Scientific QA

Large language models (LLMs) should abstain from scientific multiple-choice questions when no option is valid, but frequent abstention alone does not demonstrate sensitivity to answer availability. We introduce ArcticQA, a dataset of 194 questions derived from primary Arctic research, with automated checks of answer support and distractor contradiction against source evidence. We further develop ArcticAbstain, a paired benchmark comparing answer-present and answer-absent conditions, with the correct answer replaced by a distractor in the latter and an explicit abstention option in both. We evaluate eight models from the Gemini, Claude, and ChatGPT families at high reasoning effort, with three trials per condition, yielding 9,312 recorded responses. Answer-present abstention rates range from 0.0% to 63.0%, whereas replacing the correct answer increases abstention by 5.05 percentage points on average. These findings highlight substantial baseline differences and the need to evaluate abstention frequency and responsiveness jointly. The dataset and benchmark are available at https://github.com/BenWilcox8/arctic-qa.

Redpine Science gives models and agents a single access point to a wide range of peer-reviewed literature, queried directly through the Model Context Protocol (MCP) and an API. This report evaluates Redpine Science on two levels: the relevance of the retrieved chunks, and a model's answer when it has access to Redpine Science compared to web search. Both public and expert-validated benchmarks are used. Public benchmarks are a widely accepted way to test model development and are comparable across labs, but risk saturation and memorization. To address this, we complement them with an expert-validated question set. In total, this report presents four evaluations. On ScholarQABench SciFact, the public answer-quality benchmark reported here, an agent with Redpine Science answers 94.4% of claims correctly against 87.6% with no retrieval. On the expert-validated question set, an agent with Redpine Science states 80.1% of the required claims against 70.2% for an agent restricted to web search. On the 668 queries of a public retrieval benchmark whose gold paper Redpine holds, stripped of any model reasoning, Redpine Science places the correct source paper in its top ten results for 83.1% of queries (Recall@10), against 79.3% for the benchmark's creator. A blinded expert relevance panel places Redpine Science's Precision@5 at 75.2% against 39.8% for the PubMed search tool. We release the expert-validated question set and instructions to reproduce every headline result above, at https://github.com/redpine-ai/benchmarks.

Scientific language models often access literature through untyped text chunks, which fragment the functional and evidential structure required for mechanism-rich questions. We introduce an evidence-grounded mechanism knowledge substrate that organizes scientific literature into provenance-linked evidence units, role-typed entities, and directed mechanism paths. We instantiate it as MS$^3$, a Material-Sensor-Signal-System schema for conductive-fiber flexible sensors, over 13,689 papers, 131,083 evidence items, and 26,648 mechanism objects. On in-domain and coverage-shift question-answering benchmarks, we compare closed-book generation, Web search, Raw-PDF RAG, and MS$^3$ retrieval across ten language models. MS$^3$ improves macro-averaged scientific correctness. It also improves citation entailment and answer completeness. These results support mechanism substrates as a reliable representation layer for scientific language models and motivate a source-repair workflow in which insufficient MS$^3$ evidence triggers targeted retrieval from its linked papers rather than assuming that a user has already supplied the correct PDFs.

Bengali secondary education lacks curriculum-grounded benchmarks for STEM question-solving, and general-purpose language models struggle with the precise terminology, unit conventions, and derivations that physics problems demand. We introduce PhysicsMate, a benchmark of 1834 question-answer pairs built from the National Curriculum and Textbook Board (NCTB) Grade 9-10 physics syllabus and grounded in a multi-relational knowledge graph of 1760 nodes and 2600 edges across ten ontological types. We Low-Rank Adapt at 0.6B, 1.7B, and 4B parameters, with a unified recipe and demonstrate a significant increase in closed-book accuracy in all scales (+5.5, +15.0, and +23.3 percentage points). A node-type analysis shows that the most benefited by adaptation is the structured curricular knowledge, which consists of physical quantities and named laws, while the least benefited is the loosely specified entity-level knowledge. The 4B model has been adapted and quantized to a small offline binary that can be used for local inference in resource constrained environments and offers a viable path to curriculum aligned physics support in environments with limited connectivity and hardware.

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.

Final-answer accuracy does not reveal whether a scientific-search agent failed to encounter a target paper, attempt to inspect it, or return an accepted answer after inspection. We introduce decision checkpoints that record observations and tool actions without benchmark labels during inference, then join target identities and evaluator labels to assign outcome categories from recorded events. Across five conditions on 540 answerable AutoResearchBench Deep questions in a fixed, target-enriched environment, keyword search achieves 24.6% accuracy, compared with 17.8% for raw search. The keyword condition has fewer incorrect answers with neither target exposure nor inspection, but more incorrect answers after the target is exposed and left uninspected. Compared with keyword search, read-first has 27.4% more recorded evidence-search calls. Target inspection attempts occur on 199 questions under read-first and 191 under keyword search; both conditions achieve 24.6% accuracy. The checkpoint protocol makes these question-level differences explicit, distinguishing target exposure and inspection from aggregate accuracy and total tool use.

Retrieval-Augmented Generation (RAG) is now the standard way to ground Large Language Models (LLMs) in external knowledge, yet the design space of retrieval pipelines is large and the trade-offs between variants are not well understood, especially on domain-specific corpora at realistic scale. In this work, we present a controlled comparison of six retrieval strategies for scientific question answering: (i) classic top-k dense retrieval, (ii) LLM-based query rephrasing, (iii) query rephrasing followed by LLM-based reranking, (iv) multi-query fusion via Reciprocal Rank Fusion (RRF), (v) an agentic tool-call pipeline in which the generator decides for itself whether to retrieve, and (vi) late-interaction retrieval with ColBERTv2. All six pipelines share the same generator (Meta-Llama/Llama-3.1-8B-Instruct), prompt, and evaluation protocol; the five single-vector pipelines additionally share SPECTER2 embeddings and a Chroma vector store; and all six retrieve from the full corpus of 463,971 arXiv papers dated 2024-2025. To support reproducible, large-scale evaluation, we also release a synthetic question dataset of 19,484 problem-statement and methodology questions generated by Llama-3.1-8B-Instruct from a random sample of 10,000 papers across academic domains (query generation succeeded for 9,742 of them), and every strategy is evaluated on this same query set. We describe the architecture and implementation of each pipeline, release the code and the synthetic question dataset, and evaluate each strategy with an LLM-as-a-judge protocol along multiple quality dimensions, together with direct gold-paper retrieval metrics. The result is an open testbed for studying the cost and quality trade-offs of RAG design choices on a research-literature corpus, and a basis for future work on faithfulness, retrieval robustness, and agentic retrieval.

Agentic tasks require a large language model to interact with the world, navigating information and gathering evidence across multiple steps with restricted resources. Due to this complexity, agentic task failures arise from various sources, and pinpointing these failure causes is essential to diagnose and improve agentic systems. Existing benchmarks, however, tend to focus on a single leaderboard score, leaving the underlying failure modes opaque. To fill this gap, we introduce AgentHop, a diagnostic benchmark of 1,011 multiple-choice questions paired with a controlled seven-tool sandbox under fixed token, turn, and tool-call constraints. AgentHop reveals model vulnerabilities by dissecting a single accuracy score along four axes of agent operation: retrieval, synthesis, tool-call, and resource management. Across 19 models, we find that behavior clusters by model family, with tool-call signatures revealing distinct family fingerprints: GPT models commit early, Anthropic and GLM checkpoints verify before committing, DeepSeek and Kimi over-search, and Gemini-3 Pro stays balanced. Decomposed axes further expose within-family structure: Claude Opus 4.6 and Sonnet 4.6 land within one accuracy point yet diverge on retrieval-versus-synthesis emphasis, with Opus retrieving more and Sonnet synthesizing better. We release the full benchmark set and the harness to support diagnostic agent benchmarking.

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 our system for LitTraceQA (GroundLM @ EMNLP 2026): given a research question, retrieve the relevant papers from a pool of 27,487, cite the page and the table or figure where the answer lives, and answer in a requested format. Our main finding is that evidence grounding is limited by retrieval, not by reading. The page selector put the annotator's page, which we call the gold page, in front of the model that locates evidence only about half the time (52.6% gold-page recall), while that model, given the page, cited the right one in 45 of the 48 locators it emitted (94%). When the page was missing it rarely said so: of 45 such cases it returned nothing 14 times, a wrong page 24 times, and a correct page 7 times, so the pipeline failed quietly almost twice as often as it failed visibly. Since the failure was that the right page was never shown, the fix is to stop choosing: each retrieved paper fits in the model's context, so we show it whole. Page ranking survives only as a fallback inside papers too long to fit, which no test-split paper was, and gold-page recall reaches 100% on the papers we can parse. Separately, questions that identify their target by position rather than content, such as "the first author of the 24th reference", are served by parsing rather than retrieval: we resolve the bibliography into an addressable list, which also supplies identifiers the evidence metric scores. The final system scores 0.762 paper $F_1$, 0.441 evidence $F_1$ and 0.920 multiple-choice accuracy on the held-out test split. Because the pipeline depends on a closed model without seed control, we release a harness that verifies the paper's central claims against committed artifacts.

Domain-specialized language models are widely used for scientific question answering, but stronger general-purpose systems raise a sharper question: when does domain-specific fine-tuning remain valuable for open-ended scientific reasoning? We study this in astronomy with a curated QA benchmark from publicly available 2017--2026 Olympiad-style materials. The free-response subset contains 300 questions, including 204 text-only and 96 image-linked examples. We compare open-weight and API-served general-purpose, multimodal, and astronomy-specialized models using judge-based correctness and complementary reference metrics. Strong general-purpose models establish the highest correctness baseline in this testbed, while analyses of metric agreement, judge sensitivity, benchmark composition, and modality reveal variation not captured by a single leaderboard. These results motivate treating domain specialization as a task- and deployment-dependent property and highlight the role of domain-specific evaluation in determining which models, capabilities, and evaluation criteria are appropriate for scientific workflows.

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.

Scientific papers require models to integrate evidence across text, equations, figures, tables, code, and datasets while preserving its provenance. Beyond answer correctness, scientific reading requires verifiable outputs from operations such as evidence localization, definition extraction, and consistency checking. We introduce SciDocBench, a workflow-centered benchmark targeting these operations through 124 expert-authored and difficulty-screened questions across seven research-assistant capability groups, 19 subtasks, and five scientific domains. Each question is instantiated in four matched settings formed by pairing its bilingual variants with the All Images First and Markdown Interleaved document representations, yielding 496 evaluation instances. The strongest evaluated model, Claude-Opus-5, scores 62.6 out of 100, with remaining gaps in evidence localization, structured information extraction, cross-document synthesis, and robustness to document representation. To convert these diagnostics into scalable training signals, we introduce SciDocIR, a structured representation of scientific document objects, layout and cross-reference relations, and provenance. Using SciDocIR, we construct SciDocDataset, which contains 4K supervised fine-tuning instances and 10K reinforcement-learning instances, built on 14 verifiable training subtasks. Post-training Qwen3.6-27B on task-aligned data improves its SciDocBench score from 40.03 to 45.33 with supervised fine-tuning and to 45.74 with subsequent reinforcement learning. Both adapted models preserve DocVQA and InfoVQA performance and improve ChartQA accuracy over the original model by 0.80 and 3.40 points, respectively. Together, SciDocBench, SciDocIR, and SciDocDataset connect capability diagnosis with verifiable training-data construction for scientific-document assistants.

Vision-language models (VLMs) have demonstrated strong performance in visual question answering with natural images. However, they continue to struggle with scientific diagrams, which are designed to convey functional or relational meaning rather than literal scenes. We therefore introduce a framework for generating large-scale diagram-grounded instruction data by leveraging terminology derived from scientific curricula. Our approach systematically extracts domain concepts, synthesizes atomic facts, retrieves relevant diagrams from the web, and generates multimodal supervision in the form of diagram captions and multiple-choice questions. Using this pipeline, we construct SciGram, a dataset of over 194K diagrams and 1.4M visual instructions across life, earth, and physical sciences. Despite relying on noisy web data and synthetic annotations, models fine-tuned on SciGram achieve substantial improvements on diagram-centric benchmarks, including TQA, ScienceQA, and AI2D, outperforming or matching state-of-the-art VLMs while using fewer training instances. Furthermore, augmenting existing models such as LLaVA OneVision with SciGram establishes new state-of-the-art performance on diagram question answering. Our results highlight the effectiveness of terminology-grounded instruction generation as a general strategy for improving vision-language reasoning in scientific domains. To support future research in scientific diagram understanding, we release both the SciGram dataset and models.

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.

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.

The web is increasingly accessed by AI agents rather than humans. Every agent needs knowledge, especially in the life-sciences, where agentic pipelines are growing fast. Access to the literature is a crucial part of that need, and resources such as Europe PMC, with over 40M indexed records, are widely used to meet it. Yet these resources were not built for AI agents: they take keywords and complex syntax and return whole papers, so every agent must learn the syntax, issue several searches, and read full papers to find the evidence it needs. We introduce EMBL AI Librarian, a knowledge layer that upgrades the Europe PMC interface for AI agents: an agent asks in natural language and receives evidence that answers it. A single LLM orchestrates the whole knowledge retrieval process: it plans complementary subqueries executed by the live Europe PMC search engine, then reads the selected papers and locates the relevant evidence. We evaluate Librarian across four benchmarks: literature synthesis, claim verification, open-domain question answering, and downstream biology tasks such as protocol questions and sequence manipulation. On ScholarQABench, Librarian improves Citation F1 by more than $16$ points over strong recently published baselines. Used as the retrieval layer of an existing claim-verification pipeline, it increases agreement with expert consensus; and on the open-form LitQA2 benchmark, a GPT-5.4 agent scores about $8$ points higher when grounded in Librarian than with web search. Overall, our results show that equipping life-science agents with the Librarian knowledge layer improves performance across a range of tasks. We release our code publicly at https://github.com/petroni-lab/librarian

Scientific datasets are commonly organized as hierarchical repositories containing heterogeneous and interdependent files, making their inspection, integration, and analysis labor-intensive and reliant on domain expertise. Although large language model (LLM) agents have advanced substantially in planning, reasoning, and tool use, existing research has largely overlooked their ability to interact with real scientific data assets through executable environments. We introduce Deep Scientific Data Exploration, an agentic task paradigm in which agents navigate repositories, interpret heterogeneous files and schemas, execute analyses, integrate cross-file evidence, and produce conclusions grounded in executed observations. To operationalize this paradigm, we present SciDataSailor, a framework for synthesizing tool-interactive trajectories by balancing broad exploration with targeted exploitation. SciDataSailor instantiates trajectory synthesis as Monte Carlo Tree Search (MCTS) with four task-specific mechanisms: difficulty-stratified exploration seeds, dual-feedback first-play urgency, hierarchical strategy-to-tool action generation, and entropy-guided branching. Using this framework, we construct SciDataSailor-SFT-2K for supervised fine-tuning and SciDataSailor-Bench for evaluation, with the latter comprising 627 meta-information summarization tasks and 586 scientific question-answering tasks across 27 datasets spanning the life, earth, and physical sciences.

Scientific user facilities accumulate decades of operational knowledge that no single search index covers: electronic logbooks, technical documents, internal wikis, operations chat messages, maintenance records, and live control-system data. We present APS-RAG, Advanced Photon Source Retrieval Augmented Generation, a deployed platform that makes the institutional knowledge at the Advanced Photon Source (APS) accessible to staff through natural-language queries, along with an operations-grounded evaluation. The retrieval engine fuses dense, sparse, and knowledge-graph (KG) channels with query-type-adaptive reciprocal-rank fusion, adds a corrective agentic loop, and runs a native-tool ReAct executor over a Model Context Protocol (MCP) tooling layer. We construct APS-Bench, a 50-question, question-answering (QA) dataset with auditable gold answers. Every retrieval-augmented variant numerically improves strict vital-nugget recall over a naive BM25 baseline (63.8%), with the full corrective Agentic GraphRAG scoring (70.3%). The cross-encoder reranker contributes significantly to answer quality: removing it and allowing the LLM to score relevance drastically reduces strict vital recall by 32.8%. The graph channel and corrective loop contribute positively as expected, but the performance gains are marginal. Additionally, we also compare the performance of open-source and closed-source LLMs in final answer synthesis. We release the APS-Bench construction methodology, the six-layer evaluation harness, and the underlying codebase, along with the '/aps-rag' retrieval agent skill framework, to support reproduction and adoption at other facilities. Together, the deployed platform and its operations-grounded evaluation present a promising workflow for trustworthy, statistically grounded AI assistance in facility operations, transferable to other large scientific instruments.

Scientific question answering requires a retrieval system to solve two distinct problems: identifying which papers are relevant and locating the supporting evidence within those papers. Conventional retrieval-augmented generation typically addresses both through similarity search over fixed-length passages, flattening document structure and separating scientific claims from their methodological and argumentative context. We present VecTree-RAG, an agentic framework that assigns these tasks to complementary retrieval mechanisms. Vector search ranks compact document and section representations across the corpus, whereas reasoning-guided traversal of source-verified section trees localizes evidence within shortlisted papers. Full text is retained in a page store and exposed progressively only after structural localization. We evaluate VecTree-RAG on 300 QASPER questions, an open-access subset of 54 LitQA2 questions, and 49 multi-document MOSAIC questions. Compared with Dense RAG, reranked Dense RAG, RAPTOR, and Search-o1, VecTree-RAG obtained the highest observed answer score on all three benchmarks, reaching 0.800 LLM-judge correctness on QASPER, 0.925 accuracy on LitQA2, and a 0.547 composite score on MOSAIC. On QASPER, its evidence-page precision was 0.274, compared with 0.046--0.071 for the baselines. LitQA2 ablations further showed that the complete vector--tree architecture required fewer inference tokens than variants without tree navigation or corpus-level vector routing. These results indicate that vector retrieval narrows the corpus-level search space and tree navigation concentrates reading on structurally relevant evidence. Although multi-turn inference remains more expensive than single-call retrieval, VecTree-RAG provides a structure-aware and traceable architecture for scientific literature question answering.

Visual diagrams, figures, and tables are central to scientific papers, and convey information beyond what is captured in text. While blind or low-vision (BLV) scientists have traditionally relied on static alternative text to access figures in papers, the rise of artificial intelligence (AI) has made interactive question-answering (QA) a feasible paradigm for visual exploration; yet little is known about how scientists use visual QA in practice or how to improve its accessibility. In this work, we interview five BLV and five sighted scientists across different STEM fields to understand how they use two AI tools, ChatGPT and Gemini, to query multimodal scientific documents. Our findings characterize how scientists review multimodal content, including existing practices (along with accessibility workarounds) for engaging with visuals, and feedback on the suitability of AI-generated responses to multimodal queries. We further find that vague or incomplete image descriptions, as well as incorrect AI outputs more broadly, can cause both BLV and sighted scientists to abandon AI workflows. To support future research, we additionally contribute a dataset of 115 queries and responses from our participants' interactions with the AI tools for papers in their field. We close by discussing implications for AI-powered scientific QA systems, emphasizing considerations for access across abilities and domains.

This paper describes DS@GT ARC's submission to the CLEF 2026 LongEval Task 4 on Retrieval-Augmented Generation (RAG). In this submission, we examine a divergence between traditional natural language evaluation metrics and citation integrity as applied to RAG QA systems. We evaluate a corrective pipeline using Corrective RAG (CRAG) and CiteFix against baseline and frontier model benchmark RAG QA scores. While frontier models maximized answer relevance and fluency scores, our RAGAs LLM-as-judge diagnostics indicate that frontier models would correctly identify relevant documents without using their context in answer generation. Conversely, by filtering chunks pre-generation and enforcing strict entailment of generated claims to the cited material post-generation, our corrective pipeline marginally improved citation faithfulness and answer grounding. We propose that evaluation of trustworthy RAG QA requires metrics that reward strict answer grounding.

Large language models are increasingly used to assist scientific reading, but existing evaluation methods often fail to detect whether answers are supported by verifiable citations. We introduce ResearchQA, a benchmark of 6,211 single-paper question-answer pairs from 494 open-access papers spanning eight domains and four question types: lookup, comprehension, multi-hop, and adversarial. ResearchQA is designed for citation-grounded evaluation: it permits multiple valid supporting passages for a claim and rewards grounded refusal when the source paper does not support an answer. We evaluate eight leading closed- and open-weight models in a citation-grounded chat-with-paper setting using a deterministic citation matcher and an LLM-based rubric evaluator. Citation-based metrics separate systems more clearly than LLM-evaluator scores: section coverage and citation accuracy vary substantially across models, while evaluator scores remain tightly compressed. We further find that open-weight models approach the best closed-model citation accuracy while achieving 3 to 6 times lower per-example latency. We release the benchmark, evaluation harness, and evaluator prompt.

Large language models (LLMs) have demonstrated strong performance across a wide range of tasks, but ensuring their reliability in highly technical domains remains a significant challenge. In nuclear engineering, problem solving often requires not only factual knowledge but also quantitative reasoning and conceptual understanding. To address the need for systematic evaluation in this domain, we introduce NuclearQAv2, a benchmark for assessing LLMs on nuclear engineering knowledge. The benchmark comprises approximately 1,240 question-answer pairs spanning three categories: boolean, numeric, and verbal. NuclearQAv2 is constructed using a hybrid pipeline that combines expert-authored questions, existing datasets, and LLM-assisted generation from domain-specific technical corpora. By leveraging structured prompting for both automated question generation and response evaluation, the proposed framework enables scalable benchmark construction and evaluation. We evaluate a diverse set of LLMs using NuclearQAv2 and observe substantial performance differences across task types. While the models generally perform well on factual questions, quantitative reasoning and conceptual understanding remain considerably more challenging. These results highlight the importance of multi-faceted evaluation frameworks and establish NuclearQAv2 as a scalable benchmark for assessing LLM capabilities in technical domains.

Muon collider research spans accelerator physics, detector instrumentation, and high-energy phenomenology, with relevant evidence scattered across a rapidly expanding and heterogeneous body of scientific literature. As high-energy physics (HEP) increasingly explores agent-assisted analysis workflows, efficiently locating, integrating, and verifying scientific evidence becomes an essential capability. While retrieval-augmented generation (RAG) offers a promising framework for scientific question answering, integrating agentic reasoning without compromising retrieval precision remains a key challenge. In this work, we present agentic hybrid RAG, an evidence-grounded RAG framework for muon collider research. The framework combines a hybrid retriever, integrating sparse lexical and dense semantic retrieval, with an agentic reasoning module for query decomposition, evidence expansion, and grounded answer generation. To enable systematic evaluation, we construct the first benchmark for retrieval-augmented scientific question answering in the muon collider domain, comprising a curated literature corpus together with dedicated retrieval and answer-generation benchmarks covering major detector and physics research topics. Extensive evaluation shows that hybrid retrieval provides the strongest retrieval backbone, while agentic reasoning is most effective for controlled evidence expansion and answer synthesis. Built on this principle, agentic hybrid RAG consistently outperforms representative retrieval and RAG baselines in retrieval effectiveness, answer quality, evidence coverage, and factual grounding. Together, the benchmark and framework provide a foundation for evidence-grounded scientific question answering and future HEP analysis agents operating over large-scale scientific literature. Code is available at this URL.

Climate change research increasingly requires AI systems that reason across text, dynamic visual content, and scientific figures, yet existing climate QA benchmarks are small, mostly textual, and cover a narrow range of models. We introduce MMClima, a large-scale multimodal climate question answering framework with 104k+ expert-validated question-answer pairs spanning articles, video transcriptions, and figures across five core climate science domains. MMClima is constructed via automated claim extraction and QA synthesis with human-in-the-loop validation to ensure both scale and reliability. Using MMClima, we benchmark state-of-the-art multimodal language models on tasks requiring factual recall, visual interpretation, and cross-modal synthesis. We additionally fine-tune on the textual split to produce mmclima-70b-txt, a domain-adapted baseline that outperforms strong open- and closed-source models on textual QA. We release the dataset, evaluation pipeline, fine-tuned model weights, and data creation framework to support standardized multimodal evaluation for climate science.

This paper presents an agentic multimodal retrieval-augmented generation (RAG) framework for domain-specific literature reasoning, instantiated on a curated corpus of several thousand papers in intelligent tires, vehicle dynamics, vehicle control, sensing, estimation, and machine learning. Unlike conventional single-pass RAG systems, the proposed architecture uses an autonomous, evidence-gated pipeline that classifies query intent, generates separate text and visual query rewrites, performs hybrid text retrieval with FAISS and BM25 followed by cross-encoder reranking, expands evidence through graph-guided chunk traversal over a Neo4j knowledge graph, and retrieves visual document evidence using ColSmol late-interaction embeddings with MUVERA fixed-dimensional encoding, approximate nearest-neighbor search, and MaxSim reranking. The framework scores evidence sufficiency using a 100-point rubric with hybrid rule-based/LLM review, retries retrieval through drift-guarded reformulation, searches external academic databases through optimize--search--vet loops, merges and deduplicates multimodal evidence, verifies citation integrity, and generates cited answers through Planner, Researcher, Writer, and Critic agents with self-correcting revision. Key contributions include: (i) a scalable multimodal retrieval architecture combining text, graph, and visual evidence over 40,000 document pages; (ii) an interpretable evidence sufficiency and retry mechanism; (iii) a multi-agent generation pipeline with evidence mapping and critic-driven revision; (iv) a domain knowledge graph with LLM-based entity extraction, OpenAlex author validation, and intra-corpus citation resolution; and (v) a route-dependent external search architecture for targeted literature expansion. The result is a practical, evidence-gated, multimodal agentic RAG architecture for technical reasoning over specialized research corpora.

Protein-language systems are often evaluated by whether they generate plausible biological text, but a structural question has a sharper semantics: it denotes a measurement in a 3D coordinate system. We introduce ProtStructQA, an executable benchmark for protein structural question answering in which each natural-language question is generated from a hidden typed domain-specific language (DSL) program and the answer is obtained by executing that program on an AlphaFold-predicted structure. ProtStructQA releases 382.2K questions covering confidence, distances, predicted aligned error (PAE), solvent exposure, secondary structure, topology and contacts, and held-out compositions: a 330K active benchmark over 10K proteins from four species, plus a 52.2K hard-negative robustness pool. Without fine-tuning, we evaluate Qwen3 models from 0.6B to 8B under direct prompting, chain-of-thought, grammar-constrained executable voting, executable voting with chain-of-thought, and multi-turn ReAct-style tool use, and replicate the headline finding on Gemma-3-1B and Gemma-3-12B. We find a capability-dependent denotation threshold between Qwen3-1.7B and Qwen3-4B: below it, tool-mediated ReAct dominates because models often fail to produce executable denotations; above it, chain-of-thought flips from mostly harmful to strongly beneficial and becomes the strongest strategy on most splits. Parse-failure and family-level analyses show that the threshold is a transition from unparseable language to executable structural denotation, while grammar and execution remain selectively valuable for PAE and secondary-structure queries. ProtStructQA reframes scientific QA as compilation from language to measurement and provides a diagnostic testbed for when language models can map words to executable 3D structural measurements.

As multimodal language models play an increasingly important role in scientific research, materials science offers a critical testbed due to its interdisciplinary, multimodal, and application-driven nature. However, existing materials benchmarks mainly focus on property prediction, knowledge QA, or characterization understanding, leaving the broader reasoning process from materials knowledge to application underexplored. To fill this gap, we present OmniMatBench, a human-calibrated multimodal reasoning benchmark for materials science. OmniMatBench contains 3,171 expert-curated QA and calculation problems across 19 materials-science subfields, spanning fundamental materials knowledge, structural and engineering materials, materials processing and manufacturing, and functional and applied materials. We evaluate 13 open-source and closed-source MLLMs and find that the best model achieves only a 0.372 overall score, revealing a substantial gap in current materials-science reasoning. Further analysis shows strong variation across subfields, fixed reasoning heuristics, uneven materials knowledge, and limited high-level knowledge application under formula-, retrieval-, and code-assisted settings. OmniMatBench provides crucial insights into the capabilities and limitations of current MLLMs and establishes a foundation for reliable AI assistants in materials-science research.