Deep Research, Shallow Evaluation: A Case Study in Meta-Evaluation for Long-Form QA Benchmarks
Authors: Jena D. Hwang, Varsha Kishore, Amanpreet Singh, Dany Haddad, Aakanksha Naik, Malachi Hamada, Jonathan Bragg, Mike D'Arcy, Daniel S. Weld, Lucy Lu Wang, Doug Downey, Sergey Feldman
Recent advances have made long-form report-generating systems widely available. This has prompted evaluation frameworks that use LLM-as-judge protocols and claim verification, along with meta-evaluation frameworks that seek to validate these methods. Many of the meta-evaluations estimate an evaluation quality's by comparing its assessments against human pairwise preferences. Prior work, however, suggests that human pairwise preference may be overly simplistic and can fail to capture nuances of expert expectations. We conduct a case study in meta-evaluation for long-form QA benchmarks using ScholarQA-CS2, a benchmark designed for assessing retrieval-augmented deep-research QA in the scientific domain. We comprehensively validate the benchmark through human pairwise preference judgments, then critically examine the strengths, weaknesses, and confounders of this approach. We show that pairwise preference rankings are best suited for system-level evaluation, while explicit metric-wise annotations and expert annotators are critical for reliable metric-level assessment, with subjectivity remaining a key challenge. Based on our findings, we offer practical guidelines for designing future meta-evaluations that better align evaluation methods, annotator expertise, and reporting practices. By surfacing these methodological challenges, we aim to advance evaluation standards for deep-research systems.
Figures & tables
Human Meta-Evaluation
(Expert Agreement w/ LLM-judge)
Evaluation
Dom
Input Source
Ret Src
Metrics Used
Expert Eval
PPR
Metric -Wise
Reported Comp.
Qs Assign
# Sys Comp.
IAA
OA
ScholarQA-CS2 ( Bragg et al., 2025 ) + present study
Sci:CS
real user queries
PI
AR,RCC, CP,CR
✓
✓
✓✓
SC,IC, OA,MA, MC
R,C,A
6
55.0%
51.6%
OpenScholar ( Asai et al., 2024 )
Sci
written queries
PI
RCC,CP, CR,AQ
✓
✓
✓ *
OA
R
3
68%
50%
DeepResearchGym ( Coelho et al., 2025 )
Gen
real user queries
WI
FC,AQ, CP,CR
✓
✓
✓ *
SC,OA
R
7
0.87 Cohen κ
0.72 Cohen κ
DeepResearch Bench ( Du et al., 2025 )
Gen
curated queries
WS
RC,CP, CR
✓
✓
-
SC,OA
R
4
68.4%
71.3%
Table 1: We summarize benchmarks that evaluate scientific or research-oriented systems and represent the subset that are most closely related to ScholarQA-CS2 . Ordered alphabetically by author.
Figure 1: Our experimental settings for meta-evaluation of ScholarQA-CS2 . We investigate meta-evaluation that assesses agreement between evaluation score and expert preference ranking (Setting 1). We also investigate settings (Settings 2 & 3) that compare evaluation scores against metric-wise judgment annotation and control for annotator expertise level.
All Data
Expert-
(IAA: 55.0%)
Agreed
System-level Corr ( τ -b)
0.40
0.60
↪ w/o Elicit
0.70
1.00
Instance-level Corr ( τ -b)
0.25
0.36
Table 2: System and sample-level correlations (Kendall τ -b) and Human IAA. Our system-level τ s range from moderate-to-strong. The strong correlations are not reflected at instance-level comparison.
Human Score
Model Score
All Data
Expert-Agreed
Overall preference ranking
Overall Score
51.6%
62.4%
Answer Relev.
34.5%
35.2%
Answer Recall
47.3%
54.3%
Citation Prec.
42.3%
59.0%
Citation Recall
41.9%
58.4%
Table 3: Pairwise agreements between expert overall preference ranking vs. model scores. Our overall score agreement approaches IAA levels, however, individual metric comparison to human preference show lower levels of agreement.
Human-Model Score comparison
Near-Expert
Deep-Expert
Human Score
Model Score
agree.
τ -b
agree.
τ -b
Overall preference ranking
Overall score
65.0%
0.50
57.3%
0.25
Answer relev.
31.7%
0.00
22.7%
-0.02
Answer recall
25.0%
0.00
25.3%
0.09
Citation prec.
53.3%
0.38
49.3%
0.22
Citation recall
43.3%
0.31
49.3%
0.29
Table 4: Results from per metric human evaluation with expertise control. We compare instance-level agreement between model scores and two human signals: (TOP) human preference, and (BOTTOM) metric-wise human ratings collected in a setup parallel to ScholarQA-CS2 metrics. The results include thresholded ties (see § 4.1 ). Overall score (for both human and model) is the computed average of the metric scores at instance-level.
Figure 2: When evaluating answer relevance disagreements, near- and deep-experts choose to keep their own judgments at similar rates; however, when they do not, near-experts tend to defer to the LLM’s judgment more often than deep-experts.
Figure 3: Expert preference ranking vs. model scores. Model score alignments with expert preferences vary substantially across annotators.
Gemini-flash
Gemini-pro
Claude-sonnet
Claude-sonnet-r
GPT-5.1
GPT-5 (test only)
agree.
τ -b
agree.
τ -b
agree.
τ -b
agree.
τ -b
agree.
τ -b
agree.
τ -bs
overall score
51.8%
0.22
52.0%
0.24
57.1%
0.31
53.3%
0.25
55.2%
0.28
51.5%
0.24
answer relev.
29.6%
-0.07
30.4%
-0.12
24.3%
0.00
25.8%
-0.14
40.5%
0.01
39.2%
-0.03
answer recall
45.9%
0.15
48.1%
0.16
47.3%
0.14
48.4%
0.15
48.7%
0.17
44.6%
0.10
citation prec.
40.5%
0.20
41.0%
0.19
42.5%
0.25
40.8%
0.19
38.9%
0.20
43.3%
0.23
citation recall
40.2%
0.15
42.9%
0.21
44.4%
0.25
43.4%
0.18
43.8%
0.26
42.3%
0.22
Table 5: Evaluation results using six alternative LLM judges: Gemini-2.5-flash (Gemini-flash, fresh run), Gemini-2.5-pro (Gemini-pro), Claude-sonnet-4.5 with (Claude-sonnet-r) and without reasoning (Claude-sonnet), GPT-5.1 without reasoning, and reasoning GPT-5. We limit reasoning GPT-5.1 run to test set due to cost constraints. We present the agreement (TOP) and the system correlations (BOTTOM) for both all data and expert-agreed subset.
Figure 4: Expert preference ranking vs. expert’s metric-wise scores obtained in annotations settings 2 & 3. The expert preferences alignments with their own scores vary substantially across annotators.
Appendix figures & tables10 assets
Supplementary material from the paper’s appendix.
Appendix
Figure 5: Human annotation is conducted as a 3-way comparison. The results are converted into pairwise judgments, and is compared to the model scores for score (dis)agreements.
Figure 6: Annotation Procedure and Screenshots
Figure 7: rubric comparison
Figure 8: The annotation UI used to collect validation data from CS researchers regarding the quality of the citation evaluation quality.
IAA
Agree.
2 systems
55.3%
43.4%
3 systems
57.0%
44.6%
all 6 systems
55.0%
51.6%
↪
w/o Elicit
57.0%
58.9%
Appendix
Table 6: Comparing most competitive or "best" systems. 3 systems : ScholarQA-CS2 , ScholarQA-CS2 -SFT, OpenAI-DR; 2 systems : ScholarQA-CS2 , ScholarQA-CS2 -SFT.
Table 8: Final rankings based on human overall preference ratings for the full dataset.
Figure 9: Analysis of qualitative assessments shows that each annotator calibrates what constitutes a good answer differently.
Figure 10: Cross-correlation heatmap for Pearson ρ coefficient. Cross-correlation analysis indicates that all models are highly correlated with one another, and that our findings are robust across evaluator choice.
Human Meta-Evaluation
(Expert Agreement w/ LLM-judge)
Evaluation
Dom
Input Source
Ext. Src
Metrics Used
Expert Eval
PPR
Metric -Wise
Reported Comp.
Qs Assign
# Sys Comp.
IAA
OA
ScholarQA-CS2 ( Bragg et al., 2025 ) + present study
Sci:CS
real user queries
PI
AR,RCC, CP,CR
✓
✓
✓✓
SC,IC, OA,MA, MC
R,C,A
6
55.0%
51.6%
OpenScholar ( Asai et al., 2024 )
Sci
written queries
PI
RCC,CP, CR,AQ
✓
✓
✓ *
OA
R
3
68%
50%
Deep Research Bench ( Bosse et al., 2025 )
Gen
synthetic queries
WS
RC,CP
-
-
-
-
-
DeepResearchGym ( Coelho et al., 2025 )
Gen
real user queries
WI
FC,AQ, CP,CR
✓
✓
✓ *
SC,OA
R
7
0.87 Cohen κ
0.72 Cohen κ
Appendix
Table 9: Related Deep Research Evaluation Literature. Ordered alphabetically by author.
Recent advances in large language models have enabled deep research systems that generate expert-level reports through multi-step reasoning and evidence-based synthesis. However, evaluating such reports remains challenging: report quality is multifaceted, making it difficult to determine what to assess and which criteria to use; LLM-based judges may miss errors that require domain expertise to identify; and because deep research relies on retrieved evidence, report-wide claim verification is also necessary. To address these issues, we propose DEER, a benchmark for evaluating expert-level deep research reports. DEER systematizes evaluation criteria with an expert-developed taxonomy (7 dimensions, 25 subdimensions) operationalized as 101 fine-grained rubric items. We also provide task-specific Expert Evaluation Guidance to support LLM-based judging. In addition to rubric-based assessment, we propose a claim verification architecture that verifies both cited and uncited claims and quantifies evidence quality. Experiments show that current systems produce structurally plausible, evidence-citing reports, but still struggle to fully satisfy expert-level user requests and achieve logical completeness. Beyond performance comparisons, DEER makes system strengths and limitations interpretable and provides diagnostic signals for improvement.
Janghoon Han, Heegyu Kim, Changho Lee +6
LG AI Research · University of Illinois Chicago · University of Michigan, Ann Arbor
Deep Research Agents (DRA) aim to help users search the web, synthesize information, and deliver comprehensive investigative reports. Prior benchmarks often either under-evaluate a system's ability to produce meaningful insights and high-quality writing, or adopt coarse or LLM-defined criteria that are hard to verify and can diverge from human expert judgment. To address these issues, we introduce Deep Research Bench II, a new benchmark for evaluating DRAs. It contains 132 grounded research tasks across 22 domains; for each task, an agent must produce a research report that is evaluated by a set of 9,430 fine-grained binary rubrics in total, covering three dimensions: information recall, analysis, and presentation. All rubrics are derived from carefully selected expert-written investigative articles and are constructed through a four-stage LLM+human pipeline that combines automatic extraction with over 400 human-hours of expert review, ensuring that the criteria are verifiable and aligned with human expert judgment. We evaluate several state-of-the-art deep-research agents on Deep Research Bench II and find that even the strongest models satisfy fewer than 50% of the rubrics, revealing a substantial gap between current DRAs and human experts. We release the benchmark, evaluation scripts, and all rubrics at https://github.com/imlrz/DeepResearch-Bench-II to facilitate future research on deep-rearch agents.
Ruizhe Li, Mingxuan Du, Benfeng Xu +3
University of Science and Technology of China · Metastone Technology, Beijing, China
Recent progress in deep research systems has been impressive, but evaluation still lags behind real user needs. Existing benchmarks predominantly assess final reports using fixed rubrics, failing to evaluate the underlying research process. Most also offer limited multimodal coverage, rely on synthetic tasks that do not reflect real-world query complexity, and cannot be refreshed as knowledge evolves. To address these gaps, we introduce MiroEval, a benchmark and evaluation framework for deep research systems. The benchmark comprises 100 tasks (70 text-only, 30 multimodal), all grounded in real user needs and constructed via a dual-path pipeline that supports periodic updates, enabling a live and evolving setting. The proposed evaluation suite assesses deep research systems along three complementary dimensions: adaptive synthesis quality evaluation with task-specific rubrics, agentic factuality verification via active retrieval and reasoning over both web sources and multimodal attachments, and process-centric evaluation audits how the system searches, reasons, and refines throughout its investigation. Evaluation across 13 systems yields three principal findings: the three evaluation dimensions capture complementary aspects of system capability, with each revealing distinct strengths and weaknesses across systems; process quality serves as a reliable predictor of overall outcome while revealing weaknesses invisible to output-level metrics; and multimodal tasks pose substantially greater challenges, with most systems declining by 3 to 10 points. The MiroThinker series achieves the most balanced performance, with MiroThinker-H1 ranking the highest overall in both settings. Human verification and robustness results confirm the reliability of the benchmark and evaluation framework. MiroEval provides a holistic diagnostic tool for the next generation of deep research agents.