arXiv subjects

Nazia Riasat

Publications and source records attributed to Nazia Riasat.

3 recordsLinked to original sources

arXiv2026

SciSchema.org: A Multidisciplinary Collection of Schemas for Structured Scientific Process Descriptions

Scientific processes are often described in heterogeneous article discourse, with details needed for comparison, reproducibility, reuse, and automation dispersed across prose, tables, figures, protocols, and supplementary files. We present the first release of SciSchema.org, a multidisciplinary collection of 16 expert-annotated schemas spanning Biology & Biotechnology, Materials & Chemistry, Imaging & Measurement, Physics, and Psychology. Each schema defines reusable fields for describing process instances, including inputs, outputs, materials, instruments or software, parameters, conditions, procedural steps, measurements, and provenance-related information. The schemas were created through a human-in-the-loop schema-mining workflow in which large language models generated candidate structures from process specifications, scientific articles, and expert feedback, followed by domain-expert construction of final master schemas. The dataset contains final schemas in JSON Schema and SHACL formats, intermediate model-generated schemas, expert-feedback records, source-paper metadata, community-development materials, and analysis scripts. Technical validation assessed schema structure, development provenance, expert review, and syntactic conformance. The collection supports structured annotation, metadata enrichment, scientific knowledge graphs, information extraction, semantic publishing, and cross-study comparison.

cs.DL↗

arXiv2026

When Marginals Match but Structure Fails: Covariance Fidelity in Generative Models

Generative models are increasingly deployed as substitutes for real data in downstream scientific workflows, yet standard evaluation criteria remain focused on marginal distribution matching. We argue that this represents a fundamental gap: downstream inference is rarely a marginal operation, and a model that passes every univariate diagnostic can still produce structurally unreliable synthetic data. We introduce covariance-level dependence fidelity, measured by D_Sigma(P,Q) = ||Sigma_P - Sigma_Q||_F, as a principled, computable criterion for evaluating whether a generative model preserves the joint structure of data beyond its univariate marginals. Three results formalise this criterion. First, marginal fidelity provides no constraint on dependence structure: D_Sigma can be made arbitrarily large while all univariate marginals match exactly. Second, covariance divergence induces quantifiable downstream instability, including sign reversals in population regression coefficients. Third, bounding D_Sigma provides positive stability guarantees for dependence-sensitive procedures such as PCA via Davis-Kahan-type bounds. Empirical validation across three domains, image data (Fashion-MNIST VAE, n = 60,000), bulk RNA-seq (TCGA-BRCA, n = 1,111), and a small-sample stress test (Alzheimer's gene expression, n = 113), shows that D_Sigma/delta consistently distinguishes structure-discarding from structure-preserving generators in cases where standard marginal diagnostics show little separation, confirming that covariance-level fidelity provides information orthogonal to existing evaluation metrics across domains and sample sizes.

stat.ML↗

arXiv2026

When Stability Fails: Hidden Failure Modes Of LLMS in Data-Constrained Scientific Decision-Making

Large language models (LLMs) are increasingly used as decision-support tools in data-constrained scientific workflows, where correctness and validity are critical. However, evaluation practices often emphasize stability or reproducibility across repeated runs. While these properties are desirable, stability alone does not guar- antee agreement with statistical ground truth when such references are available. We introduce a controlled behavioral evaluation framework that explicitly sep- arates four dimensions of LLM decision-making: stability, correctness, prompt sensitivity, and output validity under fixed statistical inputs. We evaluate multi- ple LLMs using a statistical gene prioritization task derived from differential ex- pression analysis across prompt regimes involving strict and relaxed significance thresholds, borderline ranking scenarios, and minor wording variations. Our ex- periments show that LLMs can exhibit near-perfect run-to-run stability while sys- tematically diverging from statistical ground truth, over-selecting under relaxed thresholds, responding sharply to minor prompt wording changes, or producing syntactically plausible gene identifiers absent from the input table. Although sta- bility reflects robustness across repeated runs, it does not guarantee agreement with statistical ground truth in structured scientific decision tasks. These findings highlight the importance of explicit ground-truth validation and output validity checks when deploying LLMs in automated or semi-automated scientific work- flows.

cs.LG↗