Answering clinicians' questions over trial evidence tables with verifiable, feedback-driven language models
Authors: Manan Roy Choudhury, Suparno Roy Chowdhury, Swastik Sahoo, Muhammad Ali Khan, Kaneez Zahra Rubab Khakwani, Mohamad Bassam Sonbol, Irbaz Bin Riaz, Vivek Gupta
Organizations: Arizona State University, Tempe, Arizona, USA · Mayo Clinic, Phoenix, Arizona, USA
Systematic reviews condense clinical trials into evidence tables, yet clinicians can interrogate these tables only through database queries, and many questions concern attributes that the table does not record, such as a drug's target class or a harmonised endpoint. Here we introduce FD-SCoPE, a language-model framework that answers both kinds of question, exposes the query, the selected trials and the derivation rule behind every answer, and learns from expert corrections. On an oncology evidence table of 159 immune checkpoint inhibitor trial records, FD-SCoPE completed all 140 clinician-style tasks (alternatives, 90.7-97.9%). For questions needing derived attributes it retrieved 99.3% of relevant trial records at a positive predictive value of 89.8% and outperformed four alternative approaches (derived-value F1 77.7% versus 64.8-73.4%). Corrections on 299 questions, simulated from reference answers, raised F1 on 1,201 unseen questions from 77.9% to 84.9%. Language models coupled with executable queries, verified programs and expert feedback can give clinicians auditable access to trial evidence.
Figures & tables
Figure 1: FD-SCoPE architecture. Following a safety check, clinical questions are routed through direct SQL retrieval or a hybrid pathway that combines trial selection with derivation of variables not explicitly stored in the database. Expert feedback updates reusable SQL examples and derivation programs to improve subsequent answers.
Question set
n
What it tests
Example
Recorded fields (benchmark)
1,500
Retrieving trials and fields stored in the table
“Show trials of CTLA-4 for non-small cell lung cancer that began in 2018 or later.”
Derived attributes (benchmark)
1,500
Selecting trials, then deriving a value that is not stored (31 families)
“In small cell lung trials, classify the ICI by target class from its generic name as PD-1, PD-L1 or CTLA-4.”
Clinician-style tasks
140
Look-ups, counts, evidence landscapes and trial listings
“Which bladder cancer trials published in 2018 or later enrolled more than 500 patients?”
Table 1: Question sets used in the evaluation.
Figure 2: Clinician-style tasks and benchmark questions about recorded fields. a , Share of 140 clinician-style tasks answered correctly by FD-SCoPE and seven alternatives using the same language model; few-shot, zero-shot and chain-of-thought are the prompting baselines. b , The same result by task type, with the number of tasks in brackets; each grey dot is one alternative, and ‘Control’ denotes listings of trials with a comparator other than chemotherapy. c , Exact-match accuracy on the 1,500 benchmark questions. d , Execution F1 on the same questions. e , Exact-match accuracy with two language models. Bars are 95% confidence intervals (Wilson in a , bootstrap in c – e ). Values are in Supplementary Tables 4 and 4 .
Figure 3: Questions that require an attribute not stored in the table (n = 1,500). a , Derived-value F1 for FD-SCoPE and four alternatives using the same language model. b , Share of questions for which every row of the answer was correct. c , Share of questions for which exactly the reference set of trial records was returned. d , Sensitivity and positive predictive value for retrieving the relevant trial records. e , Flow of the 1,500 questions through FD-SCoPE: the value was computed by a verified program reused from an earlier question, derived row by row by the model, or computed by a newly induced and verified program, or no trial matched the question; band width is proportional to the number of questions, and blue bands lead to answers that were correct in every row. Bars in a – d are bootstrap 95% confidence intervals. Values are in Supplementary Tables 4 and 4 .
Figure 4: Effect of corrections on held-out questions. Corrections on 299 questions were simulated from reference answers; results are for the 1,201 questions not used for feedback. a , Question-level measures before and after feedback. b , Accuracy of individual derived values for all trials, and for trials excluded from learning when corrections were drawn from half of the trials. Numbers beside the points are the change in percentage points. Values are in Supplementary Table 4 .
Figure 5: Derived-value F1 by derivation family and approach. Each cell is the derived-value F1 (%) on the same 1,201 held-out questions, for the four alternative approaches and for FD-SCoPE before and after feedback; darker cells are higher and the number of questions in each family is in brackets. Families are ordered by the change that feedback produced. Questions in the endpoint-role family do not state which endpoint field is meant and were not answered correctly by FD-SCoPE in either condition. Values are in Supplementary Table 4 .
Figure 6: Component analysis and robustness to phrasing. a , b , Derived-attribute questions (304-question subset): derived-value F1 and share of questions with every row correct for the full system and with one component removed or replaced. c , Recorded-field questions (300 held-out benchmark questions): exact-match accuracy with one component removed. d , Exact-match accuracy as a function of the share of the approved-example bank that is available; the band is the bootstrap 95% confidence interval. e , f , Exact-match accuracy and execution F1 on original and reworded questions with the reference answer unchanged; numbers in brackets are question counts and numbers beside the points are the change in percentage points. Bars in a – c are bootstrap 95% confidence intervals. Values are in Supplementary Tables 4 , 4 , 4 and 4 .
Exact match
Execution F1
Query
Executable
Tokens per
System
(95% CI)
(95% CI)
similarity
queries
question
FD-SCoPE
58.9 (56.3–61.5)
67.4 (65.1–69.6)
89.8
100.0
5,864
DAIL-SQL style
55.2 (52.4–57.7)
67.1 (64.8–69.3)
89.9
100.0
3,004
Zero-shot prompting
49.9 (47.2–52.4)
57.8 (55.4–60.1)
55.3
100.0
2,099
Few-shot prompting
49.3 (46.7–51.9)
63.3 (61.0–65.5)
84.3
100.0
2,491
DIN-SQL style
48.1 (45.6–50.5)
62.6 (60.3–64.8)
86.4
100.0
6,508
Table S1: Accuracy on the 1,500 benchmark questions about recorded fields
Sensitivity
Positive predictive value
Exact trial set
System
(95% CI)
(95% CI)
(% of questions)
FD-SCoPE
67.4 (65.0–69.5)
73.7 (71.5–75.8)
63.3
DAIL-SQL style
68.6 (66.4–70.7)
74.7 (72.6–76.8)
64.6
Zero-shot prompting
64.0 (61.6–66.2)
69.5 (67.2–71.6)
57.3
Few-shot prompting
65.2 (62.8–67.4)
71.5 (69.3–73.7)
59.9
DIN-SQL style
65.5 (63.3–67.7)
71.9 (69.5–73.9)
60.9
Table S2: Trial-level retrieval on the benchmark questions about recorded fields
Derived-value F1
F1,
Every row correct
Table
Exact
Tokens per
System
(95% CI)
exact
(95% CI)
F1
table
question
FD-SCoPE
77.7 (75.7–79.4)
62.1
67.0 (64.6–69.2)
87.6
52.3
8,592
BlendSQL style
73.4 (71.4–75.3)
56.6
59.1 (56.6–61.5)
83.9
44.1
3,827
Code agent
67.9 (65.8–69.8)
51.8
50.6 (48.1–53.0)
79.7
38.5
6,329
Row-retrieval QA
66.1 (64.1–67.8)
50.9
35.1 (32.6–37.4)
74.0
25.4
7,515
Whole-table prompting
64.8 (62.8–66.7)
49.5
35.5 (33.1–37.7)
73.8
25.7
28,503
Table S3: Accuracy on the 1,500 questions that require a derived attribute
Row-selection
Sensitivity
Positive predictive
Exact trial set
System
F1
(95% CI)
value (95% CI)
(95% CI)
FD-SCoPE
88.1
99.3 (98.9–99.7)
89.8 (88.4–91.1)
84.3 (82.3–86.2)
BlendSQL style
84.8
97.0 (96.1–97.7)
87.0 (85.6–88.6)
76.6 (74.4–78.7)
Code agent
81.7
94.4 (93.1–95.5)
82.7 (81.0–84.3)
70.9 (68.5–73.1)
Row-retrieval QA
75.7
87.6 (86.3–88.8)
75.8 (74.4–77.4)
44.0 (41.5–46.4)
Whole-table prompting
77.6
90.5 (89.2–91.8)
74.4 (72.6–76.1)
46.1 (43.5–48.4)
Table S4: Trial-level retrieval on the questions that require a derived attribute
Before
After feedback on
After feedback from
Measure
feedback
299 questions
half of the trials
Derived-value F1 (95% CI)
77.9 (75.8–80.0)
84.9 (83.2–86.6)
83.4 (81.4–85.1)
Derived-value F1, exact
62.6
77.6
78.6
Every row correct (95% CI)
67.1 (64.4–69.7)
75.8 (73.3–78.2)
73.8 (71.3–76.2)
Evidence-table F1
87.7
89.5
89.3
Exact table match
52.6
68.5
68.5
Table S5: Effect of feedback on the 1,201 held-out questions
Alternative approaches
FD-SCoPE
Derivation family
n
Whole
Row
Code
Blend-
Before
After
table
retrieval
agent
SQL
feedback
feedback
Change
Dosing schedule
31
0.0
0.0
23.6
0.4
21.0
93.1
+72.1
Named control regimen
31
6.3
5.2
6.9
5.7
18.6
71.7
+53.1
Chemotherapy backbone
31
10.8
7.5
9.2
2.7
13.9
66.1
+52.2
Composite endpoint components
32
48.3
56.3
51.3
53.2
52.0
91.9
+39.9
Table S6: Derived-value F1 (%) by derivation family on the held-out questions
Exact match
Execution F1
Tokens per
Configuration
(95% CI)
(95% CI)
question
Full system
62.0 (56.7–67.3)
71.5 (66.9–75.9)
5,859
Without catalogue grounding
64.0 (58.7–69.3)
73.0 (68.4–77.2)
5,703
Without model decomposition
60.0 (54.7–65.3)
71.8 (67.2–76.0)
3,271
Without exemplar retrieval
56.0 (50.3–61.3)
69.9 (65.3–74.3)
5,139
Without context-field completion
55.0 (49.7–60.3)
69.1 (64.7–73.6)
5,785
Table S7: Component analysis for questions about recorded fields (300 held-out benchmark questions)
Derived-value F1
Every row correct
Exact
Trial
Exact
Configuration
(95% CI)
(95% CI)
table
PPV
trial set
Full system
78.0 (73.7–81.8)
66.8 (61.2–71.7)
52.3
92.4
87.5
Without program induction
77.9 (73.7–81.8)
66.8 (61.5–71.7)
53.6
92.4
87.5
Without output normalisation
76.7 (72.4–80.6)
62.2 (56.6–67.4)
45.4
91.8
82.2
Without planner
72.0 (67.3–76.3)
61.2 (55.9–66.4)
47.7
92.4
87.5
Model selects the rows
67.6 (63.2–71.6)
37.8 (32.6–42.8)
28.9
77.6
53.0
Table S8: Component analysis for questions that require a derived attribute (304-question subset)
Table S10: Exact-match accuracy (%) of FD-SCoPE on reworded questions
Difference, points
Questions
Questions
Comparison
n
(95% CI)
better
worse
Recorded-field questions: FD-SCoPE vs an alternative
DAIL-SQL style, exact match
1,500
+3.7 (+1.9 to +5.5)
123
67
DAIL-SQL style, execution F1
1,500
+0.3 ( − 0.5 to +1.1)
162
83
Few-shot prompting, exact match
1,500
+9.6 (+7.7 to +11.5)
193
49
Few-shot prompting, exact match (Gemma-3-27B)
1,500
+5.1 (+2.7 to +7.6)
227
150
Table S11: Paired differences between two systems on the same questions
Scope check on
Scope check off
Unsafe
Category
Prompts
Declined
Answered
Declined
Answered
statements
Request to modify the table
12
12
0
0
12
0
Prompt injection
10
10
0
0
9
0
Request for clinical advice
8
8
0
0
8
0
Request for patient-level data
6
6
0
0
6
0
Valid evidence question (control)
10
0
10
0
10
0
Table S12: Safety set of 46 prompts
Setting
Qwen3.8-27B
Gemma-3-27B-it
Numerical precision
bfloat16
bfloat16
Served context limit
40,000 tokens
24,000 tokens
Temperature
0.0
0.0
Top- p
1.0
1.0
Thinking mode
Disabled
Not applicable
JSON-constrained output
Enabled
Enabled
Table S13: Language-model serving and inference settings
Approach
Settings
Zero-shot prompting
One call; schema and up to 24 observed values per field; 400 new tokens.
Few-shot prompting
As zero-shot, with four fixed expert examples; 400 new tokens.
Chain-of-thought prompting
Reasoning scaffold with worked examples; 2,500 new tokens.
DIN-SQL style
Four calls: schema linking (400 tokens), difficulty classification (10), generation (500) and self-correction (1,200); the corrected query is kept only if it executes.
DAIL-SQL style
Eight examples chosen by similarity of the question with literals masked, most similar last; schema given as a table definition; 500 tokens.
C3 style
Zero-shot prompt with clear layout and tips; ten samples at temperature 0.7; the result shared by most executable samples is returned.
We study clinical trial table reasoning, where answers are not directly stored in visible cells but must be reasoned from semantic understanding through normalization, classification, extraction, or lightweight domain reasoning. Motivated by the observation that current LLM approaches often suffer from "bad reasoning" under implicit planning assumptions, we focus on settings in which the model must recover implicit attributes such as therapy type, added agents, endpoint roles, or follow-up status from partially observed clinical-trial tables. We propose SCOPE (Structured Clinical hybrid Planning for Evidence retrieval in clinical trials), a multi-LLM planner-based framework that decomposes the task into row selection, structured planning, and execution. The planner makes the source field, reasoning rules, and output constraints explicit before answer generation, reducing ambiguity relative to direct prompting. We evaluate SCOPE on 1,500 hybrid reasoning questions over oncology clinical-trial tables against zero-shot, few-shot, chain-of-thought, TableGPT2, Blend-SQL, and EHRAgent. Results show that explicit multi-LLM planning improves accuracy for reasoning-based questions while offering a stronger accuracy-efficiency tradeoff than heavier agentic baselines. Our findings position clinical trial reasoning as a distinct table understanding problem and highlight hybrid planner-based decomposition as an effective solution
Suparno Roy Chowdhury, Manan Roy Choudhury, Tejas Anvekar +5
Structured extraction of evidence from clinical trial publications underpins systematic reviews and clinical guidelines, yet large language models are adopted for it only hesitantly: their outputs are difficult to verify, their use commonly requires transmitting documents to proprietary services, and they do not improve from the corrections their users make. We present EviSearch, a multi-agent system that addresses these three obstacles. Three tool-augmented agents with complementary access to a publication extract every column of an evidence table, and a value is admitted only after an attribution verifier has read it on its cited page, so that every value carries a page-level attribution. Disagreement between independent agents directs human review to the cells most likely to be wrong, and reviewer feedback refines the schema definitions and a curation knowledge base without updating model parameters. The agentic system runs entirely offline on open-weight models. On a clinician-annotated benchmark of randomized-trial publications, EviSearch attributes 100.0% of its values, reaches 91.70% accuracy autonomously, and reaches 95.22% after review of 15.6% of cells, exceeding random review of the strongest single agent at equal effort by 1.75 points.
Naman Ahuja, Abhijit Chakraborty, Muhammad Ali Khan +4
Clinicians exploring oncology trial repositories often need ad-hoc, multi-constraint queries over biomarkers, endpoints, interventions, and time, yet writing SQL requires schema expertise. We demo FD-NL2SQL, a feedback-driven clinical NL2SQL assistant for SQLite-based oncology databases. Given a natural-language question, a schema-aware LLM decomposes it into predicate-level sub-questions, retrieves semantically similar expert-verified NL2SQL exemplars via sentence embeddings, and synthesizes executable SQL conditioned on the decomposition, retrieved exemplars, and schema, with post-processing validity checks. To improve with use, FD-NL2SQL incorporates two update signals: (i) clinician edits of generated SQL are approved and added to the exemplar bank; and (ii) lightweight logic-based SQL augmentation applies a single atomic mutation (e.g., operator or column change), retaining variants only if they return non-empty results. A second LLM generates the corresponding natural-language question and predicate decomposition for accepted variants, automatically expanding the exemplar bank without additional annotation. The demo interface exposes decomposition, retrieval, synthesis, and execution results to support interactive refinement and continuous improvement.
Suparno Roy Chowdhury, Tejas Anvekar, Manan Roy Choudhury +5