research software developers

Abstract: The research idea in a published paper is rarely the project's initial idea. Between the two lies a closed-loop process in which researchers run experiments, derive insights, identify challenges, explore the literature, and revise the idea, with each step motivated by evidence and reasoning they can articulate. We call the path one idea takes through this process, with the evidence and reasoning behind each step, its authentic research trajectory. Although it underlies every scientific contribution, it is rarely recorded. Existing LLM-based research agents generate an idea once, refine it against reviews, literature, or their own experimental results, or search over candidate ideas and experiments. In all of them the text of the idea evolves, while the evidence and reasoning that connected one version to the next are discarded. We propose the Research Progress Graph (RPG), a representation of authentic and complete research trajectories. An RPG records the evolution of an idea as typed research states connected by cognitive transitions, each annotated with a temporal index and the reasoning behind it, which makes this evolution an explicit object of study. We ground the representation in authentic trajectories whose steps their authors justify in annotations and papers. Comparing the representations of thirty-five research agents with the RPG, we find that each is an incomplete RPG; none keeps the state that changed, the evidence that changed it, and the reasoning connecting them as one evolving record. Modeling ideation with the RPG changes how research agents should be designed, evaluated, and trained. Agents predict the next research state instead of a complete idea, ideas are evaluated as trajectories instead of final texts, and authentic trajectories serve as training data. These directions shift research agents from generating static ideas to modeling how ideas evolve.

Abstract: Many scientific advances come from cross-pollination, carrying an idea from one field over to a problem in another. Yet retrieving papers across fields remains underexplored, with existing benchmarks confined to a narrow range of fields. We study cross-pollination retrieval, the problem of identifying transferable ideas across research fields, and introduce CPR-Dataset, a large-scale dataset constructed by mining cross-topic citations. Its evaluation split CPR-eval has 1,300 queries in 26 fields, and its training split CPR-train has 10,573 pairs. On CPR-eval, the best of eleven existing retrievers reaches a Recall@10 of only 0.26, whereas an LLM reranker reaches 0.81. Standard contrastive fine-tuning on CPR-train raises Recall@10 to as high as 0.70. The gain carries over to domains held out from training and to analogy and reasoning-intensive retrieval. On AnaloBench, it raises nDCG@10 by up to 33% over the untrained retriever, whereas training on three existing retrieval datasets lowers it. On BRIGHT, it raises nDCG@10 by up to 70%, more than twice the gain from those datasets. CPR-Dataset is available at https://huggingface.co/CPR-Dataset, and the code at https://github.com/SeokwonJung-Jay/Cross-Pollination-Retrieval.

Abstract: The rapid expansion and specialization of scientific literature make it increasingly difficult to identify not only what is known, but where new and still supportable knowledge may emerge. We introduce Knowledge Manifold Optimization (KMO), a discovery-oriented extension of the Knowledge Manifold framework that treats scientific discovery as a multiobjective search over a continuous, literature-derived knowledge space. Candidate locations are evaluated using four complementary objectives: persistent knowledge-regime boundary strength, band-pass white-space novelty, semanticgradient magnitude, and evidential support. Rather than collapsing these criteria into a single weighted score, KMO identifies Pareto-optimal Supported Knowledge Gaps, defined as corpus-relative unoccupied regions that remain sufficiently supported by surrounding literature. The method is demonstrated on a 99-paper corpus in aerodynamics and aerodynamic design. On a 21 x 21 grid, exact Pareto analysis produced 19 non-dominated points, of which 16 formed the practical front after excluding points with zero white-space score. These solutions exhibited distinct discovery modes, including methodology bridges, aero-structural topology/FSI integration, functional aerodynamic-device integration, and rear-wake/vehicle flow-control integration. A distance-maximization baseline preferentially selected extrapolative regions with substantially lower support and reliability, demonstrating why emptiness alone is insufficient. Representative Pareto locations were converted into auditable evidence packages and then verbalized by a constrained large language model into candidate research hypotheses. The results show that scientific discovery can be formulated as structured multi-objective search in an explicit knowledge space, while keeping novelty corpus-relative and separating numerical discovery from downstream language generation.

Abstract: Recent advances in artificial intelligence have contributed to several information-theoretic results through genuinely different modes: a language model may suggest a proof, participate in an extended mathematical dialogue, coordinate computation, or operate as one component of a search harness. Treating all of these as "AI-discovered mathematics" obscures distinctions that matter for scientific reliability, attribution, and reproducibility. This article examines a set of recent cases through a four-stage pipeline: how the problem was formulated; how AI participated in finding a solution; how the resulting analytical and computational claims were verified; and how machine-generated outputs were translated into mathematical exposition for human understanding. Based on these cases, we recommend that research publications (1) disclose the nature and extent of AI assistance at each stage, (2) report verification of analytical reasoning separately from certification of numerical computations, and (3) place more emphasis on articulating the underlying ideas, techniques, and interpretations.

Abstract: AI-assisted research leaves instructions, computations, artifact revisions and checks whose relationships matter when another researcher receives the work. We present AIPOCH Open-Science, an open-source research workbench with portable .science session packages, and specify an exchange contract for these recorded relationships. Version and assessment targets remain attributable while receiving-workspace identifiers can be remapped, eligible contents can be omitted explicitly, and imported history remains separate from a writable fork. A controlled session tested an incorrect first version, a reviewed correction, an unreviewed revision and a planned but unexecuted step. We compared complete and partial exports with source records extracted independently of the exporter, then inspected imports into separate projects within the same installation. Both conditions retained the tested version and review associations, kept the unreviewed revision distinct from earlier assessments and represented excluded content as unavailable. A documentation-rich ordinary directory also supplied evidence for all seven static inspection questions. A separate registry case connected a table to its recorded task, execution and review; offline execution of its retained script and fixed input reproduced two saved CSV tables byte for byte. The study contributes an implemented exchange contract and a controlled examination of its preservation rules, content-selection constraints and interpretation boundaries.

Abstract: Research software sustainability is often assessed through the FAIR principles: findability, accessibility, interoperability and reusability. While important, FAIR does not cover all relevant sustainability concerns. Research software should also be environmentally responsible and secure over time. Excessive resource consumption increases environmental cost, while insecure software creates maintenance overhead, technical debt and barriers to reuse. To this end, in this paper, we extend a previously proposed fitness function framework for sustainable research software beyond FAIR. We introduce two additional sets of fitness functions: environmental functions targeting resource efficiency and execution footprint, and security functions targeting dependency health, vulnerability exposure and secure configuration. Together, these functions broaden continuous software assessment from FAIR compliance to a more complete view of sustainability. The resulting framework treats research software sustainability as a multidimensional property that includes FAIR, environmental responsibility and long-term security.

Abstract: Software is both a foundational tool and a primary output of modern computational research, yet citation practices for software remain inconsistent, incomplete, and rarely machine-actionable. Existing infrastructure designed for paper and data citation does not adequately serve the distinct needs of software citation, leaving a gap that impedes reproducibility, misattributes scholarly credit, and obscures the labor embedded in research pipelines. Drawing on a NASA-funded community workshop held in April 2026, we present an analysis of four interconnected themes: (I)~the cultural barriers to consistent citation practice; (II)~the need for clearer community norms and conventions; (III)~gaps in existing technical infrastructure and workflow; and (IV)~the emerging challenges posed by AI-assisted research. For each theme we identify targeted interventions and assign responsibility across stakeholder groups. We conclude that meaningful progress requires simultaneous action on technical and cultural fronts. Journal editors and publishers represent the single highest-leverage point for accelerating this change, and correct citation must become the path of least resistance within researchers' existing workflows.

Abstract: Scientific literature search often begins with an open research problem rather than a known target paper or a fixed candidate set. We introduce INSPIRE, a benchmark for evaluating agents that search prior literature to make progress on solution-redacted research problems. Each instance pairs a research brief with a target-specific cutoff three months before a later paper and evaluates ranked outputs against graded cited antecedents from that paper's realized research lineage. Search proceeds over an open corpus, while the identity of the target paper and membership of its cited antecedents remain hidden from the agent. Beyond end-to-end retrieval quality, INSPIRE uses logged search trajectories to distinguish three coupled stages: resource exposure, whether useful antecedents are surfaced during search; selection, whether exposed antecedents are retained; and ranking, how effectively retained papers are ordered. Across 476 computer-science targets under a shared search interface and budget, the strongest evaluated agent achieves 0.284 nDCG@10. Results show that current agents more readily recover an isolated antecedent than assemble a broader portfolio of relevant prior work. The stagewise analysis identifies resource exposure as the largest observed bottleneck, with further losses in selection and ranking. We additionally construct replay-valid hindsight demonstrations and show that they improve held-out search without changing test-time information, establishing that the benchmark provides an actionable learning signal. INSPIRE therefore enables both end-to-end comparison and stage-resolved diagnosis in a setting where the agent must construct its own working criterion of relevance.