Evaluating vision-language models (VLMs) in scientific domains like mathematics and physics poses unique challenges that go far beyond predicting final answers. These domains demand conceptual understanding, symbolic reasoning, and adherence to formal laws, requirements that most existing benchmarks fail to address. In particular, current datasets tend to be static, lacking intermediate reasoning steps, robustness to variations, or mechanisms for verifying scientific correctness. To address these limitations, we introduce PRiSM, a synthetic, fully dynamic, and multimodal benchmark for evaluating scientific reasoning via grounded Python code. PRiSM includes over 24,750 university-level physics and math problems, and it leverages our scalable agent-based pipeline, PrismAgent, to generate well-structured problem instances. Each problem contains dynamic textual and visual input, a generated figure, alongside rich structured outputs: executable Python code for ground truth generation and verification, and detailed step-by-step reasoning. The dynamic nature and Python-powered automated ground truth generation of our benchmark allow for fine-grained experimental auditing of multimodal VLMs, revealing failure modes, uncertainty behaviors, and limitations in scientific reasoning. To this end, we propose five targeted evaluation tasks covering generalization, symbolic program synthesis, perturbation robustness, reasoning correction, and ambiguity resolution. Through comprehensive evaluation of existing VLMs, we highlight their limitations and showcase how PRiSM enables deeper insights into their scientific reasoning capabilities.

AI Scientific Assistant Core (AISAC) is an integrated multi-agent system developed at Argonne National Laboratory for scientific and engineering workflows. AISAC builds on established technologies - LangGraph for orchestration, FAISS for vector search, and SQLite for persistence - and integrates them into a unified system prototype focused on transparency, provenance tracking, and scientific adaptability. The system implements a Router-Planner-Coordinator workflow and an optional Evaluator role, using prompt-engineered agents coordinated via LangGraph's StateGraph and supported by helper agents such as a Researcher. Each role is defined through custom system prompts that enforce structured JSON outputs. A hybrid memory approach (FAISS + SQLite) enables both semantic retrieval and structured conversation history. An incremental indexing strategy based on file hashing minimizes redundant re-embedding when scientific corpora evolve. A configuration-driven project bootstrap layer allows research teams to customize tools, prompts, and data sources without modifying core code. All agent decisions, tool invocations, and retrievals are logged and visualized through a custom Gradio interface, providing step-by-step transparency for each reasoning episode. The authors have applied AISAC to multiple research areas at Argonne, including specialized deployments for waste-to-products research and energy process safety, as well as general-purpose scientific assistance, demonstrating its cross-domain applicability.

Large language models (LLMs) are increasingly used in scientific domains. While they can produce reasoning-like content via methods such as chain-of-thought prompting, these outputs are typically unstructured and informal, obscuring whether models truly understand the fundamental reasoning paradigms that underpin scientific inference. To address this, we introduce a novel task named Latent Reasoning Chain Extraction (ARCHE), in which models must decompose complex reasoning arguments into combinations of standard reasoning paradigms in the form of a Reasoning Logic Tree (RLT). In RLT, all reasoning steps are explicitly categorized as one of three variants of Peirce's fundamental inference modes: deduction, induction, or abduction. To facilitate this task, we release ARCHE Bench, a new benchmark derived from 70 Nature Communications articles, including more than 1,900 references and 38,000 viewpoints. We propose two logic-aware evaluation metrics: Entity Coverage (EC) for content completeness and Reasoning Edge Accuracy (REA) for step-by-step logical validity. Evaluations on 10 leading LLMs on ARCHE Bench reveal that models exhibit a trade-off between REA and EC, and none are yet able to extract a complete and standard reasoning chain. These findings highlight a substantial gap between the abilities of current reasoning models and the rigor required for scientific argumentation.

The deep-research framework orchestrates external tools to perform complex, multi-step scientific reasoning that exceeds the native limits of a single large language model. However, it still suffers from context pollution, weak evidentiary support, and brittle execution paths. To address these issues, we propose DualResearch, a retrieval and fusion framework that matches the epistemic structure of tool-intensive reasoning by jointly modeling two complementary graphs: a breadth semantic graph that encodes stable background knowledge, and a depth causal graph that captures execution provenance. Each graph has a layer-native relevance function, seed-anchored semantic diffusion for breadth, and causal-semantic path matching with reliability weighting for depth. To reconcile their heterogeneity and query-dependent uncertainty, DualResearch converts per-layer path evidence into answer distributions and fuses them in log space via an entropy-gated rule with global calibration. The fusion up-weights the more certain channel and amplifies agreement. As a complement to deep-research systems, DualResearch compresses lengthy multi-tool execution logs into a concise reasoning graph, and we show that it can reconstruct answers stably and effectively. On the scientific reasoning benchmarks HLE and GPQA, DualResearch achieves competitive performance. Using log files from the open-source system InternAgent, its accuracy improves by 7.7% on HLE and 6.06% on GPQA.

Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples generated from templates and grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.

The complexity of modern bioinformatics analysis has created a critical gap between data generation and developing scientific insights. While large language models (LLMs) have shown promise in scientific reasoning, they remain fundamentally limited when dealing with real-world analytical workflows that demand iterative computation, tool integration and rigorous validation. We introduce K-Dense Analyst, a hierarchical multi-agent system that achieves autonomous bioinformatics analysis through a dual-loop architecture. K-Dense Analyst, part of the broader K-Dense platform, couples planning with validated execution using specialized agents to decompose complex objectives into executable, verifiable tasks within secure computational environments. On BixBench, a comprehensive benchmark for open-ended biological analysis, K-Dense Analyst achieves 29.2% accuracy, surpassing the best-performing language model (GPT-5) by 6.3 percentage points, representing nearly 27% improvement over what is widely considered the most powerful LLM available. Remarkably, K-Dense Analyst achieves this performance using Gemini 2.5 Pro, which attains only 18.3% accuracy when used directly, demonstrating that our architectural innovations unlock capabilities far beyond the underlying model's baseline performance. Our insights demonstrate that autonomous scientific reasoning requires more than enhanced language models, it demands purpose-built systems that can bridge the gap between high-level scientific objectives and low-level computational execution. These results represent a significant advance toward fully autonomous computational biologists capable of accelerating discovery across the life sciences.

Scientific reasoning requires not only long-chain reasoning processes, but also knowledge of domain-specific terminologies and adaptation to updated findings. To deal with these challenges for scientific reasoning, we introduce RAISE, a step-by-step retrieval-augmented framework which retrieves logically relevant documents from in-the-wild corpus. RAISE is divided into three steps: problem decomposition, logical query generation, and logical retrieval. We observe that RAISE consistently outperforms other baselines on scientific reasoning benchmarks. We analyze that unlike other baselines, RAISE retrieves documents that are not only similar in terms of the domain knowledge, but also documents logically more relevant.

Large language models (LLMs) have demonstrated remarkable capabilities in natural language understanding, reasoning, and problem-solving across various domains. However, their ability to perform complex, multi-step reasoning task-essential for applications in science, medicine, and law-remains an area of active investigation. This paper examines the reasoning capabilities of contemporary LLMs, analyzing their strengths, limitations, and potential for improvement. The study uses prompt engineering techniques on the Graduate-Level GoogleProof Q&A (GPQA) dataset to assess the scientific reasoning of GPT-4o. Five popular prompt engineering techniques and two tailored promptings were tested: baseline direct answer (zero-shot), chain-of-thought (CoT), zero-shot CoT, self-ask, self-consistency, decomposition, and multipath promptings. Our findings indicate that while LLMs exhibit emergent reasoning abilities, they often rely on pattern recognition rather than true logical inference, leading to inconsistencies in complex problem-solving. The results indicated that self-consistency outperformed the other prompt engineering technique with an accuracy of 52.99%, followed by direct answer (52.23%). Zero-shot CoT (50%) outperformed multipath (48.44%), decomposition (47.77%), self-ask (46.88%), and CoT (43.75%). Self-consistency performed the second worst in explaining the answers. Simple techniques such as direct answer, CoT, and zero-shot CoT have the best scientific reasoning. We propose a research agenda aimed at bridging these gaps by integrating structured reasoning frameworks, hybrid AI approaches, and human-in-the-loop methodologies. By critically evaluating the reasoning mechanisms of LLMs, this paper contributes to the ongoing discourse on the future of artificial general intelligence and the development of more robust, trustworthy AI systems.