Researchers organize the papers they collect into personal folder hierarchies in reference managers, and route each new paper into the folder where it belongs. This task differs from standard hierarchical text classification. A user's folder hierarchy is not a fixed, shared taxonomy but a private and evolving folksonomy whose folder meanings may be topical, shorthand, venue-based, or process-oriented, and are often defined by the papers already stored inside them. We formalize this setting as personalized hierarchical paper routing (PHPR): assigning an incoming paper to folders in a user-specific hierarchy without per-user training. We propose PaperRouter-Agent, a training-free LLM agent that grounds routing decisions in folder members rather than folder names alone. The agent first narrows the candidate hierarchy, retrieves folder-specific evidence, verifies fit by inspecting member papers, and incorporates similarity-gated feedback from past user rejections. A formative study on real personal libraries shows that PaperRouter-Agent raises overall Recall@1 from 0.39 to 0.61 and Recall@3 from 0.57 to 0.83, with the largest gains on organizational folders defined by metadata such as venue or year, where single-shot methods collapses (Recall@1 0.09 to 0.50). On the public LaMP-2 benchmark, the same approach improves accuracy from 44.5% to 51.5% (+9.0 macro-F1) over a single-shot baseline, while remaining low-cost for practical use.
Academic paper search is a core step in scientific research, and LLM-based search agents are emerging as a promising paradigm for iterative, intent-driven literature exploration. However, existing benchmarks are insufficient for systematically evaluating agentic academic search under realistic open literature environments. We propose ScholarQuest, a large-scale, taxonomy-guided benchmark for agentic academic paper search. ScholarQuest is constructed from over 1,000 computer science topics and four representative research intents, including method-oriented, setting-anchored, comparison-based, and scope-controlled queries. It further provides scalable answer construction and a shared retrieval backend ScholarBase for reproducible evaluation. Benchmarking results show that agentic methods outperform single-shot retrieval baselines, yet the best-performing agent only achieves 0.314 Recall@100 and 0.355 Recall@All, indicating substantial room for improvement. In addition, analyses of search efficiency, intent-level robustness, and failure cases further highlight the benchmark's ability to provide multi-dimensional evaluation signals for academic paper search agents.
Scientific literature search often requires more than retrieving papers from a single query: users' intents are underspecified, preference-dependent, and evolve through interaction. Existing search agents typically rely on fixed pipelines or implicit language-only reasoning, making their search strategies difficult to control, inspect, and refine. We introduce PaperPilot, a multi-turn literature search agent that frames scientific search as workflow induction. Given an anchor paper and a user query, PaperPilot constructs an executable DAG of paper-search operators, including keyword search, citation expansion, filtering, scoring, reranking, and evidence extraction. User feedback is then used to refine both the query and the workflow itself. We train PaperPilot with supervised workflow imitation and preference optimization over controlled workflow corruptions. Experiments show that PaperPilot-9B improves over the base Qwen3.5-9B toolset agent under multi-turn interaction, increasing Hit@5 from 58.0 to 77.0, MRR from 47.5 to 59.4, and nDCG@10 from 26.8 to 32.5, while reducing workflow execution errors from 9.5% to 0%. These results show that explicit, editable search workflows provide an effective and controllable interface for aligning literature search agents with complex scientific intent.
Research artifacts are distributed primarily as reader-oriented documents like PDFs. This creates a bottleneck for increasingly agent-assisted and agent-native research workflows, in which LLM agents need to infer fine-grained, task-relevant information from lengthy full documents, a process that is expensive, repetitive, and unstable at scale. We introduce Knows, a lightweight companion specification that binds structured claims, evidence, provenance, and verifiable relations to existing research artifacts in a form LLM agents can consume directly. Knows addresses the gap with a thin YAML sidecar (KnowsRecord) that coexists with the original PDF, requiring no changes to the publication itself, and validated by a deterministic schema linter. We evaluate Knows on 140 comprehension questions across 20 papers spanning 14 academic disciplines, comparing PDF-only, sidecar-only, and hybrid conditions across six LLM agents of varying capacity. Weak models (0.8B--2B parameters) improve from 19--25% to 47--67% accuracy (+29 to +42 percentage points) when reading sidecar instead of PDF, while consuming 29--86% fewer input tokens; an LLM-as-judge re-scoring confirms that weak-model sidecar accuracy (75--77%) approaches stronger-model PDF accuracy (78--83%). Beyond this controlled evaluation, a community sidecar hub at https://knows.academy/ has already indexed over ten thousand publications and continues to grow daily, providing independent evidence that the format is adoption-ready at scale.