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01.
arXiv (CS.LG) 2026-06-18

KEPLA: A Knowledge-Enhanced Deep Learning Framework for Accurate Protein-Ligand Binding Affinity Prediction

arXiv:2506.13196v5 Announce Type: replace Abstract: Accurate prediction of protein-ligand binding affinity is critical for drug discovery. While recent deep learning approaches have demonstrated promising results, they often rely solely on structural features of proteins and ligands, overlooking their valuable biochemical knowledge associated with binding affinity. To address this limitation, we propose KEPLA, a novel deep learning framework that explicitly integrates prior knowledge from Gene Ontology and ligand properties to enhance prediction performance. KEPLA takes protein sequences and ligand molecular graphs as input and optimizes two complementary objectives: (1) aligning global representations with knowledge graph relations to capture domain-specific biochemical insights, and (2) leveraging cross attention between local representations to construct fine-grained joint embeddings for prediction. Experiments on two benchmark datasets across both in-domain and cross-domain scenarios demonstrate that KEPLA consistently outperforms state-of-the-art baselines. Furthermore, interpretability analyses based on knowledge graph relations and cross attention maps provide valuable insights into the underlying predictive mechanisms.

02.
arXiv (CS.LG) 2026-06-19

A Hybrid GNN-FEM Framework for Phase-Field Fracture Simulation. Physics-Preserving Hybridization for Generalizable Surrogate Modeling

arXiv:2606.19378v1 Announce Type: new Abstract: Scientific machine learning (SciML) has emerged as a promising approach for accelerating simulations of complex physical systems, yet achieving physically consistent and generalizable predictions for nonlinear, history-dependent problems remains a central challenge. In this study, we propose a hybrid GNN–FEM framework for efficient and generalizable phase-field fracture modeling. While phase-field approaches provide a robust variational framework for simulating complex crack evolution, their high computational cost limits practical applications because they require solving coupled, nonlinear, and history-dependent systems within an incremental finite element procedure. To address this challenge, a graph neural network surrogate is integrated into the conventional staggered scheme, replacing the phase-field update at each load increment while retaining the FEM-based displacement solver to enforce mechanical equilibrium and boundary conditions. By preserving the incremental solution structure, the framework remains consistent with history-dependent fracture evolution without requiring the surrogate to approximate the full solution trajectory. This selective surrogate strategy emphasizes the identification of a physically meaningful and incrementally structured learning target, rather than relying on brute-force data generation to learn the full fracture process. The proposed framework achieves strong generalization across varying geometries, loading conditions, material properties, and discretizations through dimensionless feature design, a graph-based formulation on mesh-based domains, and a physics-informed loss derived from the governing phase-field equation. Numerical experiments demonstrate that the hybrid approach reduces computational cost while maintaining accuracy compared with conventional FEM, and exhibits robust predictive performance across diverse problem settings.

03.
arXiv (quant-ph) 2026-06-15

Quantum codes and optimal pure quantum $(r,\delta)$-LRCs via the MP construction

arXiv:2606.14253v1 Announce Type: new Abstract: In this paper, we employ MP codes whose defining matrices are $\tau$-optimal defining ($\tau$-OD) matrices to construct new quantum codes and quantum $(r,\delta)$-LRCs. Specifically, we report the following results: We establish a unified $\tau$-monomial decomposition theorem for invertible self-adjoint matrices over finite fields of arbitrary characteristic, which generalizes the result in "Quantum codes using the $\tau$-OD MP construction" where the characteristic was required to be odd. Based on this theorem, we prove the existence of $\tau$-OD matrices over $\mathbb{F}_{q^2}$ for any characteristic and demonstrate that there exist several new infinite families of $\tau$-OD matrices over $\mathbb{F}_{q^2}$ of characteristic $2$. As an application of MP codes involving $\tau$-OD matrices, we construct several infinite families of quantum codes with flexible parameters. Within this framework, we present $222$ record-breaking quantum codes that surpass the best-known records maintained in Grassl's database. We propose two effective schemes for constructing optimal pure quantum $(r,\delta)$-LRCs via MP codes. Accordingly, we construct four new infinite families of optimal pure quantum $(r,\delta)$-LRCs with flexible parameters. Notably, we report an interesting phenomenon by exhibiting $30$ optimal pure quantum $(r,\delta)$-LRCs derived from our framework; that is, there exist quantum codes that are not only optimal pure quantum $(r,\delta)$-LRCs but also, according to Grassl's database, best-known, optimal, or record-breaking quantum codes. To the best of our knowledge, the new discovery that quantum codes are simultaneously optimal pure quantum $(r,\delta)$-LRCs and record-breaking quantum codes has not been previously reported in the literature.

04.
medRxiv (Medicine) 2026-06-18

Hospital staff views on the visibility, role and impact of Acute Learning Disability Liaison Services in Wales: a service evaluation

People with a learning disability experience marked health inequalities. In Wales, Acute Learning Disability Liaison Services (ALDLS) are delivered by specialised learning disability services, and all roles within them are undertaken by Learning Disability Liaison Nurses (LDLN). These services aim to enable access to, and delivery of, secondary care by supporting reasonable adjustments, facilitating communication, and coordinating care for people with learning disability during hospital encounters. However, independent evidence of the impact of ALDLS on patient care remains limited. This evaluation tries to address this evidence gap by examining hospital staff perceptions of the visibility, role, and impact of ALDLS across Welsh Health Boards, with the aim of informing service design and development and improving secondary care access and care for people with learning disability. The service evaluation used a qualitative approach involving interviews and a focus group with hospital staff across the seven Welsh Health Boards who had experience working with or interacting with ALDLS staff to care for patients with learning disability. Findings cover six key areas including i) visibility and delivery of ALDLS, ii) Barriers and challenges to effective ALDLS delivery, iii) Enablers of effective ALDLS delivery, iv) Positive impacts for patients with learning disability, v) Negative impacts and unintended consequences when the service is absent or limited, and vi) Participants recommendations for future improvements of ALDLS. To synthesise the findings, we developed an overview diagram, which illustrates how ALDLS may influence care quality in acute hospitals. The overview places the liaison service at the centre, showing how organisational enablers and barriers shape its delivery, and how its core functions support improvements in safety, timeliness, effectiveness, efficiency, equity, and patient-centred care. From the findings we have identified recommendations for practice and policy. These include that ALDLS should be recognised as a core, safety-critical component of acute hospital care for people with a learning disability, rather than an optional add-on. In practice, services should be more visibly embedded within routine pathways, with consistent site-based presence, clear referral criteria, early identification through electronic flagging and notification systems, and routine involvement in multidisciplinary planning for complex admissions and procedures. At policy level, ALDLS provision should be recognised within equality and patient safety frameworks as an essential service requiring sustained investment, national minimum configuration standards, adequate staffing, and better-integrated digital systems to support continuity, equitable access, and person-centred care.

05.
arXiv (CS.CV) 2026-06-16

Intrinsic Gradient Suppression for Label-Noise Prompt Tuning in Vision-Language Models

Contrastive vision-language models like CLIP exhibit remarkable zero-shot generalization. However, prompt tuning remains highly sensitive to label noise, as mislabeled samples generate disproportionately large gradients that can overwhelm pre-trained priors. We argue that because CLIP already provides a near-optimal initialization, adaptation should be inherently conservative, particularly against the extreme gradient updates common in noisy settings. To this end, we propose Double-Softmax Prompt Tuning (DSPT), a hyperparameter-free method for intrinsic gradient suppression. By applying a sequential probabilistic normalization, DSPT induces a self-adaptive saturation zone that suppresses gradients from high-error noisy samples while maintaining informative updates. We also provide both theoretical analysis and empirical evidence about how this mechanism achieves adaptive suppression. This design transforms ``gradient vanishing'', traditionally a training bottleneck, into a principled noise-filtering shield for label-noise prompt tuning. Extensive experiments confirm that this simple, drop-in design achieves state-of-the-art robustness across various noisy benchmarks, outperforming methods with complex architectures and handcrafted hyperparameters.

07.
arXiv (CS.CV) 2026-06-15

TSA: Temporal Slot Activation for Persistent Object-Centric Video Representation

Unsupervised video object-centric learning aims to decompose dynamic scenes into temporally persistent entity representations. Existing recurrent video slot-attention methods propagate a fixed set of slots across frames, but typically assume unconditional slot propagation: every slot is updated and decoded at every frame, regardless of whether its corresponding object is visible. We show that this design violates a basic lifecycle requirement for persistent slots: when an object is absent or fully occluded, its slot should preserve its previous state and avoid explaining unrelated visible content. Instead, unconditional propagation creates two failure pathways: update-induced state drift, where current-frame evidence overwrites the absent object's representation, and decoder-induced reconstruction interference, where the inactive slot remains coupled to reconstruction through decoder attention. We propose Temporal Slot Activation (TSA), a mechanism that learns a per-slot, per-frame activation score $\alpha_{k,t} \in (0, 1)$ without visibility supervision. TSA uses this activation as a shared latent control variable for slot lifecycle modeling. When a slot is inactive, TSA anchors its state to the previous slot via activation-gated updating and suppresses its decoder participation through an activation-dependent additive bias on attention logits before softmax normalization. This jointly reduces state drift and reconstruction-driven interference. To improve decisions under partial occlusion and gradual reappearance, TSA further conditions activation prediction on a per-slot temporal memory produced by a Temporal Context Encoder. We evaluate TSA on MOVi-C/E, YT-VIS, and OVIS benchmarks using both standard and tracking-based metrics (FG-ARI, mBO, IDF1, HOTA). TSA consistently improves object decomposition and temporal identity preservation, with large gains on long, heavily occluded videos.

08.
arXiv (quant-ph) 2026-06-16

Detecting basis-dependent hardware errors through spatio-temporal quantum steering

arXiv:2606.16451v1 Announce Type: new Abstract: Spatio-temporal quantum steering provides a framework for benchmarking the nonclassicality of general quantum state transfer processes. A central diagnostic is the no-signaling-in-time (NSIT) condition, whose violation can indicate basis-dependent hardware errors. However, finite measurement statistics may also yield apparent violations, thereby obscuring the detection of basis-dependent hardware errors. To address this, we construct a statistical hypothesis test under the null hypothesis that NSIT violations arise solely from statistical fluctuations. Combining the statistical properties of NSIT violation under the null hypothesis with Chebyshev's inequality, we obtain a distribution-free upper bound on the $p$-value without parametric assumptions. We apply this method to two examples. For a single-qubit state-transfer experiment on a superconducting processor, we observe several instances that the NSIT violation is observed and the null hypothesis is simultaneously rejected by a small $p$-value, providing statistical evidence of basis-dependent hardware errors. For a seven-qubit Hayden-Preskill teleportation protocol on IonQ devices, the null hypothesis is also rejected even when the average fidelity exceeds the classical threshold, while the associated nonclassicality measure vanishes. Our results highlight the necessity of statistical hypothesis testing for detecting basis-dependent errors in near-term quantum devices.

09.
arXiv (math.PR) 2026-06-11

Stochastic Reaction Networks Within Interacting Compartments with Content-Dependent Fragmentation

arXiv:2511.10223v4 Announce Type: replace Abstract: Stochastic reaction networks with mass-action kinetics provide a useful framework for understanding processes – biochemical and otherwise – in homogeneous environments. However, cellular reactions are often compartmentalized, either at the cell level or within cells, and hence non-homogeneous. We investigate a model of compartmentalization in which the rate of fragmentation of a compartment depends on the abundance of some designated species inside that compartment. The particular model of study is part of a general framework for compartmentalized chemistry with dynamic compartments that was proposed in (Duso and Zechner, PNAS, 2020). This paper builds on (Anderson and Howells, Bull. Math. Biol., 2023) where the special case where the compartment dynamics do not depend on their contents was studied mathematically. In particular, we demonstrate that the explosivity characterization from (Anderson and Howells, Bull. Math. Biol., 2023) fails in this setting and provide new sufficient conditions for non-explosivity and positive recurrence, under the assumption that the underlying CRN admits a linear Lyapunov function. These results extend the theoretical foundation for modeling content-mediated compartment dynamics, with implications for systems such as cell division and intracellular transport.

10.
medRxiv (Medicine) 2026-06-17

Diagnostic Concordance of Immediate Versus 1-Hour Technetium-99m Hydroxydiphosphonate Scintigraphy in Suspected Transthyretin Amyloid Cardiomyopathy

Background Bone-avid tracer myocardial scintigraphy for the diagnosis of transthyretin amyloid cardiomyopathy (ATTR-CM) has traditionally employed imaging at one or 3-hour intervals. Technetium-99m hydroxydiphosphonate (99mTc-HDP) has unique characteristics that may enable earlier imaging. We investigated the diagnostic concordance of immediate versus 1-hour acquisitions. Methods Consecutive patients with suspected ATTR-CM underwent planar imaging and SPECT/CT immediately and at 1-hour following the administration of 99mTc-HDP. Perugini grades and heart to contralateral lung (H/CL) ratios were assessed. Target-to-background ratios (TBRs) were calculated on the SPECT/CT acquisitions using the left ventricular (LV) septum and three background regions: aorta, LV blood-pool, and vertebrae. We assessed diagnostic concordance using Cohen's Kappa ({kappa}), temporal stability using paired t-tests, and correlation between timepoints using Pearson's coefficient (r). The 1-hour SPECT/CT interpretation served as the protocol reference standard. Results Forty-eight patients (83% male; median age, 80 [73-85] years) were evaluated. One-hour SPECT/CT identified 19 positive and 29 negative cases. Immediate SPECT/CT demonstrated 100% diagnostic concordance with the 1-hour reference standard ({kappa} = 1.000; 95% CI: 1.00 to 1.00; p < 0.001). The LV septum/LV Blood-Pool TBR showed the highest correlation (r = 0.956; 95% CI: 0.922 to 0.975; p < 0.001). The LV Septum/Aorta TBR demonstrated high correlation (r = 0.918; 95% CI: 0.857 to 0.953; p < 0.001) and remained stable in the ATTR-negative cohort (-0.02; 95% CI: -0.08 to 0.04; p = 0.54). Significant decrease in the LV Septum/Vertebrae TBR in the ATTR-negative (-0.55; 95% CI: -0.64 to -0.47; p < 0.001) and ATTR-positive cohorts (-1.14; 95% CI: -1.39 to -0.89; p < 0.001) was observed. Conclusions Immediate 99mTc-HDP SPECT/CT is diagnostically concordant with standard 1-hour protocols. By leveraging SPECT/CT and the favorable kinetics of 99mTc-HDP, immediate-phase imaging can accurately reproduce 1-hour acquisitions in cases of suspected ATTR-CM. This expedited approach may improve nuclear laboratory throughput and patient satisfaction.

11.
arXiv (CS.AI) 2026-06-18

Structured Cognitive Loop for Behavioral Intelligence in Large Language Model Agents (Extended Revision: From Behavioral Architecture to Epistemic Accountability)

作者:

arXiv:2510.05107v5 Announce Type: replace Abstract: The central challenge for AI agents is not only performance but accountability. Agents that act through opaque prompt sequences may produce correct outputs, but they provide little basis for verifying why an action was permitted, where an error occurred, or how responsibility should be assigned. This paper presents the Structured Cognitive Loop as an architecture for accountable behavior in large language model agents. SCL separates cognition, memory, control, and action into distinct modules. The language model proposes. External memory preserves verified state. A lightweight controller checks preconditions, prevents redundant actions, and authorizes execution before tools are used. We evaluate SCL against ReAct and common LangChain agent variants across travel planning, conditional email drafting, and constraint guided image generation. Across 360 episodes, SCL achieves 86.3 percent task success compared with 70.5 to 76.8 percent for prompt based baselines. It also improves goal fidelity, reduces redundant tool calls, increases reuse of intermediate state, and lowers unsupported assertions. This extended revision situates SCL within a broader architecture of epistemic accountability. Subsequent extensions integrate context aware Human in the Loop control, Pool Gated Retrieval, and the Horizon Warrant Commitment framework. Together these components define an agent architecture in which the model proposes, structure decides, evidence is warranted before use, and human judgment is embedded in the trace rather than imposed after the fact. The result is a foundation for AI agents whose decisions are not only effective but also authorized, inspectable, and accountable.

12.
medRxiv (Medicine) 2026-06-11

Advancing Clinical Implementation of Cardiovascular Polygenic Risk Scores Through Patient-Level Robustness Assessment

Background and Aims: Polygenic risk scores (PRSs) for atherosclerotic cardiovascular disease (ASCVD) can perform equivalently at the population level yet disagree for individual patients. We examined whether such intra-individual variability reflects genuinely complementary risk information or mainly statistical and methodological uncertainty, and whether it affects clinical classification once PRSs are integrated into SCORE2-OP. Methods: In 4,137 ASCVD-free participants of the CoLaus|PsyCoLaus cohort (478 incident events over a median 14.4 years), we identified 16 ASCVD-PRSs with practically equivalent population-level performance using Bayesian equivalence testing. We quantified intra-individual variability (standard deviation, coefficient of variation, intraclass correlation, Cohen's kappa, extreme discordance), tested whether discordance exceeded chance, decomposed scores into shared and unique genetic components, and assessed variability after integration into SCORE2-OP, benchmarked against perturbation of systolic blood pressure. Results: For a typical individual, risk estimates varied by 18 percentile points across PRSs. Discordance matched chance expectations under a shared-signal model, with no distinct phenotypic profile among discordant individuals, and predictive power resided overwhelmingly in the shared genetic component. Variability tracked PRS size and weighting rather than distinct variants. After integration into SCORE2-OP, 75.6% of participants were placed in different categories by at least one model and 54.6% as both low and high risk; instability was concentrated near guideline thresholds and far exceeded that from blood-pressure measurement error. Conclusions: Equivalent population-level performance is not sufficient to treat PRSs as interchangeable at the individual level, and methodological standardisation and pragmatic clinical trials remain necessary to determine whether PRS integration improves long-term cardiovascular outcomes.

13.
arXiv (CS.CV) 2026-06-16

Timestep Rescheduling in Diffusion Inversion

Diffusion inversion, which maps images back to the Gaussian latent space of a diffusion model, is a critical task for image reconstruction and editing. While DDIM enables fast deterministic inversion, it inherently introduces deviations that accumulate into noticeable inversion errors. Existing methods often address this by solving a fixed-point problem but largely overlook how the selection of the diffusion timestep in the noise scheduler influences inversion fidelity. In this work, we reveal that the deviation scale in diffusion inversion is strongly dependent on the timestep size, and exhibits a parabolic trend, with larger errors concentrated at both small and large timesteps. Based on this finding, we propose a simple yet effective nonuniform timestep scheduler that integrates a global rescaling with a local dynamic programming based rescheduling, enabling a strategic allocation of computational effort that minimizes the overall inversion error and preserves higher inversion accuracy. Our method serves as an off-the-shelf enhancement for existing inversion techniques and requires no extra parameters or computational overhead. Through extensive experiments, we verify that integrating our scheduler consistently boosts the performance of existing inversion methods, achieving superior results in image reconstruction and editing.

14.
arXiv (CS.CL) 2026-06-15

FineDialFact: A benchmark for Fine-grained Dialogue Fact Verification

Large language models are known to produce hallucinations - factually incorrect or fabricated information - which poses significant challenges for many natural language processing applications, such as dialogue systems. As a result, detecting hallucinations has become a critical area of research. Current approaches to hallucination detection in dialogue systems primarily focus on verifying the factual consistency of generated responses. However, these responses often contain a mix of accurate, inaccurate or non-verifiable facts, making the use of a single factual label overly simplistic and coarse-grained. In this paper, we introduce a benchmark, FineDialFact, for fine-grained dialogue fact verification, which involves verifying atomic facts extracted from dialogue responses. To support this, we construct a dataset based on publicly available dialogue datasets and evaluate it using various baseline methods. Experimental results demonstrate that methods incorporating Chain-of-Thought reasoning can enhance performance in dialogue fact verification. Despite this, the best F1-score achieved on the HybriDialogue, an open-domain dialogue dataset, is only 0.74, indicating that the benchmark remains a challenging task for future research. We release our dataset and code at https://github.com/XiangyanChen/FineDialFact.

15.
arXiv (CS.AI) 2026-06-16

HCP-MAD:Heterogeneous Consensus-Progressive Reasoning for Efficient Multi-Agent Debate

arXiv:2604.09679v2 Announce Type: replace-cross Abstract: Multi-Agent Debate (MAD) is a collaborative framework in which multiple agents iteratively refine solutions through the generation of reasoning and alternating critique cycles. Current work primarily optimizes intra-round topologies and inter-round interactions separately, limiting the adaptation of token costs to task complexity. This work introduces Heterogeneous Consensus-Progressive Reasoning for Efficient Multi-Agent Debate (HCP-MAD), leveraging consensus as a dynamic signal to facilitate progressive reasoning. The core motivation is that a majority of straightforward tasks can be effectively resolved via lightweight pair-agent debates, while complex tasks require expanded collaboration. Firstly, Heterogeneous Consensus Verification conducts rapid consensus verification using a pair of heterogeneous agents for early stopping. Next, Heterogeneous Pair-Agent Debate applies an adaptive stopping criterion to terminate mutual critique of reasoning traces. Finally, the unresolved tasks are addressed through Escalated Collective Voting by aggregating diverse perspectives from additional agents. Experiments across six benchmarks show that HCP-MAD enhances accuracy while substantially reducing token costs. Code is https://github.com/fuyu66/HCP-MAD.

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

SegTME-UNI2: A Foundation Model-Based Framework for Generalisable Multiclass Cell Segmentation and LLM-Driven Tumour Microenvironment Characterisation in Histopathology

Characterising the tumour microenvironment (TME) from routine H&E-stained histology images requires simultaneous cell segmentation, feature extraction, and interpretable clinical reporting. We present SEGTME-UNI2, a unified framework addressing these requirements. Its core is UNI2-UPERHOVER, a dual-head segmentation model pairing the UNI2-H pathology foundation model (ViT-Giant, pretrained on >100M tiles from 100K slides) with two parallel UperNet decoders: one for six-class semantic segmentation and one for horizontal-vertical gradient regression enabling watershed-based nuclear instance separation. To address the lack of pixel-level annotations in large real-world repositories, UNI2-UPERHOVER undergoes a three-stage progressive pseudo-label curriculum. Each stage trains a fresh model without weight transfer, driving improvement entirely via increased pseudo-label quality: Stage 1: Uses human-annotated PanNuke (7,901 images, 189,744 nuclei, 0.25 um/pixel). Stage 2: Uses entropy-filtered pseudo-labels from the Stage 1 model on 271,711 TCGA-UT scale-0 patches (0.5 um/pixel). Stage 3: Uses pseudo-labels from the Stage 2 model on all 1,608,060 TCGA-UT patches across six resolution scales (0.5-1.0 um/pixel). Segmentation outputs feed a structured TME feature extraction pipeline computing 20+ per-patch compositional, morphological, spatial entropy, and intercellular distance metrics. These are encoded as JSON and passed to a fine-tuned NVIDIA BioNeMo GPT model to generate clinically interpretable TME narratives. Preliminary validation on held-out PanNuke and TCGA-UT partitions demonstrates framework feasibility and internal consistency. The pseudo-labelled TCGA-UT dataset and UNI2-UPERHOVER checkpoint are publicly released to support large-scale TME profiling and spatial biology research.

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

We Need to Rethink Benchmarking in Anomaly Detection

arXiv:2507.15584v2 Announce Type: replace Abstract: Despite the continuous proposal of new anomaly detection algorithms and extensive benchmarking efforts, progress seems to stagnate, with only minor performance differences between established baselines and new algorithms. In this position paper, we argue that this stagnation is due to limitations in how we evaluate anomaly detection algorithms. In current benchmarks, a trivial algorithm that only checks for extreme values in individual features performs competitively with state-of-the-art deep learning methods, despite failing on simple cases such as anomalies within an annulus of normal points. Moreover, existing benchmarks do not adequately reflect the diversity of anomaly detection applications, making it difficult for practitioners to reliably select algorithms for their applications. Consequently, we need to rethink benchmarking in anomaly detection. In our opinion, anomaly detection should be studied using scenarios that group applications sharing relevant characteristics, defined through a common taxonomy. Benchmarking within scenarios enables scenario-specific choices for preprocessing, metrics, and model selection, clarifying which advances transfer across similar applications and providing practitioners with reliable guidance for their specific contexts.

18.
arXiv (CS.AI) 2026-06-15

Applicability Condition Extraction for Therapeutic Drug-Disease Relations

arXiv:2606.14031v1 Announce Type: new Abstract: Identifying conditions that a certain drug takes therapeutic effect on a target disease is crucial for clinical decision-making support. However, most existing biomedical information extraction methods have focused on identifying only relations between drugs and diseases, while largely overlooking the context-specific conditions where such relations can apply. To address this problem, we introduce the task of applicability condition extraction for therapeutic drug–disease relations from biomedical research literature. We create the first dataset that has manually annotated triples of drugs, diseases, and applicability conditions on biomedical paper abstracts with 1,119 drug-disease pairs. Using this dataset, we systematically evaluate the performance of a range of existing methods. In addition, we propose a new method that enhances LoRA to consider relations between drugs and diseases. Our method consistently outperforms strong baselines across different evaluation settings. The source code and dataset of this paper can be obtained from: https://github.com/guantingluo98/Drug-ACE

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

Improving Lunar Topography with Deep Learning Schrödinger Bridges

Increasing the resolution of planetary topography models can enable a better understanding of surface processes and geomorphology; however, existing analytical super-resolution methods are expensive and difficult to apply at large scales. Generative models provide the tools to learn complex relationships within data and can be applied at scale due to hardware accelerators and parallelization. We present a diffusion-based Schrödinger Bridge (SB) generative modeling approach for lunar topography super-resolution, connecting the distribution of low-resolution topography to that of high-resolution topography, incorporating physically-constraining optical imagery. Our approach is inspired by existing Shape-from-Shading methods, which improve a priori low-resolution topography by using optical images at the target resolution. We train SBs on a novel dataset of rendered lunar topography, emulating optical imagery from the Lunar Reconnaissance Orbiter Narrow Angle Camera. The result is a flexible approach for topography super-resolution which can provide pixel-level uncertainties in the reconstruction.

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

Virtual Speech Therapist: A Clinician-in-the-Loop AI Speech Therapy Agent for Personalized and Supervised Therapy

This paper develops Virtual Speech Therapist (VST), an intelligent agent-based platform that streamlines stuttering assessment and delivers customized therapy planning through automated and adaptive AI-driven workflows. VST integrates state-of-the-art deep learning-based stuttering classification, and multi-agent large language model (LLM) reasoning to support evidence-based clinical decision-making. The VST begins with the acquisition and feature extraction of patient speech samples, followed by robust classification of stuttering types. Building on these outputs, VST initiates an agentic reasoning process in which specialized LLM agents autonomously generate, critique, and iteratively refine individualized therapy plans. A dedicated critic agent evaluates all generated therapy plans to ensure clinical safety, methodological soundness, and alignment with peer-reviewed evidence and established professional guidelines. The resulting output is a comprehensive, patient-specific therapy draft intended for clinician review. Incorporating clinician feedback, the system then produces a finalized therapy plan suitable for patient delivery, thereby maintaining a clinician-in-the-loop paradigm. Experimental evaluation by expert speech therapists confirms that VST consistently generates high-quality, evidence-based therapy recommendations. These findings demonstrate the system's potential to augment clinical workflows, reduce clinician burden, and improve therapeutic outcomes for individuals with speech impairments. An interactive user interface for the proposed system is available online at: https://vocametrix.com/ai/stuttering-therapy-planning-agent , facilitating real-time stuttering assessment and personalized therapy planning.

21.
arXiv (CS.LG) 2026-06-18

Anomaly Detection for Sparse and Irregular Multivariate Time Series with Latent SDEs

arXiv:2606.18898v1 Announce Type: new Abstract: Multivariate time series anomaly detection (MTSAD) is critical for a wide range of application areas, such as industrial monitoring, cybersecurity, or healthcare. Real-world data is often sparse, irregularly sampled or partially observed, yet existing methods assume uniformly sampled time series. We propose a generative approach based on Latent SDEs that projects the observed time series on a continuous-time stochastic dynamical system, directly being able to handle missing observations and irregular sampling, while also naturally capturing possible cyclic behavior that many real-world use cases inherently possess. Experiments on six anomaly benchmark datasets show that our proposed method ranks first among state-of-the-art baselines. We further demonstrate that our method remains robust under severe data sparsity, while performance significantly degrades for the tested baseline methods. These results highlight latent SDEs as a natural inductive bias for anomaly detection in multivariate time series, especially in presence of real-world irregularities.

22.
arXiv (CS.CL) 2026-06-16

How Far Can Machine Translation Quality Take You? Extrinsic Discourse Evaluation in Goal-Oriented Setups

Existing machine translation (MT) metrics and discourse-focused evaluations primarily assess translation quality intrinsically, without measuring the downstream consequences of translation errors. In this work, we focus on extrinsic discourse evaluation of machine translation under two distinct regimes: static and interactive. Under the static regime, we propose an entity counting task as a probe of referential consistency in discourse. We show that high intrinsic MT quality does not reliably predict downstream discourse success and strong MT systems still produce referential inconsistencies. For the interactive regime, we study the goal-oriented multi-agent Welfare Diplomacy game as a probe of long-horizon communication and coordination. We find that interaction-specific translation failures impact downstream coordination. Our results highlight goal-oriented environments as a viable framework for discourse-sensitive extrinsic MT evaluation.

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

Self-Preference Is Weak or Absent in Verifiable Instruction-Following Revision: A Four-Model Test Under Genuine Authorship

Large language models (LLMs) increasingly review and revise text, including their own. A documented self-preference bias (models favoring their own generations when acting as judges) raises the question of whether models also resist valid corrections to their own writing. We test this in a setting where "valid" is decided not by another model but by a deterministic verifier: instruction-following revision on IFEval. A model writes a draft; the official IFEval checker confirms the draft violates a constraint and that a candidate edit fixes it; the model then accepts or rejects that edit either as the genuine in-context author or as a fresh model that sees the draft neutrally. Across four mid-tier model families and 85 author-versus-fresh comparisons, we find no detectable self-preference: authors reject verified-good fixes to their own drafts at essentially the same rate as fresh models judging the same drafts (gap -5.1 pp, 95% CI [-12.9, +2.7]). A self-skepticism hint from a smaller pilot did not replicate at scale. The one robust observation is qualitative: when authors do reject a verified-good fix, 97% of their stated reasons are flaw-catching rather than preference, that is, about the character of rejections, not an elevated rate. Effects smaller than ~13 pp cannot be excluded at this sample size.

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

ARTEMIS: Agent-guided Reliability-aware Temporal Mask Evolution for Imperfectly Supervised Video Polyp Segmentation

Imperfectly supervised video polyp segmentation (VPS) aims to learn dense, temporally consistent masks from inexpensive supervision, including weak annotations (points, scribbles) and semi-supervision with few densely labeled frames. This setting is clinically valuable but challenging due to weak contrast, ambiguous boundaries, motion blur, and specular highlights, compounded by sparse pixel-level guidance. While SAM2 can generate dense masks from sparse inputs, direct pseudo-labeling often yields geometry-degraded masks with boundary leakage, underutilizes temporal consistency, and ignores reliability. To address these issues, we propose ARTEMIS, a unified framework for imperfectly supervised VPS driven by agent-guided reliability-aware temporal mask evolution. ARTEMIS initializes coarse masks from available supervision: SAM2 converts points/scribbles, while dense labels serve as reliable anchors. A debate-and-judge vision-language agent selects reliable temporal anchors under weak supervision, which are propagated bidirectionally with SAM2 to refine unreliable or unlabeled frames. Finally, ARTEMIS trains the segmenter using temporal reliability-aware robust learning, incorporating reliability-guided reference selection, a Reference Prototype Transport Module, and reliability-aware robust loss. These components assess mask reliability, evolve anchors over time, transport target identity across frames, and down-weight noisy supervision instead of discarding difficult samples. Experiments on SUN-SEG and CVC-ClinicDB-612 under scribble, point, and limited-label settings demonstrate that ARTEMIS achieves state-of-the-art performance. Code will be released at https://github.com/wangtong627/ARTEMIS.

25.
arXiv (CS.CL) 2026-06-16

AthDGC: An Open Diachronic Greek Treebank with Indo-European Parallels

AthDGC ("Athens-PROIEL") is an open, end-to-end workflow and dataset. It is, to the best of our knowledge, the first openly licensed dependency-parsed treebank of Greek that spans eight diachronic periods, namely Archaic, Classical, Koine, Late Antique, Byzantine, Late Byzantine, Early Modern, and Modern Greek, under a single PROIEL XML 2.0 schema, with verse-level cross-alignment of the New Testament to Latin (Vulgate), Gothic (Wulfila), Old Church Slavonic (Marianus), and Classical Armenian. AthDGC builds on the PROIEL Treebank Family (Haug and Johndal 2008; Eckhoff et al. 2018), which established the schema and the Koine-Greek reference set for the project. Annotation uses the Stanford Stanza PROIEL-trained workflow; sentence-level alignment uses LaBSE, a multilingual sentence-embedding model; word-level alignment uses multilingual-BERT attention through the AwesomeAlign procedure. The v0.4 release provides curated samples and the open-source toolkit; the full annotated corpus partitions remain under v0.5 audit on the Greek national HPC. Quantitative scale, per-witness verse counts, and per-period annotated-row counts are reported in the v0.5 release notes, after the audit pass completes. Concept DOI: 10.5281/zenodo.20439182.