PRAISE: A Reproducible Workflow for Non-Programmer Scientists to Implement Published AI Models
Authors: Max Achterweust, Stefan Groot Nibbelink, Vincent J. de Beer, Stefan Schipper, Zeynep Yüksektepe, Pedro Andrade da Silva, Aurelia Peppelaar, Martijn J. van der Willigen, Christophe B. Minkenberg, Robert F. van der Willigen
Organizations: HR Datalab EAS, School of Engineering and Applied Sciences, Rotterdam University of Applied Sciences, Rotterdam, the Netherlands · Department of Chemistry, School of Engineering and Applied Sciences, Rotterdam University of Applied Sciences, Rotterdam, the Netherlands · Department of Electrical Engineering, School of Engineering and Applied Sciences, Rotterdam University of Applied Sciences, Rotterdam, the Netherlands · Department of Biology and Medical Laboratory Research, School of Engineering and Applied Sciences, Rotterdam University of Applied Sciences, Rotterdam, the Netherlands · Data Supported Healthcare: Data-Science Unit, Research Center Innovations in Care, Rotterdam University of Applied Sciences, Rotterdam, the Netherlands · School of Communication, Media and Information Technology, Rotterdam University of Applied Sciences, Rotterdam, the Netherlands · HR DataLab AI SusTech, Centre of Expertise HRTech, Rotterdam University of Applied Sciences, Rotterdam, the Netherlands
Artificial Intelligence (AI) models are increasingly developed, published and used across scientific fields. Researchers, students and industry professionals who want to apply these models to their own research questions often lack the programming and data science expertise to do so. Existing guidelines cover single steps, but not the route from a published model to working predictions on one's own data. Here we present the hands-on workflow PRAISE, a Practical, Reproducible AI-model Implementation for Science and Education, that helps non-programmers implement published AI models step by step. Because implementations rarely work the first time, PRAISE anticipates common failures and provides a fallback route for each. As a proof of principle, three BSc chemistry students and their tutor applied PRAISE without prior programming or data science knowledge. They reproduced, validated and extended a state-of-the-art model that predicts enzyme-substrate interactions. This shows that with PRAISE, implementing an AI model from the literature becomes a learnable skill, one that turns non-programmer scientists from users into evaluators and improvers of AI models.
Figures & tables
Figure 1: Visualization of the computational stack required to execute an AI model (left), and the tools that configure the stack (right). During a run, information flows from the top to the bottom of the stack and back. All layers and dependencies must be installed and compatible before the AI model can run. Users primarily work in the development tool and in the environment and package manager. Generative AI (GenAI) can help the user to develop the model and stack.
Figure 2: PRAISE (Practical, Reproducible AI-model Implementation for Science and Education) workflow for implementing scientific AI models to practical case studies, assuming no issues arise. Outputs and checks per step are given. Troubleshooting steps for common issues are shown in Section 5 .
Figure 3: AI use case formulation guide. An AI use case can be constructed by bringing together both problem and solution discovery, until a candidate model is found that fits a defined knowledge gap. The regulatory compliance is performed afterwards.
Figure 4: The PRAISE workflow for implementing scientific AI models to practical case studies, extended with troubleshooting routes. When a checkpoint is not met, the arrow marked with a cross leads to a decision point that helps decide which solution is required. These bring the user one or more steps back, depending on the issue. Such iterations are common in AI model implementations.
Figure 5: Implementation of an AI model to predict enzyme-substrate interactions following the PRAISE workflow. Colored arrows mark the first pass and the four iterations that followed, numbered in the order they occurred. First pass: the initial implementation of ProSmith, which stopped at the first issue. First iteration: the switch from Windows to a cloud-based Linux OS. Second iteration: the retraining on a dataset supplemented with data gathered manually from the literature. Third iteration: the retraining on an additional dataset containing true-negative data. Fourth iteration: the changes to the training pipeline to investigate suspected data leakage.
Model
Iteration
Accuracy
Precision
ROC-AUC
MCC
Standard ProSmith Windows
Original
0.93
n.d.
0.96
0.80
Standard ProSmith Linux
Install & computing → infrastructure selection
0.92
0.94
0.95
0.80
ProSmith manually supplemented database
Validation → data preparation
0.91
0.92
0.95
0.76
ProSmith supplemented with VIPER database
Validation → data preparation
0.93
0.83
0.95
0.75
Standard ProSmith suspected data leak fix
Validation → install & computing
0.90
0.92
0.95
0.74
Table 1: Outcomes of five different ProSmith model training sessions and the corresponding validation scores. Each training was performed once, and the values are only indicative. The suspected data leak fix was investigated and found not to be data leakage.
AI models underpin data-centric applications from image and text processing to scientific discovery in biology, physics, and chemistry. Yet developing them remains heavily manual, requiring practitioners to design architectures, build training pipelines, and iteratively refine solutions, making it challenging for natural scientists without specialized AI engineering expertise to build the high-performing models their research demands. To reduce this burden and broaden access to AI for scientific discovery, agents that automatically build AI models have been proposed. However, the performance of these agents is largely limited by the parametric knowledge of their underlying large language models, which is static, often outdated, and sparse on practical AI model engineering know-how. To address this limitation, we introduce AIBuildAI-2, a knowledge-enhanced agent with an external, evolving knowledge system for automatically building AI models. The knowledge system of AIBuildAI-2 is hierarchical, organizing curated AI development knowledge into high-level knowledge instructions over topical categories and low-level knowledge documents under each category, from which the agent dynamically loads only the context relevant to its current state and the AI task being solved, grounding each design and implementation decision in concrete, externally verifiable expertise. The system is initialized by collecting and cleaning AI-development-related documents from the web and organizing them into the corresponding categories, and continually evolves from the agent's own experience by distilling each completed run on an AI task into structured takeaways that are written back into the knowledge system. AIBuildAI-2 achieves state-of-the-art results, ranking first on MLE-Bench with a 70.7% medal rate and placing in the top 6.6% among 4,370 human-expert teams in a heart disease prediction competition.
Ruiyi Zhang, Peijia Qin, Qi Cao +2
Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA 92093, USA · Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
Bold projections that artificial intelligence will accelerate scientific discovery have raced ahead of evidence from working scientists, and the field still lacks large-scale, scientist-in-the-loop tests of these claims. Here we mount the largest such evaluation to date and map what AI cannot yet do for science. We invited authors of 121,640 recent preprints across biology, medicine, chemistry, and the social sciences to judge ideas that large language models (LLMs) generated from the context and puzzles of their own papers. 6,749 scientists returned 25,139 sets of ratings on novelty, empirical feasibility, probability of being true, and favorability of adoption. Three patterns emerge. First, non-reasoning LLMs collapse into a narrow "hivemind" of similar ideas; reasoning models roam a wider hypothesis space, yet no model class spontaneously proposes null hypotheses -- a move humans make more freely. Second, scientists reward ideas that resemble their own and prize probability over novelty, though social scientists tolerate risk more readily than life scientists. Senior social scientists are the harshest critics, and their skepticism is well-earned: LLMs falter most in pluralistic fields like the social sciences that demand context-aware interpretation and evolving theories. Third, automated evaluators on which the community currently relies -- LLM-as-a-judge, artificial metrics, and even state-of-the-art (SOTA) models -- agree only weakly with expert judgment, and retrieval augmentation and scientist persona prompting yield only marginal gains. A Qwen3-14B reward model we post-trained on human ratings captures field taste nuances, beats SOTA models by up to 27%, and closes the gap to the inter-rater consistency of independent peer reviewers. For all the hype, today's scientific AI still represents a collaborator whose imagination, outputs and judgment benefit from human grounding.
Honglin Bao, Siyang Wu, Xiao Liu +3
Data Science Institute, University of Chicago · Knowledge Lab, University of Chicago
The automation of science is a long-standing ambition in the field of AI. While the community has made significant progress in automating individual components of the scientific process, a system that autonomously navigates the entire research lifecycle -- from conception to publication -- has remained out of reach. Here, we present the strongest demonstration to date toward automating the entire process end-to-end. We present The AI Scientist, which creates research ideas, writes code, runs experiments, plots and analyzes data, writes the entire scientific manuscript and performs its own peer review. Its ideas, execution, and presentation are of sufficient quality to produce a manuscript generated by an AI system that passes the first round of peer review at a major machine learning conference workshop. The workshop has an acceptance rate of 70 percent. Our system leverages modern foundation models within a complex agentic system. We evaluate The AI Scientist in two settings: a focused mode using human-provided code templates as an initial scaffold to conduct research on a specific topic, and a template-free, open-ended mode that leverages agentic search for wider scientific exploration. Both settings produce diverse ideas and automatically test, report on, and evaluate them. This achievement demonstrates AI's growing capacity for scientific contribution and signifies a potential paradigm shift in how research is conducted. As with any impactful new technology, there could be significant risks, including taxing overwhelmed review systems and adding noise to scientific literature. However, if developed responsibly, such autonomous systems could greatly accelerate scientific discovery.
Yutaro Yamada, Robert Tjarko Lange, Cong Lu +5
Sakana AI, Tokyo, Japan · University of British Columbia, Vancouver, Canada · Vector Institute, Toronto, Canada +1