scientific software developers

Abstract: Scientific research increasingly relies on large, heterogeneous data sources, motivating interest in retrieval-augmented generation (RAG) systems that provide natural language access to scientific knowledge and research workflows. Researchers are exploring the viability of these systems as natural language interfaces for document search and for generating analysis code and pipeline components. At the same time, concerns about data privacy and control over research infrastructure have motivated interest in open-weight models and open-source deployments hosted within research institutions. In astronomy, this development follows a long history of computational infrastructure development, from archival databases and SQL-based systems to LLM-assisted research tools. This paper presents a domain-expert evaluation of faithfulness for AquiLLM, an open-weight, offline RAG-LLM platform designed to support scientific research groups in the use and preservation of tacit and formal knowledge. We define faithfulness as the extent to which generated responses remain grounded in retrieved scientific context without unsupported claims or omissions. We report results from an astronomy case study evaluating AquiLLM across retrieval and scientific analysis tasks. AquiLLM performs most reliably on explicit retrieval-oriented questions grounded in the RAG collection, while faithfulness degrades for queries requiring synthesis or ambiguity resolution. These results highlight both the promise and limitations of open-weight RAG-LLM systems for scientific research and demonstrate the importance of domain-expert evaluation beyond standard benchmark leaderboards.

Abstract: As artificial intelligence's capabilities improve, it is increasingly viewed as a general scientific method. But how true are these claims? Does AI outperform all techniques, or only some, and how is this changing? To assess the claims, we assemble a corpus of 2,507 head-to-head comparisons between AI and other scientific analysis techniques across 27 scientific disciplines from papers published between 2000 and early 2025. We find a profound dichotomy. Relative to traditional statistics, AI often outperforms, but at a significantly higher computational cost. But there are also nearly a quarter of cases where AI is both more expensive and performs worse than traditional statistical techniques and this fraction has been stable for a decade. Relative to scientific computing, AI often underperforms, but at lower computational cost. This has begun to change: since 2020, AI's performance against scientific computing has notably strengthened and it now outperforms on more than half of comparisons. These patterns suggest that AI is therefore not a universal replacement for existing methods, but rather a valuable -- and improving -- part of a new AI-enabled scientific frontier.

Abstract: Automating filament tracing in Cryo-Electron Microscopy (Cryo-EM) is essential for 3D helical reconstruction but challenged by intersecting topologies and extremely low Signal-to-Noise Ratios ($\text{SNR} = σ_s^2/σ_n^2$ < 0.1 or -10 dB). Existing paradigms fail: pixel-wise segmenters suffer from severe topological fracturing, box-based detectors face ghost center drift, sequential trackers derail due to error accumulation, and traditional active contours collapse under artificial closed-curve constraints. To resolve these bottlenecks, we present FPicker, the first topology-guided framework reconciling these incompatibilities. It unifies perception via a center-endpoint representation and an open-curve evolution module to explicitly model non-cyclic connectivity. On simulated benchmarks, FPicker outperforms top baselines by over $40\%$ relative gain in mean spatio-angular precision (mSAP) and reduces topological gap rates by over $60\%$ under extreme noise ($-20\text{ dB}$). By learning intrinsic physical geometry rather than local texture, FPicker demonstrates strong potential as a resilient geometric backbone. Its zero-shot performance on the real-world EMPIAR dataset exhibits robust topological resistance, achieving a state-of-the-art 82.9\% mSAP upon fine-tuning. Our results also suggest modeling physical priors is a highly robust path toward bridging the sim-to-real gap in signal-starved scientific imaging. The code is publicly available at: https://github.com/tomzhaosky/FPicker.