# Process-Level Representation of Scientific Protocols with Interactive Annotation

arXiv: https://arxiv.org/abs/2101.10244 · HTML: https://mlsanity.com/paper/2101.10244/

## Key facts

- Cited by 16 papers in the map (data through 14 Oct 2026).
- Builds on 17 of its 37 references that are in the map.
- First posted on arXiv 25 Jan 2021.

## Builds on (most cited first, 17 of 17)

- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [TextWorld: A Learning Environment for Text-based Games](https://mlsanity.com/paper/1806.11532/) (2018)
- [Matching the Blanks: Distributional Similarity for Relation Learning](https://mlsanity.com/paper/1906.03158/) (2019)
- [Entity, Relation, and Event Extraction with Contextualized Span Representations](https://mlsanity.com/paper/1909.03546/) (2019)
- [Discriminative Embeddings of Latent Variable Models for Structured Data](https://mlsanity.com/paper/1603.05629/) (2016)
- [A General Framework for Information Extraction using Dynamic Span Graphs](https://mlsanity.com/paper/1904.03296/) (2019)
- [Tracking State Changes in Procedural Text: A Challenge Dataset and Models for Process Paragraph Comprehension](https://mlsanity.com/paper/1805.06975/) (2018)
- [Simulating Action Dynamics with Neural Process Networks](https://mlsanity.com/paper/1711.05313/) (2017)
- [The Materials Science Procedural Text Corpus: Annotating Materials Synthesis Procedures with Shallow Semantic Structures](https://mlsanity.com/paper/1905.06939/) (2019)
- [Learning Dynamic Belief Graphs to Generalize on Text-Based Games](https://mlsanity.com/paper/2002.09127/) (2020)
- [A Dataset for Tracking Entities in Open Domain Procedural Text](https://mlsanity.com/paper/2011.08092/) (2020)
- [An Incremental Parser for Abstract Meaning Representation](https://mlsanity.com/paper/1608.06111/) (2016)
- [An Annotated Corpus for Machine Reading of Instructions in Wet Lab Protocols](https://mlsanity.com/paper/1805.00195/) (2018)
- [Annotating and Extracting Synthesis Process of All-Solid-State Batteries from Scientific Literature](https://mlsanity.com/paper/2002.07339/) (2020)
- [Playing by the Book: An Interactive Game Approach for Action Graph Extraction from Text](https://mlsanity.com/paper/1811.04319/) (2018)

## Built on by (most cited first, 16 of 16)

- [ScienceWorld: Is your Agent Smarter than a 5th Grader?](https://mlsanity.com/paper/2203.07540/) (2022)
- [PaperQA: Retrieval-Augmented Generative Agent for Scientific Research](https://mlsanity.com/paper/2312.07559/) (2023)
- [BioPlanner: Automatic Evaluation of LLMs on Protocol Planning in Biology](https://mlsanity.com/paper/2310.10632/) (2023)
- [Pre-train or Annotate? Domain Adaptation with a Constrained Budget](https://mlsanity.com/paper/2109.04711/) (2021)
- [Schema-Driven Information Extraction from Heterogeneous Tables](https://mlsanity.com/paper/2305.14336/) (2023)
- [A Systematic Survey of Text Worlds as Embodied Natural Language Environments](https://mlsanity.com/paper/2107.04132/) (2021)
- [Modeling Worlds in Text](https://mlsanity.com/paper/2106.09578/) (2021)
- [Few-Shot Anaphora Resolution in Scientific Protocols via Mixtures of In-Context Experts](https://mlsanity.com/paper/2210.03690/) (2022)
- [PcMSP: A Dataset for Scientific Action Graphs Extraction from Polycrystalline Materials Synthesis Procedure Text](https://mlsanity.com/paper/2210.12401/) (2022)
- [SynKB: Semantic Search for Synthetic Procedures](https://mlsanity.com/paper/2208.07400/) (2022)
- [Situated Language Learning via Interactive Narratives](https://mlsanity.com/paper/2103.09977/) (2021)
- [Entity Tracking via Effective Use of Multi-Task Learning Model and Mention-guided Decoding](https://mlsanity.com/paper/2210.06444/) (2022)
- [Self-Supervised Behavior Cloned Transformers are Path Crawlers for Text Games](https://mlsanity.com/paper/2312.04657/) (2023)
- [Towards Flow Graph Prediction of Open-Domain Procedural Texts](https://mlsanity.com/paper/2305.19497/) (2023)
- [Notes2Skills: From Lab Notebooks to Certainty-Aware Scientific Agent Skills](https://mlsanity.com/paper/2606.11897/) (2026)
- [Representation Alignment as a Bottleneck in LLM-Based Retrosynthesis Planning](https://mlsanity.com/paper/2609.35571/) (2026)

## Abstract (arXiv)

We develop Process Execution Graphs (PEG), a document-level representation of real-world wet lab biochemistry protocols, addressing challenges such as cross-sentence relations, long-range coreference, grounding, and implicit arguments. We manually annotate PEGs in a corpus of complex lab protocols with a novel interactive textual simulator that keeps track of entity traits and semantic constraints during annotation. We use this data to develop graph-prediction models, finding them to be good at entity identification and local relation extraction, while our corpus facilitates further exploration of challenging long-range relations.