Scientific Document Retrieval

Scientific literature in materials physics is growing faster than researchers can manually inspect it, yet most retrieval tools rely on keyword matching or generic question answering that ignores domain-specific structure in PDF files. This paper presents an end-to-end pipeline that transforms arXiv superconductivity publications into a searchable corpus with structured metadata and retrieval-augmented question answering. The system combines thematic corpus construction, domain-aware extraction of materials and superconducting transition temperatures, and hybrid retrieval that merges dense chunk embeddings with structured publication fields. We test whether normalized domain attributes improve evidence retrieval and answer groundedness relative to lexical-only and dense text-only methods. Extraction is evaluated on a manually verified gold set of 59 superconducting materials, 46 of which have confirmed experimental critical temperatures. On the 33-material primary positive subset, domain-aware pair accuracy reaches 45.5% versus 9.1% for a regex baseline. Retrieval and generation are compared under a fixed language model (qwen2.5:7b-instruct) on a 100-question benchmark, varying only the retrieval mechanism: BM25, dense, hybrid, and hybrid with domain metadata. BM25 gives the highest source recall (Recall@5 of 47%), and adding extracted metadata to hybrid retrieval does not improve it (39% versus 41%), which we attribute to noise in the extracted fields; the main bottleneck is locating the supporting span inside a correctly retrieved paper. As a materials-informatics application, literature-derived temperatures are matched to an independent theoretical reference set: 200 materials appear in both sources, and 20 have a median experimental critical temperature above the theoretical value.

Many scientific advances come from cross-pollination, carrying an idea from one field over to a problem in another. Yet retrieving papers across fields remains underexplored, with existing benchmarks confined to a narrow range of fields. We study cross-pollination retrieval, the problem of identifying transferable ideas across research fields, and introduce CPR-Dataset, a large-scale dataset constructed by mining cross-topic citations. Its evaluation split CPR-eval has 1,300 queries in 26 fields, and its training split CPR-train has 10,573 pairs. On CPR-eval, the best of eleven existing retrievers reaches a Recall@10 of only 0.26, whereas an LLM reranker reaches 0.81. Standard contrastive fine-tuning on CPR-train raises Recall@10 to as high as 0.70. The gain carries over to domains held out from training and to analogy and reasoning-intensive retrieval. On AnaloBench, it raises nDCG@10 by up to 33% over the untrained retriever, whereas training on three existing retrieval datasets lowers it. On BRIGHT, it raises nDCG@10 by up to 70%, more than twice the gain from those datasets. CPR-Dataset is available at https://huggingface.co/CPR-Dataset, and the code at https://github.com/SeokwonJung-Jay/Cross-Pollination-Retrieval.

Scientific claims shared through social media platforms frequently reference research findings without explicitly linking to the corresponding scientific publications. Automatically retrieving the correct scientific source for such claims is a challenging multilingual retrieval problem involving semantic matching, paraphrasing, noisy social media text, and cross-domain language variation. In this work, we present a multilingual two-stage retrieval framework for CLEF 2026 CheckThat! Task 1 on Source Retrieval for Scientific Web Claims. Our system combines fine-tuned dense retrieval models with cross-encoder reranking for improving multilingual scientific document retrieval. We evaluate multiple transformer-based dense retrieval architectures including multilingual-E5, BGE, and Contriever under different metadata configurations. We further investigate multilingual joint training, retrieval depth analysis, metadata enrichment, and language balancing strategies for improving retrieval effectiveness. Experimental results demonstrate that metadata enrichment consistently improves retrieval effectiveness, while fine-tuned cross-encoder reranking provides additional gains in retrieval precision. Our final multilingual system achieves MRR@5 scores of 0.6222 for English, 0.5112 for German, and 0.6254 for French, with an overall average MRR@5 score of 0.5862.

Large language models (LLMs) are increasingly used for literature search and synthesis. However, it is unclear whether they retrieve accurate bibliographic information in environmental science. Therefore, we quantitatively compared the errors of widely used LLM platforms in retrieving references related to original articles from five leading environmental science journals (Energy and Environmental Science, Nature Sustainability, Nature Climate Change, Lancet Planetary Health, and Environmental Science and Technology) published in 2024 to 2025. Claude, ChatGPT, Grok, DeepSeek, Perplexity, and Gemini were used as the LLM platforms. LLMs retrieved 10 references for each of the 50 randomly selected original article using either the article's abstract or its full-text as prompt. The retrieved references were subject to a multimetric score ratio combining validity of bibliographic data, Google Scholar link, digital object identifier, Scopus Electronic Identifier and relevance score (cited by or being the index paper), and the proportion of complete fabrication that failed all metrics. Abstract-only prompt yielded significantly higher accuracy than full-text one. This advantage was confirmed in multilevel mixed-effect multivariable regression after adjusting for journal, platform, and output order. Source journal and the position of a reference within the output list were also independently associated with retrieval accuracy, with lower-listed references associated with lower accuracy. These findings suggest that LLM assisted literature retrieval in environmental science remains moderately accurate and overall inconsistent, varying significantly by platform, journal, prompt type, and output position. Abstract-based prompting, as task-aligned information compression, may outperform full-text one in literature retrieval. Caution should be used when generalizing our findings.

Biological literature retrieval systems are often developed and evaluated using broad biomedical corpora and general-purpose search tasks. However, many curated knowledge bases operate in narrower model-organism domains, where the literature is sparse and terminology is organism-specific. We introduce a retrieval benchmark from dictyBase for Dictyostelium, a model organism in cell and developmental biology. The benchmark consists of curator-generated biological queries linked to PubMed-indexed articles, together with structured gene annotations. Using this benchmark, we study three factors in niche biological retrieval: cross-encoder reranking, gene-aware query expansion, and abstract-only versus full-text retrieval. We report that reranking and gene-aware query expansion improve retrieval selectively: reranking is most useful when the model is well suited to biological evidence matching, whereas curated annotations help clarify compact biological queries by reducing vocabulary mismatch. Full-text chunks substantially improve retrieval when abstracts omit supporting evidence, increasing both candidate recall and top-rank performance, although these cases are harder than queries supported by abstracts. Data and code are publicly available at https://github.com/fulaibaowang/dictycite, and the benchmark dataset is additionally archived on Zenodo.

What makes great scientists great? Even as AI systems start to make progress on open problems, scientists remain far ahead of them at sensing which prior idea, buried in an ever-growing archive of research, a new problem needs. To study this skill, we draw on researchers who know firsthand which earlier work advanced their completed projects, with papers serving as pointers to the ideas within. Using our automated pipeline that makes author annotation scalable, we build ScholarCatalyst by having 184 lead authors of 207 recent computer science papers label which candidates did or could have advanced their project, each with a detailed rationale. We introduce a retrieval task with author-provided judgments: given an initial research question, retrieve these papers from only the literature available when the project began. Agentic search does no better than embedding retrieval (0.42 vs. 0.48 Recall@20) despite calling that same retriever as a tool. Even an agent built on Claude Fable 5.1, which may have seen the completed papers during training, reaches only 0.51 R@20. These results highlight the need for new training recipes that equip models with expert intuition for searching broad corpora. We envision ScholarCatalyst as a step toward scientific agents that can take a half-formed idea and point to the prior research it needs.

Scientific agents can retrieve relevant passages yet still lose functional order, mix evidence across sources, or state conclusions that exceed the retrieved record. We introduce PathAnchor, a bounded scientific reasoning system built on path-structured evidence workspaces. Instead of treating passages or extracted concepts as independent units, the system retrieves source-linked Material-Sensor-Signal-System trajectories that preserve role, direction, and the evidence supporting each transition. A controller uses three read-only tools to search paper-specific trajectories, trace paths across candidate sources, and open exact evidence before producing a claim-cited answer and an explicit evidence boundary. On 120 single- and cross-paper flexible-sensor questions, PathAnchor scores 82.6% and leads six evaluated systems. Under a matched controller, corpus, and six-call budget, replacing unordered concept graphs with path-structured records raises source recall from 61.3% to 82.9%, increases answers whose claims all cite opened evidence from 69.2% to 90.0%, and reduces tool calls. These results show that evidence organization affects retrieval and citation completeness under fixed agent resources.

Scientific literature search often begins with an open research problem rather than a known target paper or a fixed candidate set. We introduce INSPIRE, a benchmark for evaluating agents that search prior literature to make progress on solution-redacted research problems. Each instance pairs a research brief with a target-specific cutoff three months before a later paper and evaluates ranked outputs against graded cited antecedents from that paper's realized research lineage. Search proceeds over an open corpus, while the identity of the target paper and membership of its cited antecedents remain hidden from the agent. Beyond end-to-end retrieval quality, INSPIRE uses logged search trajectories to distinguish three coupled stages: resource exposure, whether useful antecedents are surfaced during search; selection, whether exposed antecedents are retained; and ranking, how effectively retained papers are ordered. Across 476 computer-science targets under a shared search interface and budget, the strongest evaluated agent achieves 0.284 nDCG@10. Results show that current agents more readily recover an isolated antecedent than assemble a broader portfolio of relevant prior work. The stagewise analysis identifies resource exposure as the largest observed bottleneck, with further losses in selection and ranking. We additionally construct replay-valid hindsight demonstrations and show that they improve held-out search without changing test-time information, establishing that the benchmark provides an actionable learning signal. INSPIRE therefore enables both end-to-end comparison and stage-resolved diagnosis in a setting where the agent must construct its own working criterion of relevance.

Agentic science envisions many autonomous agents investigating concurrently while building on a shared, evolving body of scientific knowledge. This requires a knowledge foundation that supports high-concurrency access, preserves traceable and reusable reasoning, and grows incrementally. We propose the Large Knowledge Model (LKM), a growing, agent-native knowledge foundation that provides a general representation of scientific knowledge across disciplines. LKM organizes the scientific literature into reasoning graphs, with claims as the core nodes and associated reasoning chains that make explicit how premises and evidence support conclusions. These source-grounded objects are persistent and addressable; cross-paper links organize them into aligned question, workflow, and evidence views. Newly extracted papers extend the foundation incrementally while preserving existing object identities. Building on this foundation, we develop an agent-native, reasoning-aware scientific retrieval system that retrieves claims together with their reasoning chains and sources, enabling agents to inspect and reuse the evidence underlying scientific conclusions. Across benchmarks, agents using LKM retrieve more evidence, cite more faithfully, and answer scientific questions more accurately: LKM nearly doubles the known supporting and contradicting evidence retrieved on SciFact-Open (818 versus 443 claim-paper pairs), reasoning graphs raise citation F1 on ScholarQABench by more than 5 points over the same retrieved papers, and LKM retrieval improves a fixed answering model by 9.3, 4.2, and 14.7 points over no retrieval on ChemBench, PubMedQA, and SciBench. LKM lays the foundation for a scientific ecosystem in which AI scientists not only recall accumulated knowledge but also extend it, returning new questions, workflows, and evidence to a memory that every subsequent investigation can build on.

We describe tus-nlp's Lit3R (Retrieve-Relate-Read) system for LitTraceQA, a shared task for literature-grounded question answering that requires systems to retrieve relevant papers, identify supporting evidence, and generate answers. Lit3R combines off-the-shelf retrieval, reranking, and large language model (LLM) components without task-specific training. The retriever iteratively combines BM25-based sparse and dense retrieval, cross-encoder reranking, and LLM-based verification, and complements retrieval based on the question with paper-to-paper expansion. The reader first identifies supporting evidence within individual papers and then synthesizes evidence across papers to produce the final answer and evidence trace. On the official test set, our system ranked 4th on the leaderboard. Our code is available at https://github.com/tus-ist-nlp/littraceqa.

For emerging scientific research domains, local Small Language Models (SLMs) are becoming more attractive, as they offer stronger privacy control and more stable deployment pipelines than Large Language Models. However, in practice, scientific question-answering on SLMs often operates under inevitable constraints: small literature collections, fragmented evidence, limited context window and reasoning abilities. We propose the Evidence-Grounded Typed Knowledge Graph (EGT-KG), a retrieval framework to improve information retrieval with local SLMs. We assessed three question-answering settings: a vanilla Retrieval-Augmented Generation (RAG) workflow and two EGT-KG workflows: an automatically generated relation schema (AS) and an expert-defined relation schema (ES). Our experiments were evaluated with a six-dimensional evaluation framework (S3CRF: Soundness, Correctness, Completeness, Conciseness, Relevance, Fluency) on a Biopolymer-bound Soil Composite literature benchmark, showing that EGT-KG outperforms the vanilla RAG method in most settings, with the best improvement from llama3:8b: a Final Score of 70.37 (+14.67%) and 68.82 (+12.14%) by AS/ES EGT-KG variants.

Retrieved scientific literature can serve as inspiration for both human and AI scientists. Inspiration can take different forms: prior work may directly suggest how to address a problem, or surface directions at different levels of abstraction---zooming out to a more general view or zooming in to a concrete realization. We introduce RATIO (Retrieval Across Typed Ideation Operations), a large-scale benchmark in which relevance is defined by three operations which we name ideation moves: Address retrieves potential approaches for stated problems, Broaden retrieves more general formulations, and Specify retrieves concrete instantiations. RATIO is constructed from millions of full-text scientific papers across CS literature via a general recipe that extends discourse-marker distant supervision---previously used only for classification---to corpus-scale retrieval, combined with extensive LLM and human vetting. Experiments show that operation-specific fine-tuning substantially boosts retrievers and LLM reranking helps further, but much room for improvement remains. Researchers blind to condition found the fine-tuned retriever's candidates more useful as inspirations. RATIO provides a scalable training and evaluation framework for retrieval components that support literature-grounded ideation, opening up new research avenues in scientific inspiration retrieval. We release full data, code, models, and annotations.

Scientific papers may relate by problem, method, result, or contribution, but document-level retrievers collapse these into a single similarity score without saying why they are related. Citation- and similarity-based retrieval alone also confines search to the neighbourhood of what is already known, whereas generative retrieval generates document identifiers directly, enabling the exploratory retrieval that scientific discovery depends on. We connect papers in a graph whose edges are typed by these four facets, derived from facet items and citation signals, and distil it into a generative retriever whose identifiers are the papers' own facet text. Two graph properties do not survive naive distillation. First, because every training pair is an edge, naive enumeration indexes just 84% of the corpus. Coverage-aware distillation makes every paper learnable through a reverse-neighbour fallback, a minimum-coverage threshold, and edge-importance weighting. Second, constrained decoding guarantees that every generated identifier is a valid paper, but not that the graph connects it to the query. Graph-weighted reciprocal rank fusion scales each candidate's rank term by its query-candidate edge weight, dropping unsupported ones. On LitWeave, our constructed corpus of 11,359 NLP papers, Graft recovers 91% of its graph teacher's Recall@20 with no nearest-neighbour index or encoder at inference, and outperforms the graph teacher on query papers outside the corpus. It reproduces the graph's own facet labels at 0.922 precision, so every returned paper arrives labelled with the facet that surfaced it rather than an opaque score.

Scientific literature is increasingly used as a knowledge source for language models, retrieval-augmented generation systems, and research assistants, but answering research questions from papers requires more than fluent generation. A reliable system must identify the relevant papers, locate the concrete evidence that supports the answer, and produce a response that is faithful to that evidence. We present LitTraceQA, a benchmark for literature-grounded question answering over scientific papers. Given a research question and a metadata pool of papers, a system must return three connected outputs: canonical paper identifiers, supporting evidence locations, and answers in one or more requested formats, including free-form text, multiple-choice answers, and structured tables. LitTraceQA targets evidence types common in scientific reading: tables, figures, text spans, equations or algorithms, and citation contexts. The public development split contains 55 examples, including 26 hidden-source single-paper questions and 29 multi-paper questions, and provides gold papers, evidence annotations, and answers for local validation. We also analyze a larger final annotation collection with 4,978 unique-question records over 4,859 unique gold papers. By evaluating paper retrieval, evidence grounding, and answer accuracy separately, LitTraceQA provides a testbed for scientific QA systems that produce verifiable answers rather than unsupported summaries.

We introduce SciRet, a compute-aware empirical study of retrieval-augmented generation for scientific question answering over CORD-19. Rather than proposing a new model, we evaluate a fixed scientific RAG pipeline across three corpus scales: 1,034 chunks (1K papers), 5,160 chunks (5K papers), and 15,480 chunks (15K papers). The pipeline combines sentence-window chunking, BM25, BGE-M3 dense retrieval, reciprocal rank fusion, optional cross-encoder reranking, and grounded answer generation. Across these settings, hybrid retrieval is more robust than either sparse-only or dense-only retrieval in our setting, reaching Recall@10 of 1.000 at 1K and 15K. In contrast, an MS MARCO-trained cross-encoder reranker reduces precision on the scientific corpus, suggesting that domain mismatch can outweigh the benefits of stronger query-passage interaction. Generation faithfulness measured with RAGAS increases with corpus scale in our setup. Retrieval evaluation uses pseudo-relevance labels derived from the hybrid system, so we treat the results as controlled comparative evidence rather than a benchmark claim. We release code, indexes, and evaluation outputs to support replication and follow-up studies.

Chemistry literature synthesis often requires assembling specific findings scattered across many publications, yet existing literature-search systems primarily return ranked document lists. As a result, scientists and AI agents need to locate relevant information, verify their provenance, and assemble cross-paper answers manually. We present AskChem, a claim-centered infrastructure for cross-paper chemistry search. AskChem changes the unit of retrieval from the paper to the provenance-carrying claim: each paper is converted into atomic, typed claims, each grounded by a source DOI and a verbatim quote or an explicit evidence locator. Over this shared claim store, AskChem exposes complementary structures for search and synthesis: a stabilized faceted taxonomy for hierarchical retrieval and browsing, an evidence graph linking claims through relations, and an exploratory living taxonomy that situates indexed papers under scientific principles. AskChem currently indexes 2.4M claims from 147K papers and provides a web interface, as well as REST, SDK, and MCP access for AI agents. On AskChem-Bench, grounding a GPT-5.5 reader in AskChem yields 100% resolvable DOIs, compared with 88.3% without retrieval, and the highest citation density among five tested systems. AskChem is live at https://askchem.org.

Scientific research involves complex information-seeking and reasoning workflows across heterogeneous sources. However, existing benchmarks primarily emphasize general-domain retrieval or static scientific question answering, and therefore fail to assess key capabilities required in realistic scientific research workflows. We introduce SciExplore, a benchmark designed to evaluate scientific information-seeking and reasoning capabilities of LLMs and agents. SciExplore comprises four task types covering 103 expert-curated tasks across more than ten scientific disciplines: scientific database navigation, ambiguous literature retrieval, missing reference completion, and cross-source structured knowledge synthesis, which probe progressively higher-level abilities from entity-level reasoning and document-level identification to evidence-level grounding and domain-level synthesis. We evaluate over ten state-of-the-art LLMs and autonomous agents on SciExplore, revealing substantial performance gaps with performance degrading sharply as task complexity increases and extremely low accuracy on the most challenging structured synthesis tasks. These results highlight significant limitations of current models and agents in realistic scientific information-seeking scenarios.

Scientists at European XFEL conduct experiments that generate very large and complex datasets. The subsequent data analysis is challenging as scientists must combine their domain expertise with facility- and software-specific knowledge scattered across documentation, tools, and support channels. To address this problem, we designed and evaluated an agentic AI system tailored to the scientists' needs and integrated with the high-performance computing environment of European XFEL. Using a design science research approach, we conducted a rapid literature review, a systematic evaluation of 16 AI tools, multiple interviews, a focus group, and a user study with experts at European XFEL to develop and evaluate two prototypes. Our study identifies key knowledge challenges in scientific data analysis, derives requirements for an AI agent that supports knowledge retrieval and source code generation, and proposes design recommendations for a specialized system adaptable to the evolving AI tool landscape. These findings provide guidance for developing maintainable AI support in highly specialized scientific environments.

LongEval-Sci evaluates scientific retrieval under collection change, where a system should be effective on the current corpus and remain usable as documents accumulate over time. This paper reports both official Task 1 results and development diagnostics for LongEval-Sci 2026. We compare the official PyTerrier BM25 and Qwen3 dense baselines with full-text BM25, additive and router variants, temporal full-text retrieval, temporal+citation retrieval, RM3 query expansion, cross-encoder reranking, and reciprocal rank fusion (RRF). In the official DCTR evaluation, the temporalized full-text runs are our strongest submissions: FT BM25+temporal and FT BM25+temporal+citation obtain the best ARP on all three snapshots (0.285, 0.267, and 0.180 nDCG@10) and reduce snapshot-3 relative change from 0.481 for the BM25 pivot to 0.368. Citation features match the temporal-only variant but do not provide a measurable additional gain in the official summary. Our internal snapshot-1 diagnostics show a complementary pattern: full-text BM25 is the strongest single development retriever (DCTR nDCG@10 = 0.3302, MAP = 0.2853), RRF gives the best deep recall (Recall@1000 = 0.9667), and some uncalibrated overlays can sharply degrade top-rank quality. We therefore conclude that full-text retrieval is the strongest foundation, temporal integration can improve official longitudinal effectiveness when applied to that foundation, and citation evidence still requires cleaner ablation and calibration. Beyond ranking, we also report a qualitative weekly IR-system update-monitoring analysis based on ingestion velocity and stale-coverage drift.

Meta-analysis is a demanding form of evidence synthesis that combines literature retrieval, PI/ECO-guided study selection, and statistical aggregation. Its structured, verifiable workflow makes it an ideal substrate for evaluating systematic scientific reasoning, yet existing benchmarks lack ground truth across the full retrieval-screening-synthesis pipeline. We introduce MetaSyn, a dataset of 442 expert-curated meta-analyses from Nature Portfolio journals. Each entry pairs a research question with PI/ECO criteria, a retrieval corpus of 140k PubMed articles, verified positive studies, hard negatives that are topically similar but PI/ECO-ineligible, and complete search strategies and date bounds. Benchmarking twelve pipeline configurations (nine RAG variants and a protocol-driven agent) reveals a critical screening bottleneck: despite a retrieval ceiling of 90.9% recall at K=200, no system recovers more than 52.7% of ground-truth included literature. Current LLMs fail to reliably separate eligible studies from PI/ECO-failing distractors in pools of comparable topical relevance. Stage-attributed metrics capture where systems succeed and fail; a single end-to-end score does not.

The exponential growth of global academic output has confronted researchers and AI agents with an unprecedented information explosion,'' where fragmented and unstructured knowledge organization impedes deep interdisciplinary integration. Current academic retrieval tools predominantly rely on superficial keyword matching or vector-space semantic retrieval, which lack the topological reasoning capabilities required to navigate complex logical connections. Agentic deep-research-based frameworks are often prone to logical hallucinations and consuming high inference costs. To bridge this gap, in this report, we introduce SciAtlas, a large-scale, multi-disciplinary, heterogeneous academic resource knowledge graph designed as a panoramic scientific evolution network. By integrating over 43M papers from 26 disciplines, and a total of 157M entities and 3B triplets, SciAtlas provides a structured topological cognitive substrate that dismantles disciplinary barriers and furnishes AI agents with a global perspective. Furthermore, we develop a neuro-symbolic retrieval algorithm featuring tri-path collaborative recall and graph reranking, achieving a seamless transition from simple semantic matching to deterministic association discovery. We also present key application directions of SciAtlas, including literature review, automated research trend synthesis, idea positioning, and academic trajectory exploration, to demonstrate that SciAtlas can serve as an effective cognitive map'' to empower the full loop of automated scientific research while significantly reducing reasoning costs. We have released the interfaces for KG retrieval and various downstream tasks in our GitHub repo.

Vector search and retrieval-augmented generation (RAG) rest on the assumption that cosine similarity between text embeddings reflects conceptual relatedness. We measure where this assumption breaks. We build an augmented citation graph over 3.58M scientific papers and partition it via Leiden CPM at two granularities: sub-field (L1) and research-agenda (L2, hierarchical inside each L1). Four state-of-the-art embeddings (Gemini, Qwen3-8B, Qwen3-0.6B, SPECTER2) clear the L1 bar reasonably (45-52% top-10 same-rate) but stop working at L2: only 15-21% of top-10 neighbors share the query's research agenda. In absolute terms, 8 of every 10 retrieved papers are off-agenda. The failure is universal across eight scientific domains and all four models; SPECTER2, despite its citation-based contrastive training, is the weakest. As a diagnostic probe, we test whether the same augmented graph also functions as a retrieval signal: a deliberately simple citation-count rerank reaches 57.7% top-1 L2 on top of LLM-expanded Boolean retrieval and 59.6% on top of plain BM25, on 80 curated agenda queries -- about 9 points above the best cosine retriever (Gemini, 50.6%) and 20 points above BM25 alone (39.3%). The probe isolates a slice of the agenda-matching signal the graph carries but the embeddings miss, connecting recent theoretical limits on single-vector retrieval to a concrete failure mode of scientific RAG.

Autonomous scientific research is significantly advanced thanks to the development of AI agents. One key step in this process is finding the right scientific literature, whether to explore existing knowledge for a research problem, or to acquire evidence for verifying assumptions and supporting claims. To assess AI agents' capability in driving this process, we present AutoResearchBench, a dedicated benchmark for autonomous scientific literature discovery. AutoResearchBench consists of two complementary task types: (1) Deep Research, which requires tracking down a specific target paper through a progressive, multi-step probing process, and (2) Wide Research, which requires comprehensively collecting a set of papers satisfying given conditions. Compared to previous benchmarks on agentic web browsing, AutoResearchBench is distinguished along three dimensions: it is research-oriented, calling for in-depth comprehension of scientific concepts; literature-focused, demanding fine-grained utilization of detailed information; and open-ended, involving an unknown number of qualified papers and thus requiring deliberate reasoning and search throughout. These properties make AutoResearchBench uniquely suited for evaluating autonomous research capabilities, and extraordinarily challenging. Even the most powerful LLMs, despite having largely conquered general agentic web-browsing benchmarks such as BrowseComp, achieve only 9.39% accuracy on Deep Research and 9.31% IoU on Wide Research, while many other strong baselines fall below 5%. We publicly release the dataset and evaluation pipeline to facilitate future research in this direction. We publicly release the dataset, evaluation pipeline, and code at https://github.com/CherYou/AutoResearchBench.

Many recent document embedding models are trained on document-as-image representations, embedding rendered pages as images rather than the underlying source. Meanwhile, existing benchmarks for scientific document retrieval, such as ArXivQA and ViDoRe, treat documents as images of pages, implicitly favoring such representations. In this work, we argue that this paradigm is not well-suited for text-rich multimodal scientific documents, where critical evidence is distributed across structured sources, including text, tables, and figures. To study this setting, we introduce ArXivDoc, a new benchmark constructed from the underlying LaTeX sources of scientific papers. Unlike PDF or image-based representations, LaTeX provides direct access to structured elements (e.g., sections, tables, figures, equations), enabling controlled query construction grounded in specific evidence types. We systematically compare text-only, image-based, and multimodal representations across both single-vector and multi-vector retrieval models. Our results show that: (1) document-as-image representations are consistently suboptimal, especially as document length increases; (2) text-based representations are most effective, even for figure-based queries, by leveraging captions and surrounding context; and (3) interleaved text+image representations outperform document-as-image approaches without requiring specialized training.

Retrieving procedure-oriented evidence from materials science papers is difficult because key synthesis details are often scattered across long, context-heavy documents and are not well captured by paragraph-only dense retrieval. We present RECIPER, a dual-view retrieval pipeline that indexes both paragraph-level context and compact large language model-extracted procedural summaries, then combines the two candidate streams with lightweight lexical reranking. Across four dense retrieval backbones, RECIPER consistently improves early-rank retrieval over paragraph-only dense retrieval, achieving average gains of +3.73 in Recall@1, +2.85 in nDCG@10, and +3.13 in MRR. With BGE-large-en-v1.5, it reaches 86.82%, 97.07%, and 97.85% on Recall@1, Recall@5, and Recall@10, respectively. We further observe improved downstream question answering under automatic metrics, suggesting that procedural summaries can serve as a useful complementary retrieval signal for procedure-oriented materials question answering. Code and data are available at https://github.com/ReaganWu/RECIPER.

Scientific discovery requires new ideas to be situated within an ever-expanding landscape of existing knowledge. An emerging challenge is how to identify conceptually relevant prior work from rapidly growing literature, and assess how a new idea differentiates from existing research. Current embedding approaches typically conflate distinct conceptual aspects into single representations and cannot support fine-grained retrieval; meanwhile, LLM-based evaluators are subject to sycophancy biases, failing to provide discriminative novelty assessment. We introduce the Ideation Space, a structured representation that decomposes scientific knowledge into three distinct dimensions learned through contrastive training. Our framework enables principled measurement of conceptual distance between ideas and modeling of ideation transitions that capture the logical connections within an idea. Building upon this representation, we propose a Hierarchical Sub-Space Retrieval framework for efficient, targeted literature retrieval, and a Decomposed Novelty Assessment algorithm that identifies which aspects of an idea are novel. Extensive experiments demonstrate substantial improvements, achieving Recall@30 of 0.329 (16.7% over the strongest baseline), and novelty assessment achieves promising correlation with expert judgments, outperforming all open-source LLM baselines up to 70B.

Scientific paper retrieval, particularly framed as document-to-document retrieval, aims to identify relevant papers in response to a long-form query paper, rather than a short query string. Previous approaches to this task have largely focused on abstracts, embedding them into dense vectors as surrogates for full documents and calculating similarity between them. Yet, abstracts offer only sparse and high-level summaries, and such methods primarily optimize one-to-one similarity, overlooking the dynamic relations that emerge across relevant papers during the retrieval process. To address this, we propose Chain of Retrieval (CoR), a novel iterative framework for full-paper retrieval. Specifically, CoR decomposes each query paper into multiple aspect-specific views, matches them against segmented candidate papers, and iteratively expands the search by promoting top-ranked results as new queries, thereby forming a tree-structured retrieval process. The resulting retrieval tree is then aggregated in a post-order manner: descendants are first combined at the query level, then recursively merged with their parent nodes, to capture hierarchical relations across iterations. To validate this, we present SciFullBench, a large-scale benchmark providing both complete and segmented contexts of full papers for queries and candidates, and results show that CoR significantly outperforms existing retrieval baselines. Our code and dataset is available at https://github.com/psw0021/Chain-of-Retrieval-Official.