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

Input-Dependent Fisher Information for Local Sensitivity Analysis of Medical Image Classifiers

arXiv:2606.16362v1 Announce Type: cross Abstract: Deep neural networks have achieved strong performance in medical image classification, but often work like black-box. Commonly used post-hoc interpretation methods often provide heuristic visualizations whose relationship to the classifier's predictive distribution is indirect. This work introduces a local sensitivity analysis framework based on the input-dependent Fisher Information Matrix (iFIM) of a trained classifier. The iFIM characterizes how the classifier's predictive distribution changes under infinitesimal perturbations of the input image. By using a Gram-matrix formulation, the nonzero eigenspectrum of the iFIM can be recovered without explicitly forming the full image-dimensional Fisher matrix. The leading iFIM eigenspace is then used to project an input image into a high local-sensitivity component and its orthogonal component. These components provide a model-intrinsic description of local predictive sensitivity, rather than a conventional pixel-wise attribution heatmap or a causal segmentation of task-relevant anatomy. The framework is evaluated on controlled and clinical medical image classification tasks using multiple classifier architectures. Perturbation-based experiments show that high-sensitivity iFIM components are more strongly coupled to changes in predictive confidence and classification performance than lower-sensitivity complementary components. The results support the iFIM framework as a principled tool for analyzing local decision sensitivity and for complementing existing attribution-based interpretability methods in medical imaging.

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

Addressing Detail Bottlenecks in Latent Diffusion for RGB-to-SWIR Image Translation

Latent diffusion models (LDMs) enable efficient image-to-image translation but discard fine spatial details during compression, degrading downstream perception tasks. We identify two bottlenecks: the autoencoder, which loses spatial information, and the conditioning pathway, which further degrades the source signal through naive downsampling. We propose two lightweight, backbone-agnostic fixes: a Source-Conditioned Autoencoder (SCAE) that injects high-resolution source features into the decoder via skip connections, and a Learnable Guidance Encoder (LGE) that replaces naive downsampling with a learned conditioning signal. Evaluated on RGB-to-SWIR translation for driving scenes with two denoiser backbones (U-Net and DiT), our approach improves detection mAP by up to 2x over the latent diffusion baseline, with up to 3.4x gains on small objects (COCO-small,

03.
arXiv (CS.CV) 2026-06-16

Unlocking Diffusion Hierarchies: Adaptive Timestep Selection for Zero-Shot Segmentation

Zero-shot segmentation has recently shown notable improvement by leveraging the rich visual priors in large-scale text-to-image diffusion models, such as Stable Diffusion. However, current diffusion-based methods often face limitations due to the trade-off between spatial resolution and contextual information, as well as their reliance on a single static timestep for feature extraction. To overcome these challenges, our work introduces two key advancements. First, our Contextual Similarity Maps fuse high-resolution attention maps with rich U-Net encoder features, providing both fine-grained and robust per-pixel representations. Second, we identify an emergent hierarchical semantic progression within the denoising process of various diffusion models: representations transition from part-level abstractions at earlier timesteps to object-level abstractions at later stages. Leveraging this insight, we introduce a mechanism to adaptively select the optimal timestep for each pixel. Extensive experiments demonstrate that our method consistently outperforms existing zero-shot segmentation baselines, validating the efficacy of combining contextual features with dynamic, hierarchical timestep selection.

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

Keep It in Mind: User Centric Continual Spatial Intelligence Reasoning in Egocentric Video Streams

We introduce UCS-Bench, a dataset spanning 170+ hours of egocentric visual observations with 8.1K+ timestamped questions for diagnosing User-Centric Continual Spatial intelligence in egocentric video streams. UCS-Bench targets a new problem that emphasizes dynamic spatial reasoning, long-term memory, and their alignment with users' real-time locations. We propose DirectMe, a framework that incrementally constructs and maintains a structured spatial memory from streaming egocentric observations. DirectMe enables robust tracking and recall of object locations, all relative to the user's movement over time. By tightly coupling visual perception with memory updates and spatial reasoning, our approach supports long-horizon queries that require recalling interactions, resolving viewpoint-induced ambiguities, and adapting to dynamic scenes. Our experiments show that DirectMe significantly improves the spatial reasoning of leading multimodal LLMs; it also surpasses many spatially aware and long-form streaming video models. We hope our benchmark and solution will advance spatial intelligence research for egocentric AI assistants. Data and code are available at https://github.com/cocowy1/UCS-Bench.

05.
bioRxiv (Bioinfo) 2026-06-18

Bayesian modeling of longitudinal metatranscriptomes of broiler meat spoilage microbiomes shows shared predictive signature associated with spoilage at refrigerated temperatures

Microbial spoilage of packaged meat is driven by complex microbial succession and related metabolic activity, yet conventional shelf-life assessment is mainly based on shelf-life studies relying on culturing and sensory analysis. In routine quality assurance, results are obtained retrospectively, and they are only indirectly linked to the metabolic activity related to sensory deterioration. Functional, time informative approaches that capture the active metabolic state of the spoilage microbiome and predict the rate of spoilage are lacking. We developed a censoring-aware Gaussian process (CAGP) framework to model longitudinal pathway expression profiles from broiler meat metatranscriptomes collected over consecutive storage days at 4 or 6{degrees}C. Samples were annotated using odor-based sensory scores defining fresh, early-spoilage, and late-spoilage phases. Because observed zeros in pathway-level data may reflect non-detection rather than true absence, the model treats low values as left-censored observations below a detection threshold while estimating smooth temporal trajectories with uncertainty. In leave-one-out prediction within the 4{degrees}C time series, predicted sampling days differed from the true days by an average of 0.43 days, and predicted spoilage phases agreed with the sensory classification. Trajectories learned at 4{degrees}C also transferred to an independent 6{degrees}C time series at the spoilage-phase level, suggesting that shared functional spoilage programs are preserved despite temperature-dependent changes in spoilage rate. Cross-entropy ranking further identified pathway modules carrying time- and phase-informative signals across temperatures. Overall, this framework provides a probabilistic approach for linking metatranscriptomic functional dynamics to sensory spoilage progression, supporting shelf-life assessment beyond retrospective microbial enumeration.

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

GIST-CMTF: Goal-State Inference for Causal Minimal Tool Filtering in LLM Agents

arXiv:2606.16813v1 Announce Type: new Abstract: Tool-augmented LLM agents rely on runtime filtering to decide which tools should be visible at each step. Causal Minimal Tool Filtering (CMTF) reduces tool-choice confusion by exposing only the next causally necessary tool frontier, but it assumes that the user request has already been mapped to a symbolic goal state. In practice, requests such as "handle my appointment" or "take care of this email" may correspond to multiple possible goals. This creates wrong-goal execution, where an agent follows a valid causal tool path for an unintended objective. We introduce GIST-CMTF, a goal-state inference layer that predicts candidate symbolic goals over the same state-transition vocabulary used by CMTF, estimates ambiguity, and either applies CMTF or exposes clarification as a causal action that produces missing goal or state variables. We evaluate GIST-CMTF across seven model backends, six filtering methods, and 120 controlled tool-use tasks. GIST-CMTF achieves 97.0% task success, compared with 80.1% for top-goal CMTF and 82.9% for semantic-goal CMTF. It reduces wrong-goal execution from 19.4% under top-goal CMTF to 2.5%, while preserving the one-tool exposure of causal filtering and using substantially fewer tokens than all-tools exposure. These results suggest that reliable tool-augmented agents should validate goal state, not only tool relevance, before exposing external actions.

07.
arXiv (CS.CL) 2026-06-16

Oops, Wait: Discourse Tokens Matter in Reasoning Model

Recent studies suggest that even data-efficient training with ($\simeq$1K) reasoning trajectories can induce non-trivial reasoning capabilities in large language models through post-training. Such training corpora often contain iconic tokens such as "wait", "so", and "alternatively", which frequently appear in reasoning trajectories and may play a role in this process. This paper focuses on characterizing observable token-level patterns in post-training and a case study of how data-efficient supervised fine-tuning (SFT) differs from, and falls short of, large-scale post-training. To this end, we first identify tokens that correlate with correct answers along reasoning trajectories across models and training setups. We then focus on the distribution and (functional) roles of the "wait" token to primarily study the model trained in a data-efficient manner compared with the counterpart. Our study finds that discourse tokens are associated with correctness and a reasoning accuracy jump, even in data-efficient SFT. This suggests data-efficient SFT can partially reproduce discourse-token patterns to mimic meaningful reasoning behavior, but the patterns are less aligned with high-confidence answer transitions than those from large-scale post-training.

08.
arXiv (CS.CV) 2026-06-15

Orchestra-o1: Omnimodal Agent Orchestration

The recent success of agent swarms has shifted the paradigm of large language model (LLM)-based agents from single-agent workflows to multi-agent systems, highlighting the importance of agent orchestration for task decomposition and collaboration. However, existing orchestration frameworks are limited to a narrow set of modalities and struggle to generalize to more complex settings where heterogeneous modalities coexist and interact. This limitation becomes particularly pronounced in omnimodal scenarios, where tasks require the unified understanding and coordination of diverse inputs such as text, image, audio, and video. In this work, we propose Orchestra-o1, an omnimodal agent orchestration framework designed to support efficient agent collaboration across multiple modalities. Orchestra-o1 introduces a unified orchestration mechanism that enables modality-aware task decomposition, online sub-agent specialization, and parallel sub-task execution. This scalable design allows agent systems to effectively tackle complex real-world tasks involving heterogeneous information sources, surpassing the second-best approach by 10.3% accuracy on the OmniGAIA benchmark. Furthermore, we introduce decision-aligned group relative policy optimization (DA-GRPO), an efficient agentic reinforcement learning approach for training Orchestra-o1-8B, which also achieves state-of-the-art performance against all existing open-source omnimodal agents.

09.
arXiv (CS.LG) 2026-06-18

Stealthy World Model Manipulation via Data Poisoning

arXiv:2606.18697v1 Announce Type: new Abstract: Model-based learning agents use learned world models to predict future states, plan actions, and adapt to new environments. However, the process of updating world models from collected experience creates a training-time attack surface: adversarially poisoned fine-tuning trajectories can manipulate the learned dynamics and thereby corrupt downstream planning. In this paper, we propose SWAAP, the first two-stage data poisoning framework for learned world models. In the first stage, SWAAP identifies a harmful target world model that induces low-return behavior under planning while remaining close to clean dynamics, using first-order bilevel optimization enabled by a transition-gradient theorem. In the second stage, SWAAP realizes this target through stealth-constrained gradient matching, modifying only a limited fraction of fine-tuning transition targets so that the induced training gradients steer the victim model toward the adversarial target, while a prediction-error regularizer encourages the poisoned targets to remain close to the world model's natural approximation error. To assess attack stealthiness, we evaluate defenses and detectability across three stages of the poisoning pipeline: pre-training detection of poisoned transitions, robust training during fine-tuning, and test-time monitoring of the resulting world model. Across diverse continuous-control tasks, SWAAP causes substantial performance degradation while keeping poisoned transitions close to clean data and evading the evaluated non-adaptive residual/CUSUM/TRIM-style defenses. These results reveal a practical vulnerability in world-model adaptation pipelines and highlight the need for robustness methods that protect both world-model training data and learned dynamics.

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

LEAP: Layer-skipping Efficiency via Adaptive Progression for Vision Transformer Distillation

Vision Foundation Models (VFMs) with Vision Transformer (ViT) backbones, such as DINOv2, have become essential for downstream tasks like object recognition and semantic segmentation. The immense computational requirements of backbones often necessitate distillation into smaller architectures for edge deployment. Feature-based knowledge distillation (KD) often suffers from the teacher-student gap; the student struggles to imitate teacher's complex feature map due to its limited capacity. To mitigate this bottleneck, we propose LEAP: Layer-skipping Efficiency via Adaptive Progression, a training curriculum for ViT feature-based knowledge distillation. By utilizing the teacher's intermediate feature maps as a sequence of progressively more difficult targets, our curriculum allows the student to build a foundational representation before tackling higher-level abstractions. Our results demonstrate that this paradigm significantly accelerates convergence through adaptive difficulty selection across various student model sizes and dataset scales. With our curriculum, the LEAP-distilled ViT-S achieves 90.1% accuracy on ImageNet-100, a +12.24% improvement compared with baseline. On ImageNet-1K, LEAP achieves +3.84% and +7.75% improvement for the instance retrieval task on the Oxford and Paris datasets, respectively. Furthermore, the curriculum enables 25.1% savings in training FLOPs and 21% savings in training time on ImageNet-100 by implementing early-stopping for teacher inference during the initial stages of training. Code is available at https://github.com/KevinZ0217/LEAP

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

Context Compression Is Not One Thing: Readable Symbolic Re-expression vs. Coherent Summary at Matched Budget

We study context compression for multi-hop question answering with small language models. We propose Telegraph English, a readable symbolic format that rewrites retrieved passages into structured entity-relation statements, preserving reasoning evidence at lower token cost. In controlled experiments on MuSiQue, TwoWiki, and HotpotQA, Telegraph English outperforms three matched-budget compression baselines (character-level deletion, truncation, and random sub-sampling) on every dataset, with gains of 13 to 20 F1 percentage point. It also outperforms a coherent prose summary produced by the same encoder on the hardest dataset. A pre-registered depth-interaction hypothesis is null: the advantage does not grow with reasoning depth within datasets. We interpret these results as evidence that readable symbolic re-expression preserves entity content more densely than either natural language or coherent summarization at matched token budget.

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

Explosion and non-explosion in pure birth Crump–Mode–Jagers branching processes

arXiv:2601.06850v2 Announce Type: replace Abstract: In this short note, we provide an explicit sufficient condition for non-explosion of Crump–Mode–Jagers branching processes with pure birth reproduction. It shows that the standard sufficient condition for explosion, namely the convergence of the series of reciprocals of the birth rates, is – at least for rate sequences without excessive oscillations – remarkably close to being necessary. At the same time, it is not necessary in full generality: we construct a counterexample which also yields a general preferential attachment tree without fitness with an infinite path and no vertices of infinite degree, thereby answering an open question previously raised in the literature.

14.
arXiv (CS.AI) 2026-06-16

Discovering Symmetry Groups with Flow Matching

arXiv:2512.20043v3 Announce Type: replace Abstract: Symmetry is fundamental to understanding physical systems and can improve performance and sample efficiency in machine learning. Both pursuits require knowledge of the underlying symmetries in data, yet discovering these symmetries automatically is challenging. We propose LieFlow, a novel framework that reframes symmetry discovery as a distribution learning problem on Lie groups. Instead of searching for the symmetry generators, our approach operates directly in group space, modeling a symmetry distribution over a large hypothesis group $G$. The support of the learned distribution reveals the underlying symmetry group $H \subseteq G$. Unlike previous works, LieFlow can discover both continuous and discrete symmetries within a unified framework, without assuming a fixed Lie algebra basis or a specific distribution over the group elements. Experiments on synthetic 2D and 3D point clouds, ModelNet10 and a real-world MI-Motion dataset show that LieFlow accurately discovers continuous and discrete subgroups, significantly outperforming a state-of-the-art baseline, LieGAN, in identifying discrete symmetries.

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

GLACIER: A Multimodal Student-Teacher Foundation Model for Molecular Property Prediction

arXiv:2606.11382v1 Announce Type: new Abstract: Deep learning models facilitate the discovery of molecules with tailored properties among billions of candidate compounds. However, the computational burden to develop and deploy state-of-the-art models continuously increases, limiting their scalability. Most large-scale models are unimodal in nature and overlook the potential to leverage complementary molecular data modalities. To address these shortcomings, this paper introduces the Graph-Language Alignment for Chemical Inference and Exploration using Representations (GLACIER) model, a student-teacher framework that integrates molecular graphs, SMILES strings, and physicochemical descriptors to learn rich molecular embeddings. Our framework consists of three stages: (1) we pretrain three student encoders on 100,000 drug-like molecules: a message-passing neural network for molecular graphs, a transformer-based encoder for SMILES strings, and a multilayer perceptron for physicochemical descriptors, (2) we fuse these student modalities using a novel Finsler geometry-aware module, and (3) distill complementary knowledge from large teacher models, including MiniMol and MolFormer, into a single lightweight model via contrastive learning. We demonstrate that GLACIER is a robust framework that delivers high predictive performance and computational efficiency in complex molecular property prediction tasks. Our code is publicly available at https://github.com/eemokey/glacier.

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

An Empirical Analysis of Optimization Dynamics and Sparsity Boundaries in Large-Scale Pedestrian Attribute Recognition

Pedestrian Attribute Recognition (PAR) is critical for video surveillance, enabling forensic search and re-identification systems. Extreme class imbalance remains a fundamental obstacle when merging PETA and PA-100K into a 109,000-image composite corpus, where minority attributes have positive sample fractions below 1%. This causes standard BCE optimization to suppress rare traits, a phenomenon we term the majority negative class cheating trap. We present a systematic ablation of Multi-Label Focal Loss hyperparameters (alpha and gamma) on a ResNet-18 backbone. A calibrated configuration (alpha=0.50, gamma=2.0) achieves a Macro F1-score of 62.32%, matching BCE baseline while preserving superior hard-example mining and convergence dynamics. Our approach uses pure loss-function engineering with zero computational overhead for edge deployment. We identify the Sparsity Wall, a hard boundary where positive sample fractions below 0.1% make global loss reweighting ineffective, requiring instance-level intervention.

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

Understanding Truncated Positional Encodings for Graph Neural Networks

arXiv:2606.13671v1 Announce Type: new Abstract: Positional encodings (PEs) enhance the power of graph neural networks (GNNs), both theoretically and empirically. Two of the most popular families of PEs - spectral (e.g., Laplacian eigenspaces, effective resistance) and walk-based (polynomials of the adjacency matrix) - are theoretically equivalent in expressive power, with expressivity between the 1-WL and 3-WL tests. However, this equivalence assumes the GNN uses the "complete" version of these PEs, which requires $O(n^3)$ time and space complexity. Instead, practitioners commonly use truncated variants of these encodings, such as the first $k$ eigenspaces or powers of the adjacency matrix. However, the theoretical properties of these truncated PEs are unknown. In this work, we initiate the study of these truncated PEs. Theoretically, we show that, under truncation, several families of PEs are fundamentally different in expressive power. As a corollary, we show that truncated spectral PEs are no longer stronger than the 1-WL test. We also study a family of spectral PEs, the $k$-harmonic distances, to highlight the differences in expressive power of even closely related truncated PEs. Finally, we experimentally show that a mix of truncated PEs is preferable to any single family on real-world datasets.

19.
bioRxiv (Bioinfo) 2026-06-19

Accurate detection of tumor clonality and ongoing expansion mode from genomic data

Recent evidence shows that despite considerable effort, currently available algorithms for estimating intra-tumor heterogeneity (ITH) remain limited. We developed DECODE (Deciphering Cancer Origin from DNA Evolution), a novel mutation clustering method that incorporates the impact of sample-specific sequencing coverage and mutation calling biases. On synthetic data, DECODE outperformed existing methods across multiple clonality metrics and accurately detected and characterized the neutral tail in the site frequency spectrum (SFS), which encodes the tumor's ongoing expansion mode. In acute myeloid leukemia, accounting for the neutral tail enabled DECODE to yield more parsimonious clonal decompositions that align more closely with known subclonal dynamics that drive relapse. Applied to data from The Cancer Genome Atlas, DECODE not only detected a neutral SFS tail in most samples across tumor types but also uncovered a clinically meaningful link between ITH and survival in low-grade glioma. By jointly inferring clonality and expansion mode, DECODE provides two complementary and prognostically relevant readouts of tumor evolution from single tumor genomic samples.

20.
arXiv (CS.CL) 2026-06-12

MemRefine: LLM-Guided Compression for Long-Term Agent Memory

Large language model (LLM) agents are increasingly expected to operate over long-term interactions, where information from past dialogues must be preserved and recalled to support future tasks. However, as interactions accumulate, the memory store grows without bound and fills with redundant entries that inflate storage cost and degrade retrieval by crowding out the most useful evidence. Furthermore, this is especially limiting on resource-constrained platforms with hard memory budgets, motivating us to formulate storage-budgeted memory management, the task of keeping an already constructed memory store within a fixed budget while preserving information useful for future interactions. To this end, we then propose MemRefine, an LLM-guided framework that, since surface similarity poorly reflects factual value, uses similarity only to propose candidate pairs and defers delete, merge, and preserve decisions to an LLM judge based on factual content, iterating until the budget is met. Across multiple memory frameworks and long-term conversation benchmarks, MemRefine consistently meets target budgets while preserving downstream performance and outperforming rule-based baselines under tight budgets.

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

DifFRACT: Diffusion Feature Reconstruction and Attribution for Circuit Tracing

Mechanistic interpretability seeks to explain neural network behavior by decomposing model computations into interpretable features and circuits. While transcoder-based circuit tracing has recently enabled detailed causal analyses of large language models, multimodal diffusion transformers for image generation remain comparatively opaque. We still lack tools for understanding how semantic information propagates across denoising steps and how text and image representations interact within double-stream MM-DiT architectures. Existing methods provide only partial insight: attention maps expose a limited view of token interactions, while sparse autoencoders can discover interpretable features but do not directly reveal how these features are transformed and composed through nonlinear MLP layers. In this work, we extend transcoder-based circuit tracing to multimodal diffusion transformers. We train timestep-conditioned transcoders that faithfully approximate the input-output behavior of MLP sublayers in FLUX.1[schnell]. By replacing MLPs with transcoders and linearizing the remaining computation, we obtain exact feature-to-feature attribution and recover compact, interpretable circuits. Empirically, our transcoders match or slightly outperform sparse autoencoders on the sparsity-faithfulness tradeoff. The resulting circuits reveal mechanisms underlying attribute binding and cross-stream semantic propagation, and provide causal explanations for systematic generation errors. Moreover, circuit-guided interventions are substantially more precise and effective than standard SAE-based steering. Our results demonstrate that transcoder-based circuit analysis is feasible for state-of-the-art diffusion transformers and provides a powerful framework for understanding and controlling multimodal generative models. The code is available at https://github.com/Artalmaz31/DifFRACT

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

A Human-in-the-Loop Label Error Detection Framework Applied to Arabic-Script HTR Datasets

Despite recent advances, Handwritten Text Recognition (HTR) for Arabic-script languages still lags behind Latin-script HTR. Part of the problem is dataset quality. To help closing this gap, we propose a two-stage framework (CER-HV) for detecting label errors. Stage 1 (CER) is a Character-Error-Rate-based noise detector built on a Convolutional Recurrent Neural Network (CRNN) architecture. Stage 2 (HV) is the Human-In-The-Loop (HITL) Verification of noisy samples detected by the first stage. Applying the CER-HV framework on multiple Arabic-script datasets can identify samples with label errors including transcription, segmentation, orientation, and non-text content errors that can markedly affect HTR performance. These errors were identified by the first stage of the framework with up to 90percent (top-50) precision. We also show that our CRNN achieves state-of-the-art performance across five of the six evaluated datasets, reaching 8.46 percent Character Error Rate (CER) on KHATT (Arabic), 8.22 percent on PHTI (Pashto), 10.59 percent on Ajami, and 10.11% on Muharaf (Arabic), all without any data cleaning. We establish a new baseline of 11.3 percent CER on the PHTD (Persian) dataset. Applying CER-HV improves evaluation CER by up to 1.8 percentage points after dataset cleaning and retraining. Although our experiments focus on documents written in an Arabic-script language, the framework is general and can be applied to other text recognition datasets

23.
arXiv (CS.CL) 2026-06-17

EmoFSM: A Finite State Machine for Emotional Support Conversation

Emotional support conversation (ESC) aims to alleviate people's emotional distress through effective conversations. Although large language models (LLMs) have made remarkable progress in ESC, most of these studies may not define the diagram from a state-model perspective, thereby providing a suboptimal solution for long-term satisfaction. To address such an issue, we leverage the Finite State Machine (FSM) on LLMs, and propose a framework called EmoFSM. Our framework allows a single LLM to bootstrap the planning during ESC, and self-reason the seeker's emotion, support strategy, and the final response upon each conversation turn. Substantial experiments in ESC datasets suggest that EmoFSM outperforms many baselines, including direct inference, self-fine, chain of thought, finetuning, and externally supported methods, even those with many more parameters.

24.
arXiv (CS.CL) 2026-06-17

LLM Features Can Hurt GNNs: Concatenation Interference on Homophilous Graph Benchmarks

Adding LLM-generated node features to graph neural networks (GNNs) is widely reported to improve accuracy on standard benchmarks. We document a contrasting observation: when LLM features are introduced through pure input concatenation (rather than joint training, distillation, or prompt-conditioning), they can systematically degrade accuracy on the same homophilous benchmarks where end-to-end LLM pipelines succeed. With an MLP backbone on the Planetoid public split and bag-of-words original features, concatenating SBERT-encoded GPT-4o-mini TAPE features reduces PubMed test accuracy by -17.0 +/- 0.3 pp and Cora by -4.3 +/- 0.6 pp (CiteSeer -0.6 +/- 0.8 pp, within seed noise). The drop attenuates as we relax each condition (GCN / GCNII / GAT backbones, random splits, smaller encoders) and reverses on medium-homophily WikiCS (+4.4 pp) and ogbn-arxiv (+11.7 pp). To predict when concatenation helps versus hurts, we report a simple measure of LLM-alone discriminability, Delta_sig. Across 9 datasets Delta_sig correlates with the concatenation cost more strongly than homophily at point estimate (r^2 = 0.38 vs. 0.06; N=9, bootstrap CIs overlap). The bootstrap-best change-point is tau = 13.8 pp, and the rule "Delta_sig

25.
arXiv (CS.AI) 2026-06-11

On the Limits of LLM-as-Judge for Scientific Novelty Assessment

arXiv:2606.12071v1 Announce Type: cross Abstract: LLMs are increasingly used to generate and judge scientific ideas. This makes novelty evaluation a central problem. Full idea evaluation is difficult because it often requires judging a method, its feasibility, and its empirical promise. We therefore study a cleaner upstream object: the research question (RQ). RQ generation is a prerequisite for scientific ideation, and RQs can be compared against questions pursued in real papers. We introduce RQ-Bench, a benchmark built from recent arXiv papers. For each paper, we reconstruct author-anchored RQs from its cited background, gaps, and contributions. These RQs are not the only valid questions for the same background. They are author-anchored reference points for testing novelty judgments. We evaluate model-generated RQs with standalone LLM judging, comparative LLM judging, and human expert evaluation. LLM judges consistently rate model-generated RQs as highly novel, producing a novelty mirage; in comparative evaluations, this preference becomes even stronger. Domain experts, however, reach the opposite conclusion and prefer the author-anchored reference questions. We further find that many generated RQs are narrow or source-bound, a dimension that LLM judges often miss unless explicitly tested. Overall, the contradictory novelty evaluations between LLM judges and human experts raise a serious concern about the reliability of using LLMs to assess the scientific novelty of research questions.