ToolFlood: Beyond Selection -- Hiding Valid Tools from LLM Agents via Semantic Covering

Large language models deployed as agents over large tool catalogs face a critical tool-retrieval bottleneck. As embedding-based retrieval approaches rely on compact encoders that may under-capture specialized tool semantics, parametric tool retrieval addresses this by encoding each tool as a virtual token appended to the LLM vocabulary, fine-tuned in two stages (memorization then retrieval SFT) to use the LLM as a retriever, achieving strong performance on standard ToolBench retrieval benchmarks. Yet these benchmarks use verbose, fully-specified queries, and their evaluation applies constrained decoding that restricts outputs to valid token paths, neither reveals whether the model actually understands its tools. We introduce ToolSense, an open-source LLM-powered diagnostic framework that takes any tool catalog as input and automatically generates three benchmarks: a Realistic Retrieval Benchmark (RRB) with queries at three ambiguity tiers, an MCQ probing benchmark, and a QA probing benchmark. Applying ToolSense to ToolBench (~47k tools) and evaluating five parametric model training configurations reveals a knowledge-retrieval dissociation: on RRB queries, several configurations collapse by ~50-64 percentage points compared to fully-specified ToolBench benchmarks, falling below the embedding-model baseline. Additionally, despite strong retrieval performance, some models score near-random on factual probes, suggesting a knowledge-retrieval dissociation. We open-source the ToolSense framework and the ToolBench diagnostic benchmarks at https://github.com/SAP/toolsense.

Before an LLM agent can use a tool, a retrieval system must decide which candidate tools to show to the agent. How long should that shortlist be? Show too many tools and the model struggles to choose. Show too few and the correct tool may not appear. Most systems apply a fixed shortlist size to every query, but no standard metric exists to evaluate whether that size was appropriate. We treat the number of tools shown to an LLM agent as the object of evaluation and we apply Bits-over-Random (BoR), a chance-corrected metric that asks whether success at a given depth is better than what random selection would achieve at that same depth. We evaluate BoR across three tool-selection benchmarks, multiple scorers, and registries ranging from 20 to 3,251 tools. We then turn the same principle into a reinforcement learning (RL) reward for choosing tool shortlist depth per query. The RL agent is deliberately simple, serving as a probe of the metric rather than a proposed system. As the shortlist grows, random chance of including the correct tool rises, so the reward naturally decreases, reducing the need for an engineered depth penalty. On BFCL (370 tools), the learned policy nearly matches the coverage of showing 50 tools ($90.3\%$ vs $90.8\%$) while presenting only 7 on average. On ToolBench (3,251 tools), a fixed shortlist of 5 tools achieves higher aggregate coverage ($64.7\%$ vs $61.9\%$) but finds nothing on hard queries (correct tool ranked 6th-20th). The BoR agent finds $16.7\%$ on those same queries by searching deeper. Downstream validation with Claude Sonnet 4.6 indicates that shorter adaptive lists also improve the LLM's ability to select the right tool: $93.1\%$ versus $87.1\%$ when always shown 5 tools, widening to $76.8\%$ vs $60.9\%$ on medium-difficulty queries where the correct tool is present but not ranked first.

Large language model (LLM) agents increasingly rely on invoking external tools to complete real-world tasks. Tool retrieval, which selects a small task-relevant subset from a library of thousands of tools before the agent acts, has therefore become a critical component of LLM agent pipelines. However, existing retrievers either score each tool in isolation or assemble the tool set sequentially, so the joint utility of a candidate set is never evaluated as a whole. In this paper, we propose HYSET, short for HYperedge-based SEt-level Tool retrieval. Our contributions are threefold: (i) we formulate tool retrieval as query-conditioned hyperedge prediction on a tool co-invocation hypergraph, under which the tool set itself becomes the unit of scoring and most existing retrieval paradigms reduce to restricted instances; (ii) we capture size-dependent tool compatibility through cardinality-specific interactions; and (iii) we design HYSET as a pre-selection module requiring no modification to the downstream agent. Experiments on ToolBench demonstrate that HYSET consistently outperforms state-of-the-art baselines in both tool retrieval performance and end-to-end task success. Beyond the in-domain setting, HYSET further supports zero-shot/few-shot transfer, generalizing to held-out tools/categories and unseen domains with minimal supervision.