#01Aug 25, 2026
cs.LG
BioKERN: Biological Kernel Regularization for Histology-to-Transcriptomics Neighborhood Retrieval
Seungik Cho, Betul Orcan-Ekmekci
Spatially resolved biology requires representations that preserve biological neighborhood structure rather than only exact cross-modal correspondences. Existing histology--transcriptomics objectives can emphasize instance-level matching even when non-paired spots share molecular or spatial context. We introduce BioKERN, a multimodal spatial representation-learning framework that incorporates biological structure as an explicit, learnable inductive bias. BioKERN constructs a training-time biological kernel by combining transcriptomic similarity and spatial proximity, then uses it to provide graded neighborhood supervision and regularize embedding geometry. Evaluation uses a fixed, model-independent biological neighborhood definition shared by all methods. Across Mouse Brain Visium and Human Liver GSE240429, BioKERN consistently improves biological-neighborhood retrieval over BLEEP in both single- and multi-scale settings. Controlled shared-architecture experiments show that most of the improvement arises from biological-kernel regularization rather than increased model capacity. These results support explicit biological geometry as an interpretable inductive bias for multimodal learning in spatial biology.
#02Aug 25, 2026
stat.ML
What FID Hides: Detecting, Ranking, and Diagnosing Deviations in Generative Evaluation
Hao Chen
Generative models are commonly ranked by Fréchet Inception Distance (FID) and Kernel Inception Distance (KID), yet FID's first-two-moment summary can miss distributional differences, and a reported scalar gap alone is not a calibrated test against sampling variation. FID's moment restriction has concrete consequences: on ImageNet, visually unrecognizable images optimized only to match the reference Inception mean and covariance obtain FID $24.7$ versus $58.6$ for held-out real images (lower is better). Moreover, FID and KID are scalar discrepancies that are unchanged when the two samples are exchanged and therefore do not encode the direction of a dispersion change: under-dispersion, as can occur in mode collapse, versus over-dispersion. We introduce \textbf{ZID} (\emph{Z-resolved Integrated Diagnostic}), which combines six standardized location- and dispersion-sensitive arms from a rank graph (RISE) and Gaussian kernels (GPK at two bandwidths). Rather than asking one scalar to serve incompatible roles, ZID reports three linked outputs: an index for ranking departure magnitude, a permutation $p$-value for testing distributional equality, and a signed dispersion readout for diagnosis. In controlled experiments, ZID detects a broad range of departures, and its score tracks increasing severity along the corresponding sweeps, including cases in which FID is flat or reversed. On DiT-XL/2 and SiT-XL/2 guidance sweeps, ZID detects departure from real data, and its signed readout labels the high-guidance diversity collapse as under-dispersion.
#03Aug 25, 2026
cs.AI
Constrained Entity Selection under Partial Knowledge for LLM-Based Knowledge Graph QA
Emanuel Kitzelmann
Large language models are increasingly used for knowledge graph question answering (KGQA), but can fail to correctly ground answers in the underlying graph. Current approaches to LLM-based KGQA either rely on full semantic parsing into executable queries such as SPARQL, which is brittle in practice due to complex schemas or incompleteness of real-world KGs, or on LLM-reasoning and answer generation over KGs, which can be more robust but lacks formal guarantees. In this work, we study a complementary setting in which \emph{candidate} answers are generated by an LLM-based system and subsequently verified using lightweight symbolic constraints derived from the question. We introduce \emph{Constrained Entity Selection under Partial Knowledge (CES-PK)}, a problem formulation that focuses on eliminating invalid answers and providing symbolic support for valid ones without requiring construction of executable logical forms. To account for incomplete KGs, we employ a three-valued constraint semantics (\emph{satisfied, violated, unknown}) that avoids incorrect rejections under open-world assumptions. To demonstrate the effects of our method, we instantiate this framework over the Hetionet biomedical knowledge graph and evaluate the impact of type, relation, and exclusion constraints. Experiments show that precision improves by filtering invalid candidates, while recall is preserved due to retaining candidates whose constraints are not explicitly violated. Satisfied constraints provide additional positive symbolic evidence to rank remaining candidates.
#04Aug 25, 2026
cs.AI
CAFE: Self-Improving Search Agents Need Co-Evolving Feedback
Boyang Liu, Senjie Jin, Peixin Wang and 15 more
Outcome-supervised search agents learn when and how to retrieve evidence, but terminal rewards neither localize intermediate errors nor redirect an ongoing trajectory before those errors compound. Treating corrective feedback as a learned in-trajectory intervention couples the two roles: the agent must decide when to request and use feedback, while the critic must infer useful corrections from outcome-confounded rollouts whose failure patterns shift as the agent improves. We introduce CAFE (Coupled Agent--Feedback Evolution), a framework in which a shared-parameter model alternates between search-agent and critic roles. CAFE initializes feedback-conditioned recovery from trajectories built around the base agent's own failures, then couples online and offline optimization. During online RL, a comparative feedback estimate uses a prompt-level call--skip success gap to shape request returns, while feedback-aware advantage shaping reweights token advantages before and after feedback. Offline, rollout-derived preference optimization learns feedback from matched successful and unsuccessful trajectories. On seven agentic search benchmarks, CAFE outperforms the evaluated RL-based search agents on average, retains its gains across all six out-of-domain benchmarks, and reduces answer-level hallucinations. One-sided ablations show that improving only the agent or only the critic eventually plateaus, whereas alternating the two updates continues to improve performance. These findings suggest that a self-improving search agent needs feedback that co-evolves with the policy it guides.
#05Aug 25, 2026
cs.LG
A Geometric Theory of Robust Fairness Audits
Binita Maity
Neighborhood-based fairness audits evaluate individual fairness by comparing predictions among similar individuals in feature space. Despite their widespread use, little is known about the robustness of the auditing procedure itself. Because these audits rely on nearest neighbor relationships, small perturbations in feature space can alter local neighborhoods and produce different fairness assessments even when model predictions remain unchanged. We develop a geometric framework for analyzing the robustness of neighborhood-based fairness audits under bounded perturbations. Our analysis establishes sufficient conditions for neighborhood invariance, quantifies how neighborhood replacement propagates to audit instability, and introduces audit volatility, a measure of the expected sensitivity of fairness audits under repeated perturbations. Experiments on benchmark datasets support the theoretical analysis and show that the proposed framework explains the observed stability of neighborhood-based fairness audits.