Bridging Through Absence: How Comeback Researchers Bridge Knowledge Gaps Through Structural Re-emergence

Scientific progress emerges from a longitudinal ecosystem in which researchers, institutions, funding agencies, collaboration networks, and the scientific literature co-evolve. As AI becomes increasingly involved throughout the scientific research cycle, understanding these interconnected and evolving processes becomes increasingly important. We introduce SciUtopia, a persistent, closed-loop LLM-agent simulation framework for studying academic research ecosystems. SciUtopia models interconnected scientific processes such as research-direction choice, collaboration, submission, peer review, resubmission, citation, funding, and researcher attrition, while maintaining evolving states across simulated years. Its configurable institutional mechanisms and information channels provide a controlled testbed for matched counterfactual experiments and targeted interventions. Across 61 simulation worlds, SciUtopia simulates over 40,000 researchers from 8,000 institutions, producing around 400,000 publication decisions and 1.2 million LLM-generated peer reviews. Using these longitudinal simulations, we find that rejection-driven resubmission substantially amplifies reviewer burden beyond population growth alone, cautious exploration balances citation impact with career success and long-term topic diversity, and resource inequality can emerge even without detectable cumulative advantage from narrowly winning early funding. Code is available at https://github.com/Ahren09/ScienceUtopia.

Can a language model recover the true research idea of a published paper when given only that paper's pre-publication bibliography? We introduce Reconstruction, a blind idea-recovery benchmark that withholds the seed paper and all contemporaneous or future literature, and asks models to propose hypotheses that an independent large language model judge matches against the held-out ground-truth idea. A strict anti-leakage protocol-temporal citation cutoff, anonymous reference IDs, and frozen per-paper bibliographies, which prevents prompt-time leakage of the seed idea. Across six scientific domains and 643 evaluated papers, seven frontier models achieve only modest Match rates (approx. 3-15%). We then evaluate a reference-only multi-agent (top 4) pipeline that combines cross-model review with a Swiss tournament over aligned hypothesis slots, without external web search. Cross-model review plus tournament selection raises Match rates to approx. 23-42% across all six domains, which is an observed approx. 2.4x lift over the best single-model baseline. This draft reports the protocol, anti-leakage design, and current results as an arXiv timestamp.

We present a semantic-structural atlas of transportation research built from 120{,}323 papers across 34 peer-reviewed journals published between 1967 and 2025, roughly an order of magnitude larger than and a decade beyond Sun and Rahwan's~(2017) coauthorship study. We use OpenAlex and Crossref as open, CC0-licensed data sources, resolve author identity through OpenAlex author IDs, ORCID records, and manual alias resolution, and embed every paper with SPECTER2 with Arora-style whitening concatenated with concept TF--IDF and venue linear-discriminant projections. On this substrate we report three findings. First, Leiden on the author-level semantic k-nearest-neighbor graph yields 23 topic communities that agree only weakly with the 172 coauthor communities (normalized mutual information $0.23$), opening room for a predictive layer that neither source encodes alone. Second, a multiplex Leiden partition combining both edge types recovers 181 communities and localizes where collaboration and topic structure decouple. Third -- the paper's core methodological contribution -- we define phantom collaborators, pairs of authors who are top-$K$ semantic neighbors yet $\geq 3$ hops apart in the coauthor graph, and show via a temporal hold-out (training cutoff 2019) that phantom pairs become real coauthors in 2020--2025 at a rate $16$ to $33$ times above random, popularity-weighted, and same-venue baselines, with a $68$-fold monotone gradient between the highest- and lowest-similarity buckets. All artifacts are released as a live, reproducible web atlas at https://choi-seongjin.github.io/transport-atlas/.