Scientific ideation aims to propose novel solutions within a given scientific context. Existing LLM-based agentic approaches emulate human research workflows, yet inadequately model scientific reasoning, resulting in surface-level conceptual recombinations that lack technical depth and scientific grounding. To address this issue, we propose MoRI (Motivation-grounded Reasoning for Scientific Ideation), a framework that enables LLMs to explicitly learn the reasoning process from research motivations to methodologies. The base LLM is initialized via supervised fine-tuning to generate a research motivation from a given context, and is subsequently trained under a composite reinforcement learning reward that approximates scientific rigor: (1) entropy-aware information gain encourages the model to uncover and elaborate high-complexity technical details grounded in ground-truth methodologies, and (2) contrastive semantic gain constrains the reasoning trajectory to remain conceptually aligned with scientifically valid solutions. Empirical results show that MoRI consistently outperforms strong commercial LLMs and complex agentic baselines across multiple dimensions, including novelty, technical rigor, and feasibility. The code is available on GitHub.
Figures & tables
Figure 1: Conceptual comparison. Unlike existing approaches that rely on pattern recombination or computationally expensive external scaffolding, MoRI internalizes scientific ideation through learning motivation-grounded reasoning. It initially identifies a Motivation ( m ) from a given Context ( x ), then generates a Reasoning Trajectory ( z ) to deduce a grounded Methodology ( y ), which is optimized via our composite RL rewards.
Figure 2: Overview of MoRI. Our framework optimizes reasoning via GRPO (Bottom) using composite rewards: Entropy-Aware Information Gain (Left) for high-entropy explanation and technical depth and Contrastive Semantic Gain (Right) for logical direction alignment, modulated by Length Anchoring (Center) to enforce reasoning depth.
Source
Overall
Novelty
Rigor
Feasibility
H
L
H
L
H
L
H
L
MoRI
2.76
3.07
2.73
3.20
2.73
3.07
2.80
2.93
AI-Scientist-V2
2.17
2.76
2.14
2.57
2.00
2.71
2.36
3.00
GPT-4o
1.75
2.17
1.50
2.00
1.75
2.25
2.00
2.25
Ground Truth
3.29
3.47
3.33
3.53
3.47
3.80
3.07
3.07
Overall
2.67
3.03
2.65
3.02
2.67
3.12
2.69
2.94
Table 1: Human-LLM alignment analysis. We report mean scores from human experts (H) and LLM judge (L) across 60 samples from three dimensions.
ICLR Test Set
NeurIPS OOD Test Set
Overall
Model
Nov.
Rig.
Feas.
Mean
Δ
Nov.
Rig.
Feas.
Mean
Δ
Nov.
Rig.
Feas.
Mean
Δ
Commercial Models
GPT-4o
2.51
2.78
2.79
2.69
+18.6%
2.57
2.87
2.88
2.77
+13.7%
2.54
2.83
2.84
2.74
+16.1%
Claude-3.5-Sonnet
3.39
3.07
2.82
3.09
+3.2%
3.42
3.03
2.94
3.13
+0.6%
3.40
3.05
2.89
3.11
+2.3%
Agentic Frameworks
AI-Scientist-V2 † (Sonnet)
3.45
3.08
2.89
3.14
+1.6%
–
–
–
–
–
–
–
–
–
–
Table 2: Main comparison across test sets. We report results on the in-domain ICLR test set (83 papers), the out-of-domain NeurIPS test set (67 papers), and their combination (150 papers). Δ denotes the relative improvement of MoRI over each baseline. Best results (excluding Ground Truth) are in bold . † denotes the use of a stronger backbone ( claude-3-5-sonnet ) for AI-Scientist-V2. For agentic frameworks, the default backbone is gpt-4o-2024-08-06 , with Haiku referring to claude-3-5-haiku-2024-10-22 .
Model
Nov.
Rig.
Feas.
Mean
Full-SFT (Direct)
2.80
2.69
2.81
2.75
Full-SFT (Two-stage)
2.85
2.76
2.94
2.85
MoRI
3.30
3.00
3.16
3.15
Table 3: Ablation on motivation conditioning (NeurIPS OOD test set). Direct: x→y ; Two-stage: x→m→y ; MoRI adds RL optimization on top of the two-stage formulation.
Figure 3: Training Dynamics. Moving average of CoT Length (a), Shaped EAIG (b), and Shaped Semantic Score (c).
ws
we
Description
Novelty
Tech. Rigor
Feasibility
Mean
0.0
1.0
EAIG Only
2.68
2.22
2.63
2.51
1.0
0.0
CSG Only
3.16
2.93
3.06
3.05
0.5
0.5
Balanced
3.32
2.96
2.98
3.09
0.7
0.3
Optimal
3.34
3.04
3.07
3.15
Table 4: Ablation on reward composition (Step 100 w/ Length Anchoring). ws and we denote weights for CSG and EAIG respectively.
Figure 4: Entropy Mask Dynamics. Moving average of CoT Length (a), Shaped EAIG (b), and Shaped Semantic Score (c).
Figure 5: Impact of Length Anchoring. Moving average of CoT Length (a), Shaped EAIG (b), and Shaped Semantic Score (c).
Config
LA
Novelty
Tech. Rigor
Feasibility
Mean
Δ
ws =0.7, we =0.3
✗
3.22
2.94
3.00
3.05
–
✓
3.34
3.04
3.07
3.15
+3.2%
ws =0.5, we =0.5
✗
2.96
2.76
2.95
2.89
–
✓
3.32
2.96
2.98
3.09
+6.9%
Table 6: Impact of Length Anchoring (Step 100). LA : Length Anchoring.
Figure 6: Overview of the Data Construction Pipeline. The process operates in three distinct phases: (1) Data Ingestion & Preprocessing , where raw ICLR PDFs are converted into text using MinerU; (2) Extraction & Cleaning , which parses the research context ( x ) and motivation ( m ), while extracting and de-symbolizing the method section ( y∗ ) to remove notation-specific noise; and (3) Posterior Reconstruction , where a reasoning chain ( z ) is synthesized by rewriting an initial thought trace ( zinit ) to logically align with the ground-truth method.
Appendix figures & tables23 assets
Supplementary material from the paper’s appendix.
Appendix
Figure 7: End-to-end example of one training/inference instance. Part (A) shows the extracted context x provided to the model; part (B) shows an abbreviated excerpt of the corresponding held-out ground-truth method y∗ ; part (C) shows the inference prompt template. Only the context in part (A) is exposed as model input, which prevents leakage of the target method.
Sub-domain
ICLR
NeurIPS
Perception & Multimodal
25.3%
16.4%
Language Reasoning & Alignment
22.9%
19.4%
Generative Modeling
16.9%
7.5%
Learning Efficiency & Foundations
16.9%
28.4%
Scientific & Interdisciplinary AI
10.8%
17.9%
Decision, Control & Safety
7.2%
10.4%
Appendix
Table 7: Sub-domain distribution of the two test sets.
Statistic
Value
Mean ± Std
1.26 ± 1.0
P25 / Median / P75 / P90
0.40 / 1.14 / 1.93 / 2.64
EAIG threshold (top-25%)
1.93
Selected tokens
36,573 (25.1%)
Appendix
Table 8: Token entropy distribution statistics over 100 training samples.
Category
Count
Sel. Rate
Mean Ent.
Technical terms
82,896
34.2%
1.52
Other
6,307
17.2%
0.93
Common words
40,279
14.5%
0.95
Whitespace
615
12.5%
0.86
Math symbols
2,240
10.8%
0.73
Punctuation
12,461
7.7%
0.87
Appendix
Table 9: Selection rate by token category under the top-25% entropy mask. Technical terms are selected at more than twice the rate of common words.
Figure 8: Annotated excerpt from a ground-truth method section. Token color indicates entropy (blue=low, red=high).
Parameter
Value
Description
max_generations
1
Ideas per topic
num_reflections
3
Reflection rounds
max_results
10
Papers per query
year_filter
-2024
Publication cutoff
overlap_threshold
0.8
Leakage filter
Appendix
Table 10: AI-Scientist-V2 parameter settings.
Stage
Original
Adapted
Problem ID
3-round iteration
Bypassed
Method Dev
3-round iteration
Preserved
Experiment
3-round iteration
Bypassed
Input
API retrieval
Regex parsing
Appendix
Table 11: ResearchAgent pipeline modifications.
Parameter
Original
Adapted
Discussion rounds
7
4
Team members
3
4
Discussion model
LLaMA-8B
GPT-4o-mini
Review model
LLaMA-70B
Qwen-72B
Final output
Abstract
Method
Appendix
Table 12: VirSci configuration comparison.
Figure 9: Complete prompt template for context-aware LLM evaluation. The prompt instructs the judge to adopt a domain expert mindset and provides detailed rubrics for each evaluation dimension.
Dimension
Pearson r
Novelty
0.613
Technical Rigor
0.684
Feasibility
0.629
Appendix
Table 13: Human–LLM alignment on an additional 60-sample NeurIPS subset.
Config
EAIG Weight
Final CoT Length
s0-e1
100%
Shortest (collapses)
s5-e5
50%
Short
s7-e3
30%
Moderate
s1-e0
0%
Preserved
Appendix
Table 14: Observed CoT length under different EAIG weights w/o Length Anchoring.
Parameter
Value
Training Dynamics
Global Batch Size
8
PPO Mini-Batch Size
4
PPO Micro-Batch Size (per GPU)
2
PPO Epochs per Rollout
1
Learning Rate
5×10−7
Appendix
Table 15: Hyperparameters for MoRI training.
Model
Novelty
Tech. Rigor
Feasibility
Overall
GPT-4o
2.54 [2.38, 2.70]
2.83 [2.71, 2.94]
2.84 [2.72, 2.97]
2.74 [2.64, 2.84]
Claude-3.5-Sonnet
3.40 [3.28, 3.52]
3.05 [2.92, 3.18]
2.89 [2.78, 2.99]
3.11 [3.02, 3.20]
AIS-v2 (GPT-4o)
2.38 [2.23, 2.53]
2.60 [2.48, 2.71]
2.82 [2.69, 2.95]
2.60 [2.49, 2.70]
ResearchAgent
2.63 [2.46, 2.80]
2.39 [2.22, 2.56]
2.50 [2.34, 2.67]
2.50 [2.35, 2.66]
VirSci
2.19 [2.08, 2.30]
2.26 [2.16, 2.36]
2.27 [2.18, 2.37]
2.24 [2.16, 2.32]
Full-SFT
2.99 [2.85, 3.13]
2.82 [2.71, 2.93]
2.99 [2.87, 3.11]
2.93 [2.84, 3.03]
Appendix
Table 16: Combined results (ICLR + NeurIPS, 150 papers) with 95% bootstrap confidence intervals (10,000 resamples). Best results (excluding Ground Truth) are in bold .
MoRI vs
Δ
p
Cohen’s d
VirSci
+0.93
< 0.001
2.000 (large)
ResearchAgent
+0.67
< 0.001
0.939 (large)
AIS-v2 (GPT-4o)
+0.58
< 0.001
1.083 (large)
GPT-4o
+0.44
< 0.001
0.874 (large)
Full-SFT
+0.24
0.003
0.458 (small)
Claude-3.5-Sonnet
+0.07
n.s.
—
Appendix
Table 17: Pairwise significance tests on the combined set (150 papers). Δ : difference in overall mean. p -values are Bonferroni-corrected.
Figure 10: Generated Motivation by MoRI for the example research idea on plan-based reasoning improvement.
Figure 11: Generated Reasoning by MoRI (representative excerpts with key insights highlighted).
Figure 12: Generated Method by MoRI (Part 1: Overview, Core Idea, and Training).
Figure 13: Generated Method by MoRI (Part 2: Solution Generation, Evaluation, and DPO Training).
Figure 14: Generated Method by AI-Scientist-V2 for the same research problem.
Figure 15: Generated Method by Claude-3.5-Sonnet for the same research problem.
Figure 16: Behavior A: Goal Decomposition with Constraint Enumeration. The model declares an objective, enumerates required properties, and narrows toward a concrete mechanism in a top-down manner.
Figure 17: Behavior B: Hypothesize–Critique–Revise Loop. The model actively discovers shortcomings in its own proposals and iterates, demonstrating self-verification rather than single-shot generation.
Figure 18: Behavior C: Paradigm Questioning via Reverse Framing. The model challenges the default methodological stance of the field before committing to a solution direction, enabling non-obvious research angles.
Large Language Models (LLMs) have demonstrated potential in automating scientific ideation, yet current approaches relying on iterative prompting or complex multi-agent architectures often suffer from hallucination or computational inefficiency. A critical bottleneck in applying Reinforcement Learning (RL) to this open-ended domain is reward hacking -- where models exploit imperfect evaluation proxies to maximize scores without producing genuine scientific innovation. To address these limitations, we propose an RL framework explicitly tailored for high-quality scientific idea generation. We propose the first multi-agent reward function designed to serve as a judge, decoupling methodological validation from implementation details while providing strict binary rewards that are robust to reward hacking. To effectively optimize against this sparse signal, we utilize an unbiased variant of Group Relative Policy Optimization to mitigate artificial length bias. We grounded our training in ICLR-320, a curated dataset of problem-solution pairs extracted from ICLR 2024 proceedings. Experiments demonstrate that our framework significantly outperforms state-of-the-art baselines across expert-evaluated metrics of novelty, feasibility, and effectiveness.
Ideation plays a pivotal role in scientific discovery. Recent LLM, especially AI Scientist systems, show promising potential for automated ideation. However, existing approaches predominantly rely on pre-defined agentic workflows. This constraint severely limits the flexibility required to navigate the vast search space of scientific literature and the complex action space of research reasoning. Recently, training Agentic LLMs has emerged as a promising direction, offering flexible reasoning frameworks and the capability for autonomous tool utilization. However, there remains a non-trivial challenge: applying previous agentic data synthesis methods to scientific ideation suffers from prohibitively high data synthesis cost. To bridge this gap, we propose Agentic-Ideation, a novel framework comprising an automated trajectory synthesis pipeline and a specialized agentic LLM trained for scientific ideation. Specifically, we first define a comprehensive tool space incorporating three external tools and three cognitive tools. Then we introduce an Oracle-Guided Data Synthesis strategy. By leveraging a reference idea as oracle guidance, this approach steers the multi-agent system to efficiently reconstruct the logical reasoning and tool invocation paths, transforming aimless trial-and-error into directed trajectory generation. Finally, we train the agent on these synthesized trajectories, employing a masking strategy on tool execution results. This ensures the model focuses on decision-making logic without interference from external feedback. Experimental results demonstrate that our method outperforms the SOTA workflow-based baseline by 11.91% in overall quality. Furthermore, our approach improves the sample efficiency of high-quality data synthesis by \textbf{over 10×}.
Keyu Zhao, Lingyan Kong, Fengli Xu +1
Department of Electronic Engineering, Tsinghua University.
Despite rapid progress in automating scientific research, generating promising and well grounded research solutions remains a central challenge. We isolate research ideation as a standalone task and build our solution on the intuition that a challenge in one field can often be addressed by a mechanism that solved an analogous challenge in another. Accordingly, we introduce IdeaScientist, which decomposes ideation into gap finding, innovation, and report writing, and trains each role with reinforcement learning. These roles identify limitations in related work, draw solution intuitions from analogous problem settings, and develop those intuitions into complete research proposals. To facilitate discovery of insights across domains, we construct the Svalbard Idea Vault, a corpus of 2.77M decomposed research ideas for retrieval, training, and temporally controlled evaluation. Our evaluation restricts access to literature available before a cutoff date and assesses how closely proposed directions align with those later explored in 15K papers authored by human researchers. On Qwen3.6-27B, IdeaScientist outperforms the strongest open-source autoresearch baseline by 14.0%, driven mainly by gains in novelty. On this 27B open backbone, IdeaScientist even outperforms Claude Code SDK with Claude-4.8-Opus and Codex SDK with GPT-5.4, by up to 5.9%.
Jiarui Liu, Renjie Tao, Yiwei Liao +15
Carnegie Mellon University · Meta Reality Labs · FAIR at Meta +5