRA-adapted ViT-B/14 backbone with a dual-head architecture that jointly learns malware classification and packing detection. A packing-aware gating mechanism conditions malware predictions on the inferred packing state, enabling distinct decision boundaries for packed and unpacked inputs. To address packing label skew during training, we employ frequency-weighted losses with stratified sampling over joint class-packing strata. Evaluated on 200,000 Windows PE byteplot images, ViPER achieves a balanced accuracy of 0.8521, ROC-AUC of 0.9260, and AUPR of 0.9279, outperforming representative state-of-the-art baselines across all primary metrics, while attaining a packing detection AUC of 0.9949.

16.
arXiv (CS.LG) 2026-06-12

QoS Improvement in Multi User Cellular-Symbiotic Radio Network Assisted by Active-STAR-RIS

arXiv:2401.08301v2 Announce Type: replace-cross Abstract: In this article, we employ active simultaneously transmitting and reflecting reconfigurable intelligent surfaces (ASRIS) to enhance the quality of 6G cellular network services. The network integrates commensal symbiotic radio (CSR) subsystems to facilitate communication between passive Internet of Things (IoT) users and active users, referred to as symbiotic backscatter devices (SBDs) and symbiotic user equipments (SUEs), respectively. Since the SBDs are passive, transmitting information to the SUEs poses significant challenges. To overcome this challenge, we harness the capabilities of massive multiple input multiple output (MIMO) antennas within the base station (BS) to relay the information transmitted by SBDs with greater power. This scheme uses the non-orthogonal multiple access (NOMA) technique for multiple access among all users, and potential interferences are eliminated using successive interference cancellation (SIC). The primary objective is to maximize the throughput between SBDs and SUEs. To achieve this, we formulate an optimization problem involving variables such as active beamforming coefficients at the BS and ASRIS, phase adjustments of ASRIS, and scheduling parameters between CSR and cellular networks. To solve this optimization problem, we used three deep reinforcement learning (DRL) methods: proximal policy optimization (PPO), twin delayed deep deterministic policy gradient (TD3), and asynchronous advantage actor critic (A3C). These methods were simulated, and the results demonstrate that A3C, TD3, and PPO have the best convergence speeds and achieve the highest increases in network throughput, respectively. Finally, the proposed scheme was evaluated using passive simultaneously transmitting and reflecting RIS (STAR-RIS), which demonstrated poorer performance compared to ASRIS.

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

Tantalum as a base material for superconducting integrated circuits

arXiv:2606.13750v1 Announce Type: new Abstract: The performance of superconducting integrated circuits for quantum applications is fundamentally limited by material-related losses. Tantalum, as an emerging material for next-generation quantum circuits, has attracted considerable attention in recent years after demonstrating breakthrough performance in both superconducting microwave resonators and qubits. Concurrently, a growing body of work is devoted to the operation of tantalum-based circuits and related fabrication techniques. This interest is further stimulated by tantalum thin films polymorphism resulting in a variety of its crystalline structure, superconducting properties, coherence, etc. Furthermore, tantalum circuits exhibit distinctive features in cryogenic experiments, which have not been observed in aluminum- or niobium-based ones. In this review, we summarize the recent research of tantalum thin films growth and phase selection mechanisms on various substrates, key aspects of fabrication and performance of superconducting circuit, including a material first-principles theoretical study. In conclusion, we address a number of open issues, including the role of \b{eta}-phase impurities, the effect of hydrofluoric acid solutions on chain characteristics, and the anomalous behavior of {\alpha}-tantalum chains at cryogenic temperatures.

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

Dynamic In-Group Persona Generation for Enhancing Human-AI Rapport

arXiv:2606.18256v1 Announce Type: cross Abstract: LLM-based chatbots are increasingly applied in interpersonal domains such as counseling and peer support, where establishing human-AI rapport is crucial yet remains challenging. In this work, we introduce a novel approach for conditioning LLMs with in-group personas, which (i) first identifies a user's primary concern and brief personal context (e.g., a computer science undergraduate worried about future career prospects), and (ii) generates a synthetic in-group persona that shares a similar primary concern while differing in background and narrative details, such as age or profession (e.g., a junior researcher at an AI startup). Furthermore, we conduct a human-subject study to systematically evaluate the effectiveness of in-group persona agents in enhancing human-AI rapport. We compare our approach against two baseline conditions: a conventional agent without persona conditioning and an agent exhibiting minimal self-disclosure (e.g., "I've felt that too"). Results from post-task questionnaires assessing rapport and user experience indicate that the in-group persona agent significantly improves perceived rapport and personal relevance compared to the baselines, and also yields more positive user experience-most notably higher engagement.

19.
PLOS Computational Biology 2026-06-02

A comparative study of simulation-based inference methods for epidemic models with identifiability considerations

作者:

by Geunsoo Jang, K. Selçuk Candan, Gerardo Chowell Epidemic models play a critical role in understanding transmission dynamics, generating forecasts, and informing public health interventions when they are properly calibrated to epidemiological data. Traditional Bayesian inference methods rely on the likelihood function to update prior knowledge using observed data. However, for realistic epidemic models, likelihood functions are often analytically intractable or computationally prohibitive, which can limit the applicability of these methods. Simulation-based inference provides a promising alternative by approximating posterior distributions through forward simulations rather than an explicit likelihood evaluation. In this study, we present a systematic comparison of four approaches: Approximate Bayesian Computation (ABC), Neural Posterior Estimation (NPE), a neural method with temporal embedding, and Preconditioned Neural Posterior Estimation (PNPE), which integrates elements of both classical and neural techniques. These methods are evaluated across epidemic models of increasing complexity under fixed simulation budgets and varying levels of observational noise, with explicit attention to both structural and practical identifiability. Our results show that neural methods generally improve posterior fidelity and predictive accuracy compared with ABC under constrained simulation budgets. PNPE achieved strong performance in several simulation settings, whereas temporal embeddings improved inference in models with complex epidemic dynamics by capturing sequential dependencies. These gains come with important trade-offs: PNPE required substantially greater computational resources and, unlike fully amortized NPE-based methods, may require reconditioning for each new observation. In contrast, ABC remained computationally efficient and provided reasonable, though often more conservative, posterior estimates. Overall, our findings highlight trade-offs among computational efficiency, posterior accuracy, uncertainty calibration, and inference reusability, suggesting that method selection should depend on model complexity, data quality, identifiability, and available computational resources.

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

Faithful Action-unit Causal Reasoning for Counterfactually Faithful Emotion Explanations

Multimodal models can name the action units (AUs) behind a facial emotion, but their AU->emotion rationales are typically plausible rather than faithful: nothing forces the AUs a model invokes to be the AUs that actually drive its prediction. We cast AU->emotion reasoning as a counterfactual-consistency problem between the rationale, the label, and a structural AU->emotion causal graph G, and propose FACR, which grounds the reasoner in an independently induced, polarity-aware G and trains a counterfactual-faithfulness objective: a do-intervention on an AU that G marks causal for a class must move the prediction, while one it marks irrelevant must leave it unchanged. Faithfulness is thereby both trainable and measurable through a matching interventional metric, which we evaluate against a known causal structure, the PSPI pain-AU composition, as no existing affective-reasoning benchmark allows. We are explicit that this metric tests fidelity to the supplied structure rather than its rediscovery: it asks whether the trained reasoner invokes the AUs the structure marks causal, on held-out subjects and a second dataset. Under subject-independent evaluation on UNBC-PAIN, the objective raises the agreement between the invoked AUs and the PSPI composition from a no-objective baseline of 0.08 to 0.57, at a small detection cost; an unfaithfulness control attributes the gain to the objective. On a cross-dataset emotion transfer, the objective likewise raises fidelity to G on a seven-class task (0.50 to 0.84). Finally, we attach a language verbalizer and extend the audit to the generated text: biasing each action unit's emission by its latent activation makes the rationale faithful by construction, so that ablating an AU removes it from the explanation, a property that transfers to a second language-model backbone, whereas a freely generated rationale is unfaithful.

21.
arXiv (CS.AI) 2026-06-15

Distributional Biases in Post-Training: A Markovian Analysis of Reasoning Trajectories

arXiv:2511.07368v3 Announce Type: replace-cross Abstract: Foundation models exhibit broad knowledge but limited task-specific reasoning, motivating post-training strategies such as RL with verifiable rewards (RLVR) and test-time scaling (TTS). While recent work highlights the role of exploration in improving pass@K, empirical evidence points to a paradox: RLVR and ORM/PRM typically reinforce existing paths rather than expanding the reasoning scope, raising the question of why exploration helps if no new patterns emerge. To reconcile this paradox, we adopt the perspective of Kim et al. (2025), viewing easy (e.g., simplifying a fraction) versus hard (e.g., discovering the some symmetry) reasoning steps as low versus high probability Markov transitions. In this tractable model, pretraining corresponds to tree-graph discovering, while post-training corresponds to CoT reweighting. We provably show that, both RLVR and ORM/PRM would favor heavily to several high-probability paths, and thereby forget rare-but-crucial CoTs. Building on this, we further prove that exploration strategies such as rejecting easy instances and KL regularization help preserve rare CoTs. Empirical simulations corroborate our theoretical results.

22.
arXiv (CS.AI) 2026-06-15

Exact Linear Attention

作者:

arXiv:2605.18848v4 Announce Type: replace-cross Abstract: This paper introduces Exact Linear Attention (ELA), a mechanism that achieves linear computational complexity for Transformer attention by exploiting the exact decomposition property of kernel functions, thereby eliminating approximation error. We identify and address two key limitations of prior linear attention – gradient explosion and token attention dilution – by imposing kernel constraints that ensure non-negativity, discriminability, and geometric interpretability. Several kernel functions are proposed, including the Hadamard Exp Kernel, Summation Squared Euclidean Distance Kernel, and Subtraction Squared Euclidean Distance Kernel, each tailored for specific attention behaviors. Beyond the core attention formulation, the paper presents three engineering innovations: (1) a Hyper-Link structure that replaces traditional residual connections to mitigate gradient degradation; (2) a Memory Lobe module based on bidirectional linear attention, which captures "transformation flow" across layers to implement qualitative memory and an implicit reinforcement learning paradigm; and (3) a routing-score-based bias mechanism for Mixture-of-Experts (MoE) to improve interpretability and semantic alignment. Experimental results demonstrate that ELA achieves up to 6x faster decoding speed and 75% reduction in KV cache memory usage compared to full attention, while maintaining comparable or superior training performance. The proposed memory module accelerates convergence and enhances generalization. Furthermore, we extend the linear attention principle to vision models, yielding YOLO-LAT, which attains up to 4.3x GPU inference speedup and 7.9x parameter reduction with competitive detection accuracy. These results underline the broad applicability of exact linear attention for scaling Transformer models to ultra-long sequences and efficient visual tasks.

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

Beyond Reasoning Gains: Mitigating General-Capability Forgetting in Large Reasoning Models

arXiv:2510.21978v2 Announce Type: replace-cross Abstract: Reinforcement learning with verifiable rewards (RLVR) has delivered impressive gains in mathematical and multimodal reasoning and has become a standard post-training paradigm for contemporary language and vision-language models. However, the RLVR recipe introduces a significant risk of capability regression, in which models forget foundational skills after prolonged training without employing regularization strategies. We empirically confirm this concern, observing that open-source reasoning models suffer performance degradation on core capabilities such as perception and faithfulness. While imposing regularization terms like KL divergence can help prevent deviation from the base model, these terms are computed on the current task and therefore do not guarantee preservation of broader knowledge. Meanwhile, commonly used experience replay across heterogeneous domains makes it nontrivial to decide how much training emphasis each objective should receive. To address this, we propose RECAP-a replay strategy with dynamic objective reweighting for general knowledge preservation. Our reweighting mechanism adapts online using short-horizon signals of convergence and instability, shifting the post-training focus away from saturated objectives and toward underperforming or volatile ones. Our method is end-to-end and readily applicable to existing RLVR pipelines without training additional models or heavy tuning. Extensive experiments on benchmarks using Qwen2.5-VL-3B and Qwen2.5-VL-7B demonstrate the effectiveness of our method, which not only preserves general capabilities but also improves reasoning by enabling more flexible trade-offs among in-task rewards.

24.
bioRxiv (Bioinfo) 2026-06-20

Evaluation of Trypanosoma brucei Phosphofructokinase Allosteric Inhibition: An In-Silico Study

Human African trypanosomiasis, caused by a protozoan parasite Trypanosoma brucei, is a neglected tropical disease for which well-tolerated, conveniently administered, and highly efficacious medicines are still missing. Previously, T. brucei Phosphofructokinase was targeted by small-molecule inhibitor development efforts. This approach has shown promise both in vitro and in vivo. In this study, we have used these wet-lab results, evaluated the compounds already characterised by Molecular Dynamics simulations, found relationships between in silico and wet-lab data and used these observations to evaluate compounds that we selected through several different approaches of virtual screens. We observed that inhibitor-ATP interactions are highly predictive of the inhibitory activity. Several compounds selected through virtual screens have outperformed previously characterised compounds.

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arXiv (CS.CV) 2026-06-16

HMR-Net: Hierarchical Modular Routing for Cross-Domain Object Detection in Aerial Images

Despite advances in object detection, aerial imagery remains a challenging domain, as models often fail to generalize across variations in spatial resolution, scene composition, and semantic label coverage. Differences in geographic context, sensor characteristics, and object distributions across datasets limit the capacity of conventional models to learn consistent and transferable representations. Shared methods trained on such data tend to impose a unified representation across fundamentally different domains, resulting in poor performance on region-specific content and less flexibility when dealing with novel object categories. To address this, we propose a novel modular learning framework that enables structured specialization in aerial detection. Our method introduces a hierarchical routing mechanism with two levels of modularity: a domain routing layer that uses latent geographic embeddings to assign inputs to domain-specialized expert modules, and a scene routing mechanism that allocates image subregions to scene-specific expert modules. This allows our method to specialize across datasets and within complex scenes. Additionally, the framework contains a conditional expert module that uses external semantic information (e.g., category names or textual descriptions) to enable detection of novel object categories during inference, without the need for retraining or fine-tuning. By moving beyond monolithic representations, our method provides an adaptive framework for remote sensing object detection. Comprehensive evaluations on four datasets highlight improvements in multi-dataset generalization, region-level specialization, and open-category detection.