Evidence-Grounded Generation

Turning a research idea into a complete paper requires more than text generation: the system must retrieve literature, design and execute experiments, revise claims according to evidence, produce publication-ready figures, and maintain consistency across a long generation process. We present Spark-to-Paper, an end-to-end research paper generation system implemented as thirteen composable skills inside an existing coding assistant, without requiring a separate agent platform or orchestration service. Spark-to-Paper separates model-based judgment from deterministic operations that can be directly executed and checked. It further separates experiment planning from reporting, so that required evidence is specified before results are observed and manuscript claims are revised according to measured outcomes. To improve reliability over long research trajectories, the system combines deterministic integrity checks with self-critique and bounds a failure mode we call the Self-Refutation Loop, in which repeated experiments continue to reject the original research objective. Spark-to-Paper also produces editable vector figures through programmatic plotting for experimental results and code-based reconstruction for generated method diagrams. Across eight controlled research topics, Spark-to-Paper achieves 99.5% citation validity and 96.4% figure editability. A controlled ablation increases fabrication detection from 14% for a single-pass draft to 92% with the full integrity and review stack, while adversarial review achieves 74% precision. The full system uses 11.9M tokens, costs $8.1 per manuscript, and requires 3.2 hours on average. These results show that end-to-end research paper generation can be implemented as a lightweight, composable workflow inside existing coding assistants while keeping experimental evidence central to how claims are accepted, revised, or abandoned.

Retrieving relevant evidence from noisy web data is challenging, particularly in sensitive domains containing incomplete reports, heterogeneous language, and irrelevant content. We present Guardian Crawler, a reproducible retrieval-first testbed for controlled experiments on knowledge discovery and evidence-grounded summarization over synthetic web-like corpora. The architecture combines BM25 retrieval with risk-aware, embedding-augmented, and hybrid reranking, followed by constrained retrieval-augmented generation with explicit document citations. Experiments on a synthetic 900-document corpus and 10 queries produced the highest descriptive retrieval scores under risk-based reranking, with P@10 = 1.00 and NDCG@10 = 0.94, compared with 0.94 and 0.81 for BM25. The best hybrid and BM25+Semantic configurations reached NDCG@10 values of 0.94 and 0.88, respectively. All 41 evaluable generated bullets passed the lexical coverage threshold; an automated LLM judge classified 36 as supported, one as partially supported, and four as unsupported. These results demonstrate the feasibility of Guardian Crawler as a controlled testbed but do not establish statistical superiority, human-validated faithfulness, or transfer to live-web investigative environments.

Retrieval-Augmented Generation (RAG) improves the factuality of large language models with external knowledge, yet conflicting evidence remains a fundamental challenge in dynamic and adversarial environments. Existing approaches often treat conflicts as static inconsistencies and select more reliable knowledge, overlooking that the same conflict may arise from legitimate knowledge evolution, malicious manipulation, or unresolved uncertainty. We formulate conflict origin attribution as a new problem in RAG: identifying which explanation of conflicting evidence is supported by observable context rather than simply which fact should be trusted. We propose EvoTrustRAG, a training-free framework for evolution-aware conflict attribution and evidence handling before answer generation. EvoTrustRAG represents span-grounded retrieved facts as a conflict evidence graph, evaluates grounded evolution and directional intervention hypotheses using temporal relations, support structure, and auxiliary consistency, and projects local decisions onto a globally consistent explanation of each conflict group. The attribution determines whether earlier and later states are preserved as temporal knowledge, an intervention candidate is separated from the primary context, or an unresolved conflict remains visible to the generator. Unlike provenance-based approaches focused on post-hoc analysis, EvoTrustRAG determines during inference whether conflicting evidence follows plausible knowledge evolution, exhibits intervention-like support, or cannot be reliably attributed. Experiments show that EvoTrustRAG achieves 81.4% average accuracy on benchmark-native conflict settings, improves attribution macro-F1 from 72.2% to 79.1% over the strongest baseline, and reduces the error rate under the strongest coordinated attack from 31.2% to 16.0%.

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.

Large language model (LLM) benchmark evaluations are routinely used to support claims about model safety, reliability, and deployment readiness. Yet most evaluations rely on a single access modality (model APIs), perform a single run per prompt, and report accuracy as the primary outcome metric, without accounting for conditions such as web search that may have effects on model behavior in deployment. We audit these assumptions for one of the most widely-used LLMs, comparing two modalities, ChatGPT's chat UI and OpenAI's API, with and without web search enabled. We use a stratified total sample of 401 prompts from two popular benchmarks, BBQ and SafetyBench, collecting 4,812 total responses across three repeated runs per prompt. Beyond standard performance measures, we evaluate model output dimensions including response consistency, response text similarity, citation grounding, and abstention behavior. For instance, chat UI responses were less accurate than API responses on both benchmarks with search disabled. Enabling web search reduced accuracy by up to 8 percentage points, and even reversed the direction of modality performance trends for one benchmark. Repeated runs of the same prompt produced inconsistent responses in up to 21% of prompts. The two modalities also grounded answers in different citations, and abstention behavior was also inconsistent across both modalities. These results illustrate that, even within a model family, reporting only simple accuracy metrics can obscure important forms of model behavioral variation relevant to AI safety assessments. We argue that AI safety evaluations should systematically account for modality, multi-run consistency, search conditions, and response-level behaviors to better reflect how deployed AI systems behave in practice.

Autonomous research agents can generate hypotheses, execute experiments, and draft manuscripts, yet their outputs often contain unsupported claims and inconsistencies between research questions, experiments, results, and conclusions. We argue that this problem is partly architectural: existing systems organize research as sequential pipelines but do not explicitly maintain or validate the evolving claim-evidence structure across stages. In this paper, we introduce EviGraph, an autonomous research framework that represents the research process as a typed evidence graph containing Problem, Gap, Hypothesis, Experiment, Finding, and Claim nodes. The graph serves as the operational state of the agent rather than a post-hoc record. EviGraph inspects evidence chains for missing dependencies, semantic misalignment, and result-claim inconsistencies, localizes the earliest weak node, and regenerates its affected downstream subgraph. Graph checkpointing prevents unsuccessful repairs from corrupting previously validated evidence. Manuscripts are generated only after every retained claim is grounded in a validated evidence chain. Experiments on ARC-Bench-ML and NanoResearch-20 show that EviGraph outperforms the compared end-to-end research-agent baselines in overall research performance, improves Claim Support Rate by 40.19% over the strongest baseline, and achieves 87.73% Experimental Data Consistency. These results demonstrate the value of explicit evidence-state maintenance for reliable autonomous research.

Abstractive summarization models remain vulnerable to factual inconsistency, redundancy, and weak length control. We propose a modular generation-and-selection framework for sentence-budget-constrained summarization. A pretrained generator produces multiple candidate summaries, which are decomposed into sentence-level candidates. A combinatorial selector then constructs the final summary by balancing relevance, factuality, and redundancy under an explicit budget. The framework supports MMR, ILP, and a DPP-inspired log-determinant objective without retraining the generator. Experiments on CNN/DailyMail, Multi-News, FaithBench, and TofuEval show consistent improvements in factuality and source-grounding metrics, especially for multi-document summarization, at the cost of lower reference-overlap scores. Human evaluation further indicates higher perceived consistency, relevance, clarity, and conciseness, with a small reduction in coherence. These results show that decoupling generation from selection provides a model-agnostic mechanism for improving factual grounding. Code is available at https://anonymous.4open.science/r/bcfs-D05E/.

Biomedical fact-checking systems must do more than predict whether a claim is supported, contradicted, or unaddressed: they should also produce evidence that is faithful, complete, and useful for verification. We study this evidence-generation setting on CARE-XAI, a unified benchmark spanning five biomedical and health fact-checking sources. We compare base instruction LLMs, PubMed retrieval-augmented LLMs, fine-tuned LLMs, label-only LLMs, and biomedical encoder classifiers under a shared evaluation protocol. Biomedical classifiers remain strongest for verdict-only prediction, while fine-tuned LLMs are the strongest evidence-generating systems. PubMed retrieval is mixed: it helps PubMed-aligned sources such as PubMedQA and SciFact, but can distract models on broader public-health claims. We introduce Bio-GRACE, a gold-reference-normalized diagnostic for measuring whether retrieved evidence recovers the decision benefit of reference evidence. Bio-GRACE shows that retrieval utility is source-dependent, motivates selective retrieval, and exposes why retrieval recall and lexical evidence overlap are insufficient for biomedical fact-checking.

Generative Artificial Intelligence (AI) is increasingly used by Muslims for religious guidance, Qur'anic interpretation, Hadith explanation, jurisprudential rulings, and Islamic education. Despite its growing adoption, there is limited empirical evidence on whether current AI systems provide authentic, verifiable, and trustworthy Islamic knowledge suitable for high-trust religious contexts. This study evaluates six leading generative AI systems using fifty realistic open-ended Islamic questions covering Qur'anic interpretation, Hadith, Fiqh, ethics, pastoral advice, and Madhhab-sensitive topics. Responses were collected under real-world conditions from participants in Australia and the United Kingdom and analysed using a mixed-method framework examining domain accuracy, citation verification, hallucinations, jurisprudential consistency, uncertainty handling, source provenance, and geographical variation. The study addresses four research questions: (1) How accurate and authentic are AI-generated responses across major Islamic knowledge domains? (2) To what extent do AI systems produce hallucinations, incomplete citations, or unverifiable religious references? (3) How consistently do models handle jurisprudential disagreement, Madhhab diversity, and uncertainty? (4) Are current AI systems sufficiently reliable for religious guidance, Islamic education, and scholarly research? Overall, current generative AI systems are valuable as assistive tools for introductory Islamic learning but should not be treated as authoritative sources for religious rulings or Islamic research without verification against authenticated primary sources and qualified scholarly expertise. This study provides one of the first comprehensive empirical evaluations of AI reliability within Islamic knowledge, offering practical guidance for researchers, educators, AI developers, and the wider Muslim community.

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

Long COVID (LC) poses a challenge for clinical decision support because relevant evidence is distributed across sources with different update cycles, evidentiary roles, and levels of clinical maturity. We present a clinician-facing chatbot that organizes four sources within a retrieval-augmented workflow: expert-curated consensus guidance, current PubMed literature, registered interventional trials, and evidence from living systematic reviews. Consensus guidance is always included to frame responses, while the remaining sources are retrieved in parallel when selected by the user. In an exploratory automated evaluation on 50 clinician-facing questions, our chatbot showed comparable mean ratings to OpenEvidence, with numerically higher scores and lower score variability in an LLM-judged comparison.

Advanced Persistent Threats (APTs) are difficult to detect and interpret due to their multi-stage and stealthy nature. While recent autonomous defense systems leverage provenance graphs and learning-based models for detection and mitigation, their outputs remain largely machine-oriented and difficult for analysts to interpret. Large language models (LLMs) offer a promising interface for report generation, but often produce hallucinated or weakly grounded content. In this paper, we propose DeepFaith, an evidence-grounded framework for faithful incident reporting in multi-stage APT defense. DeepFaith transforms structured outputs from autonomous defense and explainability modules into natural-language reports that are explicitly aligned with underlying system evidence. The framework integrates a unified evidence representation, evidence-grounded prompting, faithfulness-aware generation, and post-generation verification to ensure that all generated statements are supported. Experiments in a realistic enterprise testbed demonstrate that DeepFaith improves faithfulness from 0.68 to 0.92, reduces unsupported claims from 0.32 to 0.08, and increases temporal consistency from 0.6 to 0.88, while maintaining concise reports and lower error rates than existing template-based and LLM-based solutions. These results show that evidence-grounded generation enables reliable, interpretable, and actionable reporting for security operations centers.

Long-form question answering increasingly relies on retrieved evidence to make LLM outputs verifiable, with inline citations tracing claims to source documents. However, existing systems often attach citations that are topically related but insufficient to support their claims. We identify attribution ambiguity as a structural challenge: end-to-end generation must implicitly resolve combinatorial claim--document assignments, obscuring evidential boundaries and increasing the risk of evidence-boundary overrun, where claims exceed cited support. To address this challenge, we propose CAGE (Cognitive Attribution Graphs for Citation Generation), a two-stage framework that introduces an explicit cognitive attribution map before answer generation. CAGE first trains a plug-and-play Cognitive Map Induction Model to construct answer-centered support subgraphs, aligning each semantic answer unit with supporting documents through explicit relations. A Structured Citation Reasoning Model then realizes these units as sentence-level claims with map-aligned citations. Experiments on ASQA, ELI5, and ExpertQA show that CAGE achieves state-of-the-art performance, demonstrating the effectiveness of attribution-space contraction and map-guided citation generation.

Traditional conversational recommenders entangle retrieval and response generation within a single text interface, so exact entity cues fade as the dialogue's intent evolves, which compromises explanation credibility. We address this within the ACM RecSys Challenge 2026, which mandates both top-20 ranking and evidence-grounded response generation. This paper presents the third-place solution by team "swyoo" for the Blind-B industry track. We decouple retrieval and response into separate pipelines connected strictly via ranked tracks and metadata. Retrieval combines a hybrid lexical-dense pool for exact matching with a task-adapted pool driven by fine-tuned Qwen 8B adapters. Candidates are calibrated via LightGBM, then routed to an evidence-grounded propose-assign-select (PAS) framework to structure responses. This system also ranked second on the explanation-quality leaderboard in the final blind evaluation. Our findings demonstrate that: (i) isolating retrieval and response preserves both catalog cues and fluid intent; (ii) structuring generation via explicit evidence assignment is key to this near-best-in-class explanation reliability.

Deepfake detection is moving beyond binary classification decisions toward systems that can also explain the visual evidence supporting those decisions. This transition is important for real-world verification settings, where diverse users need to understand not only whether an image is manipulated, but also why it is considered suspicious. The Explainable Deepfake Detection Challenge at ACM Multimedia 2026 is designed to benchmark this joint capability. Built on XPlainVerse, a million-scale benchmark for explainable deepfake detection, the challenge evaluates methods on image classification and grounded natural-language explanation generation. Participants submit a real/fake label together with two explanations for each image: a detailed complex explanation for technical users and a concise simple explanation for general users. The evaluation combines classification metrics with semantic similarity, simplicity, and intent-aware grounding metrics that assess whether explanations identify the relevant manipulated entities and supporting visual evidence. The methodologies developed through the challenge will contribute to the development of next-generation explainable deepfake detectors. Evaluation script, baseline models, and accompanying code are available on https://github.com/Abhijeet8901/XPlainVerse-ACMChallenge.

Generative AI lets large language models produce scholarly-looking text within seconds, yet fluency does not equal valid explanation. The deepest risk is not factual error alone but the appearance that an explanation is already established without clear sources, page numbers, editions, or evidence. We liken the page anchor to Ariadne's thread: within the labyrinth of generative fluency, it is the thread that leads the scholar back to the source. This paper proposes Traceable Scholarship as the minimum normative condition for AI-assisted humanistic research, situating it across the three revolutions of knowledge infrastructure: print, digital, and generative AI. We introduce page anchors, dual page numbers, citation-first generation, NO_EVIDENCE, human verification, four-level compliance, and Scope Contract, and present AIH-Infra as a three-layer reference implementation: Contexture (document structuring), Open WebUI AIH-Infra (traceable knowledge base), and AIH-Infra MCP Server (agent gateway). A case study on a 29-volume Kant Akademie-Ausgabe knowledge base illustrates how traceability supports retrieval correction, evidence grading, and judgment downgrading. Traceability is not a software feature; it is the condition under which humanistic research can remain public and refutable in the age of generative AI.

This paper presents the MPR-CiteG framework, which achieved second place in the ScienceON AI Challenge by addressing two fundamental challenges in generative AI: inefficient retrieval and the absence of source verification. We propose a dual-component system, termed MPR-CiteG, in which the Multi-Portfolio Retriever (MPR) efficiently retrieves diverse and relevant information, while the Citation-Grounded Generation (CiteG) module ensures that every generated output remains factually consistent and explicitly attributed to its source. MPR-CiteG represents a significant step toward building more trustworthy and accurate LLMs that are not only capable of generating information but also of grounding their responses in reliable evidence, thereby mitigating common issues like model hallucination. Extensive experiments on the challenge dataset validate the effectiveness and reliability of our approach. Our code is available at https://github.com/2noweyh/MPR-citeG.

Generation of clear and accessible public health narratives is critical for communicating complex epidemiological projections to policymakers and the general public at large. Such narratives require more than simply reporting numbers: projections must be contextualized and quantitatively grounded across multiple dimensions. Further, projections are often derived from large ensemble datasets which combine intervention assumptions, geographic and demographic strata, outcomes, time horizons, and uncertainty quantiles. However, directly using large language models (LLMs) to summarize and contextualize such data often leads to inconsistencies, omissions, and fragile behavior. We introduce an agentic framework (EpiNarrate) for public health report generation that separates structured numerical reasoning from natural-language generation. The framework first extracts scenario axes and organizes them into a partial-order schema, enabling systematic traversal of the underlying multidimensional space. It then constructs an augmented dataset and derives valid quantitative statements through a comparison grammar that enforces semantic and arithmetic consistency. To balance coverage and non-redundancy, we introduce an interestingness-driven selection mechanism based on maximum-entropy principles. Experiments on the COVID-19 Scenario Modeling Hub demonstrate that our model produces narratives with improved factual grounding and broader coverage of salient epidemiological patterns, while preserving the style of expert-written reports.

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.

Live sports commentary is grounded generation under a deadline: statements concern real, named athletes, the grounding state changes every few seconds, and no reference text exists at generation time. We present Pitwall, a production system that generates natural-language Formula 1 strategy briefings in English, Spanish, and Portuguese, treating faithfulness as an architectural property rather than an aspiration: every published sentence is decomposed into typed factual claims (positions, gaps, tyres, pace, overtakes, race control) and each claim is verified against the probabilistic race state that prompted it. The same verifier gates the fine-tuning data: of 3,045 model-written targets, only the 81.9% whose every claim is state-supported are retained, the rest falling back to a provably faithful template, so the generator never sees an ungrounded target. Verification is meaningful because of the grounding substrate: a vectorized Monte Carlo engine (N=2,000 per-lap race continuations) calibrated on 126 races (2018-2024) and validated on fully held-out 2025-2026 seasons (winner-in-top-3 90.3% over 155 backtests; held-out Brier 0.0745). A recurring finding spans both halves of the system: virtues trade off and must be gated separately. In simulation, calibration-optimal is not decision-optimal; in generation, fine-tuning on richer targets buys vividness that collapses into hallucination when the grounding state is sparse -- a failure a four-base replication traces to base-model instruction adherence, not scale, and that sparse-context auditing removes from the production model. End-to-end operation -- live timing to verified trilingual briefings -- was confirmed at two consecutive live Grands Prix (Austria and Britain, 2026); at Silverstone a timestamped probability trace, committed to disk before the outcome was known, locked onto the eventual winner ten laps before the flag.

Synthesizing long-context supervised fine-tuning (SFT) data is a scalable way to enhance the long-context understanding of large language models (LLMs), yet existing approaches share three limitations: narrow task coverage, insufficient instruction difficulty, and a lack of faithfulness supervision. We propose \textbf{LongCrafter}, a structured synthesis framework that couples a hierarchical task taxonomy with an evidence-grounded pipeline. The taxonomy organizes long-context understanding into local/shallow and global/deep levels and yields 32 fine-grained task types that serve as a global generative prior. Guided by this taxonomy, LongCrafter constructs task-aligned long contexts, decomposes them into explicit evidence graphs that model cross-paragraph dependencies, and generates instruction--response pairs strictly grounded in the located evidence spans, ensuring both controllable difficulty and faithful, traceable reasoning. Models fine-tuned on LongCrafter data outperform all SFT baselines and even the official post-trained models on LongBench, LongBench~v2, and LooGLE across both Qwen2.5-7B and LLaMA-3.1-8B, with the largest gains on high-difficulty tasks. Further analysis shows that LongCrafter data is more diverse and better spread across difficulty levels, and that the trained models locate evidence robustly regardless of position, effectively mitigating the ``lost in the middle'' problem.

Large language models have made research ideation increasingly accessible, yet effective idea development requires more than generating candidate directions. Researchers must ground a problem in current literature, identify meaningful bottlenecks, differentiate from existing solutions, and evaluate risks before committing to implementation. We present ResearchStudio-Idea as a reusable skill suite for this first mile of research ideation. The suite includes Paper-Search, a standalone multi-source literature search skill; Scoop-Check, a standalone prior-art collision checker for novelty claims; and IdeaSpark, the end-to-end skill that composes evidence grounding, pattern-guided generation, collision retrieval, audit, and idea-card rendering into one workflow. IdeaSpark is constructed from a corpus of 1,947 machine learning conference papers collected from ICLR, ICML, and NeurIPS between 2021 and 2025, including Oral papers, a separately tracked high-citation subset, and rejected submissions. Analysis of these outcomes reveals 31 recurring ideation sub-patterns, consolidated into 15 reusable ideation patterns. Each pattern is operationalized as a structured card containing research contexts, bottleneck types, differentiation strategies, supporting precedents, and common failure modes. Given a research problem and an evidence bundle, IdeaSpark evaluates evidence readiness, reconstructs the surrounding research context, identifies unresolved bottlenecks, selects relevant patterns, instantiates one candidate direction, retrieves potentially conflicting prior work, and performs outcome-informed auditing. This workflow transforms reusable ideation patterns into traceable research proposals. Blind automated-judge evaluations show that IdeaSpark consistently produces stronger research proposals than no-skill and generic-skill baselines while maintaining competitive novelty.

We present a candidate-constrained retrieval-augmented generation system for LongEval-RAG, where each query is associated with an organizer-provided candidate set and all retrieved evidence and final citations must remain within that set. The system combines deterministic provenance tracking with passage-based retrieval, deterministic query expansion, pseudo-relevance feedback (PRF), reciprocal rank fusion (RRF), lightweight evidence reranking, citation-aware evidence aggregation, and optional MiniLM sentence reranking. We evaluate ten pipeline variants using a primary organizer evaluation and a supplementary self-generated diagnostic protocol. The primary evaluation shows that the strongest balanced variant is rule-minilm: a rule-based chunking pipeline with query expansion, PRF, RRF, reranking, citation prior, and late MiniLM sentence selection. This variant obtains the highest BERTScore, retrieval precision, nugget coverage, and average grade among our submissions. The result suggests that the main gain does not come from more complex semantic or topic-shift chunking, but from pairing stable rule-based evidence units with sentence-level neural selection before generation. The supplementary LLM-judge evaluation remains useful for early diagnosis and additional analysis, but it emphasizes different systems than the primary gold-answer and nugget-based evaluation, highlighting the need for multi-metric RAG evaluation.

Financial markets evolve in response to real-world events reported in news, yet these drivers often remain implicit in text. To better explain market dynamics, event-market relations must be explicitly modeled through factual, company-centric, and environment-aware knowledge graphs. We present FinKG-News, a framework that automatically constructs such graphs by extracting news events as anchors linked to companies. Using FinKG-News as grounded evidence that integrates events, news, and company data, we develop an in-context learning architecture for credit risk report generation across three core financial dimensions. Automatic and human evaluations show that automated hallucination detection and quality assessment remain unreliable, making expert judgment indispensable. Our approach consistently outperforms baselines, improving quality by 19%-34% while reducing hallucinations. The source code and project resources are publicly available at: https://github.com/ichise-laboratory/FINKG-news.

AI-assisted research has entered a stage in which the central question is not only whether systems can generate hypotheses, run experiments, or produce manuscripts, but whether their scientific claims are calibrated to the evidence that supports them. This Perspective-style paper develops a conceptual and methodological framework for evidence-licensed claims in AI-assisted research. Motivated by representative routes including specialized scientific foundation models, LLM research assistants, multi-agent co-scientists, AI Scientist pipelines, mathematical discovery agents, and self-driving laboratories, it represents AI-assisted research as five operators: hypothesis generation, model-mediated consequence derivation, external validation, belief update, and claim calibration. The central claim is that calibration is not merely cautious wording but a mechanism for managing scientific assertion rights: evidence licenses some forms of speech and withholds others. The paper distinguishes linguistic, consequence-based, interventional, and evidence-licensed semantics; defines the claim-evidence gap and epistemic debt; and treats minimal structural reconstruction across heterogeneous outputs as an upward form of claim calibration. AISim-Cal is included as an illustrative synthetic dynamics exercise, not as an empirical forecast or benchmark. The resulting principles are: no claim without license, validation does not determine claim level, and automation amplifies the need for calibration. Reliable AI-assisted research is therefore evaluated as a loop that generates hypotheses, derives testable consequences, accepts independent adjudication, updates beliefs, and outputs only evidence-licensed claims.

Birth defects are a major cause of fetal loss, neonatal morbidity and long-term disability. In the subset with suspected genetic etiologies, exome and genome sequencing have moved many cases from variant detection to post-sequencing interpretation: clinicians must rank patient-specific candidate variants under incomplete fetal or infant phenotypes and heterogeneous evidence from population genetics, variant-effect prediction, gene-disease validity, phenotype ontologies, cellular and pathway context, protein structure and clinical literature. We present DeepBD, a grounded agentic workflow for variant prioritization and diagnostic interpretation of genetic birth defects. DeepBD organizes the workflow into LLM-assisted case structuring, a pretrained evidence engine, specialist evidence modules and a grounded diagnostic review layer. The evidence engine learns patient-specific variant scores from structured rule evidence, sequence and variant-effect representations and phenotype-conditioned biological context, whereas specialist modules and the agentic layer provide tool-based refinement, candidate-pool review and diagnosis-oriented synthesis from ranked candidates. Developed using an in-house fetal and infant cohort comprising 18,622 cases, DeepBD achieved Recall@1/3/5/10 of 0.658/0.882/0.912/0.929 on an internal held-out solved-case benchmark, outperforming standalone Exomiser, DeepRare and prompted LLM reranking baselines evaluated on Exomiser-derived top-20 candidate variants. Ablation and overlap analyses show that rule evidence, mechanistic context, and specialist refinement provide complementary signals. These findings support a grounded agentic workflow that separates evidence integration, tool-based refinement, and LLM-assisted diagnostic review for retrospective variant prioritization in genetic birth defects.

Existing ECG report generation is tightly coupled -- interpretation and reporting fused end-to-end, so errors propagate without stage-level recourse -- while agent-based systems decouple tasks but remain single-pass, never revisiting earlier outputs. Clinical ECG reporting instead unfolds iteratively, requiring progressive context integration and bidirectional editing. We present \textsc{ATRIA}, a multi-agent ECG reporting system that mirrors the clinician's iterative workflow: it binds every report claim to its supporting evidence, flags statements unsupported by that evidence, incorporates additional context mid-session, and lets clinicians verify and revise individual findings rather than accept one opaque output. Because its agents use ECG analysis models already in clinical use, the underlying findings are clinically trustworthy; and as a cloud-based web service, \textsc{ATRIA} is ready for immediate deployment. We demonstrate \textsc{ATRIA} through four interaction cases, with a live demo and video available.

Large language models (LLMs) can produce clinically fluent recommendations for type 2 diabetes while failing to satisfy guideline constraints or explicitly justify lifestyle-related glycemic claims. We present T2D-Bench, a reproducible benchmark and evidence-gated evaluation framework for testing whether LLM outputs satisfy explicit, graph-checkable evidence requirements. T2D-Bench is built on a multi-layer clinical-lifestyle knowledge graph that combines a biomedical spine (UMLS, DrugBank, SIDER), computable ADA Standards of Care rules, and lifestyle knowledge connected through a mechanistic bridge to glycemic laboratory effects. Across 100 structured vignettes spanning diagnosis, medication safety, and adversarial lifestyle conflicts, baseline outputs failed benchmark-defined evidence-path checks in 35% of cases for GPT-4o-mini and 33% for GPT-4o. The evidence gate detects unsupported omissions and uses constrained revision to bring outputs into verifier-level compliance with benchmark-defined evidence requirements. These results show that computable evidence constraints can make unsupported clinical omissions explicit, measurable, and correctable in diabetes-focused LLM outputs.

Biomedical researchers increasingly use AI-generated analyses and reports to interpret protein-level signals, but static outputs are often insufficient for research decision-making, where users need to inspect evidence, assess uncertainty, compare mechanisms, and refine hypotheses. We present \textsc{BioInsight}, a multi-agent system that moves from static biomedical report generation to interactive evidence-centered interactive interface generation. Given a disease name, a protein association table, and optional cohort metadata, BioInsight organizes disease-specific evidence through typed intermediate artifacts, including ranked pathways, literature evidence packets, protein-level reasoning notes, citation-grounded reports, dashboard schemas, and rendered interactive interfaces. The system decomposes evidence retrieval from mechanistic reasoning, normalizes citations through deterministic components, and converts the same structured evidence used in the report into an interactive interface. We evaluate BioInsight on standardized biomedical QA, challenging protein-function reasoning, and end-to-end biomedical evidence synthesis. Results show that BioInsight achieves best, and suggest that biomedical AI systems should move beyond text-only and static reports toward provenance-preserving, interactive evidence artifacts.

Open-ended deep research (OEDR) requires systems to acquire knowledge through multi-round retrieval and generate coherent long-form reports. The outline plays a central role as a structural scaffold that coordinates retrieval, evidence organization, and generation. However, existing methods either fix the outline before writing or refine it with local heuristics, leading to scaffold drift under continuous information accumulation and delayed feedback for evaluating outline modifications. We propose ScaffoldAgent, a utility-guided dynamic outline optimization framework for OEDR. ScaffoldAgent models outline evolution as a structured decision process with three operations: Expansion, Contraction, and Revision, enabling controlled updates to the report scaffold. It further introduces a utility-guided feedback mechanism that estimates the downstream value of each outline operation from retrieval gain, structural coherence, and trial-generation quality. The resulting utility signal guides node selection, operation scheduling, and termination during inference. Experiments on DeepResearch Bench and DeepResearch Gym show that ScaffoldAgent consistently improves long-form report generation and factual grounding over existing deep research agents.