ExecRetrieval: Measuring the Functional-Correctness Gap in Code-Embedding Retrieval

Embedding-based code retrieval is a core component of coding agents and retrieval-augmented code generation, where retrieving correct code matters more than retrieving lexically similar code. Existing code-retrieval benchmarks do not plant controlled, execution-verified single-edit variants of each query's canonical implementation in the search pool, leaving the question of whether embeddings can functionally discriminate correct from near-clone-but-incorrect code unanswered in a retrieval setting. Resolving this requires a benchmark whose search pool itself contains the relevant counterfactuals -- execution-verified buggy variants near-identical to each canonical -- so that a retriever's rank ordering can be directly tested for functional discrimination rather than topical or identity overlap. We introduce ExecRetrieval, 939 Python tasks each paired with one execution-verified canonical implementation and up to four execution-verified buggy distractors, each generated by a mechanical mutation making a single targeted edit, and evaluate 23 dense embedding configurations plus BM25 under provider-native invocation with paired McNemar tests and query-level bootstrap intervals. With near-clone counterfactuals in the pool, the top hosted system reaches exec@10 = 1.00 but only exec@1 = 0.331; rank-1 misses are paired buggy variants 91.5-99.4% of the time across the four leading systems, and the canonical scores below at least one of its four paired distractors in 67-78% of queries on the leading systems. The full dataset, execution oracle, embedding matrices, environment snapshot, and pairwise statistical tests are released at the URL in Appendix D.

Do Static Embeddings Add Value to Hybrid Dutch Retrieval?

Embedding benchmarks measure standalone model quality, but they do not establish whether a low-cost retriever contributes complementary ranking information once lexical and transformer-based retrieval are already combined. We present a controlled evaluation of this question across Dutch retrieval tasks from the Massive Text Embedding Benchmark for Dutch (MTEB-NL). Weighted reciprocal rank fusion (RRF) combines Best Matching 25 (BM25), Qwen/Qwen3-Embedding-0.6B (Qwen), and two multilingual static embedding models. Five datasets comprising 14,500 queries and 786,573 documents are scored exhaustively, and fusion weights are searched on a simplex in increments of 0.1. Ten-fold query-level cross-validation selects weights on nine folds and evaluates them on the held-out fold; paired bootstrap confidence intervals and sign-randomisation tests quantify the resulting differences. Fusion improves over the training-selected individual retriever by 0.061 mean reciprocal rank (MRR) on Dutch News, 0.029 on VABB, 0.004 on WebFAQ NL, and 0.025 on Wikipedia NL, while matching BM25 on Open Tender. All four positive differences remain distinguishable from zero after Holm correction. No unrestricted fold assigns positive weight to either static retriever: all 50 selections lie on the BM25-Qwen edge, and forcing a static contribution reduces effectiveness. Leave-one-dataset-out selection chooses equal BM25-Qwen weighting in every iteration and outperforms the cross-domain-selected individual retriever on every held-out task. The results support a two-retriever lexical-transformer architecture as a robust tested default across the evaluated Dutch tasks and show that standalone benchmark performance is insufficient to establish marginal value in hybrid retrieval.

SVC-Probe: A Framework for Evaluating Perturbation Generalization in Spatial Foundation-Model Embeddings

This work examines perturbation generalization in spatial foundation-model embeddings derived from fluorescence microscopy images. Although these models can discriminate drug conditions accurately, it remains unclear whether the learned representations reflect patterns consistent with expected perturbation axes that transfer across drugs. We introduce SVC-Probe, a perturbation-aware framework that combines Subcellular Embedding Atlas Stability, Mondrian Neighborhood Graphs, and a Foundation Model Perturbation Probe to assess embedding stability, neighborhood rewiring, and centroid prediction under drug treatment. Applied to the CM4AI MDA-MB-468 chemical-perturbation atlas comprising 462 antibody labels and SubCell 1536-dimensional embeddings, SVC-Probe demonstrates that 98.6% three-way condition accuracy does not correlate with reliable cross-drug prediction, with cosine similarity diminishing from 0.944 in-domain to 0.30 under leave-one-drug-out evaluation, constituting a two-drug stress test rather than a general benchmark. Null calibration indicates that raw residual-turnover coupling is largely influenced by generic embedding structure, whereas a drug-specific signal emerges under vorinostat and is consistent with chromatin-related reorganization. In contrast, the paclitaxel axis is not robustly reconstructed, likely due to sparse coverage of microtubule-associated proteins. Together, these results introduce and demonstrate a reusable diagnostic framework for stress-testing spatial virtual-cell representations and indicate that perturbation generalization may serve as a stricter and more informative benchmark than baseline condition discrimination.

Are Time-Series Foundation Models Ready for E-Nose Data? An Empirical Assessment of Their Embeddings

Inspired by advances in natural language processing and computer vision, "time-series foundation models" (TSFMs) have recently been introduced with the promise of strong generalization across diverse time-series tasks, including forecasting, classification, and anomaly detection, as well as across domains such as healthcare, climate science, and manufacturing. However, their utility for gas-sensing data remains largely unexplored. To address this gap, this paper systematically evaluates recent TSFMs on electronic nose (E-Nose) data. In particular, we investigate whether embeddings produced by representative TSFMs, including Chronos-2 and MOMENT, provide effective representations for gas identification and concentration prediction. Specifically, we show that fine-tuning is necessary to achieve satisfactory performance on E-Nose data, and fusing TSFM embeddings with representations learned by specialized predictive models can further improve the performance, suggesting both the potential and limitations of current TSFMs for gas-sensing applications.