Seeking answers to questions within long scientific research articles is a crucial area of study that aids readers in quickly addressing their inquiries. However, existing question-answering (QA) datasets based on scientific papers are limited in scale and focus solely on textual content. We introduce SPIQA (Scientific Paper Image Question Answering), the first large-scale QA dataset specifically designed to interpret complex figures and tables within the context of scientific research articles across various domains of computer science. Leveraging the breadth of expertise and ability of multimodal large language models (MLLMs) to understand figures, we employ automatic and manual curation to create the dataset. We craft an information-seeking task on interleaved images and text that involves multiple images covering a wide variety of plots, charts, tables, schematic diagrams, and result visualizations. SPIQA comprises 270K questions divided into training, validation, and three different evaluation splits. Through extensive experiments with 12 prominent foundational models, we evaluate the ability of current multimodal systems to comprehend the nuanced aspects of research articles. Additionally, we propose a Chain-of-Thought (CoT) evaluation strategy with in-context retrieval that allows fine-grained, step-by-step assessment and improves model performance. We further explore the upper bounds of performance enhancement with additional textual information, highlighting its promising potential for future research and the dataset's impact on revolutionizing how we interact with scientific literature.

Deep Research Agents (DRAs) can autonomously conduct complex investigations and generate comprehensive reports, demonstrating strong real-world potential. However, existing benchmarks primarily evaluate DRAs on generic quality metrics and overlook personalization, a critical dimension for individual users. However, existing evaluations mostly rely on close-ended benchmarks, while open-ended deep research benchmarks remain scarce and typically neglect personalized scenarios. To bridge this gap, we introduce Personalized Deep Research Bench (PDR-Bench), the first benchmark for evaluating personalization in DRAs. It pairs 50 diverse research tasks across 10 domains with 25 authentic user profiles that combine structured persona attributes with dynamic real-world contexts, yielding 250 realistic user-task queries. To assess system performance, we propose the PQR Evaluation Framework, which jointly measures Personalization Alignment, Content Quality, and Factual Reliability. Our experiments on a range of systems highlight current capabilities and limitations in handling personalized deep research. This work establishes a rigorous foundation for developing and evaluating the next generation of truly personalized AI research assistants.

Neuroscience research publications encompass a vast wealth of knowledge. Accurately retrieving existing information and discovering new insights from this extensive literature is essential for advancing the field. However, when knowledge is dispersed across multiple sources, current state-of-the-art retrieval methods often struggle to extract the necessary information. A knowledge graph (KG) can integrate and link knowledge from multiple sources. However, existing methods for constructing KGs in neuroscience often rely on labeled data and require domain expertise. Acquiring large-scale, labeled data for a specialized area like neuroscience presents significant challenges. This work proposes novel methods for constructing KG from unlabeled large-scale neuroscience research corpus utilizing large language models (LLM), neuroscience ontology, and text embeddings. We analyze the semantic relevance of neuroscience text segments identified by LLM for building the knowledge graph. We also introduce an entity-augmented information retrieval algorithm to extract knowledge from the KG. Several experiments were conducted to evaluate the proposed approaches. The results demonstrate that our methods significantly enhance knowledge discovery from the unlabeled neuroscience research corpus. The performance of the proposed entity and relation extraction method is comparable to the existing supervised method. It achieves an F1 score of 0.84 for entity extraction from the unlabeled data. The knowledge obtained from the KG improves answers to over 52% of neuroscience questions from the PubMedQA dataset and questions generated using selected neuroscience entities.

Developing effective prompts demands significant cognitive investment to generate reliable, high-quality responses from Large Language Models (LLMs). By deploying case-specific prompt engineering techniques that streamline frequently performed life sciences workflows, researchers could achieve substantial efficiency gains that far exceed the initial time investment required to master these techniques. The Prompt Report published in 2025 outlined 58 different text-based prompt engineering techniques, highlighting the numerous ways prompts could be constructed. To provide actionable guidelines and reduce the friction of navigating these various approaches, we distil this report to focus on 6 core techniques: zero-shot, few-shot approaches, thought generation, ensembling, self-criticism, and decomposition. We breakdown the significance of each approach and ground it in use cases relevant to life sciences, from literature summarization and data extraction to editorial tasks. We provide detailed recommendations for how prompts should and shouldn't be structured, addressing common pitfalls including multi-turn conversation degradation, hallucinations, and distinctions between reasoning and non-reasoning models. We examine context window limitations, agentic tools like Claude Code, while analyzing the effectiveness of Deep Research tools across OpenAI, Google, Anthropic and Perplexity platforms, discussing current limitations. We demonstrate how prompt engineering can augment rather than replace existing established individual practices around data processing and document editing. Our aim is to provide actionable guidance on core prompt engineering principles, and to facilitate the transition from opportunistic prompting to an effective, low-friction systematic practice that contributes to higher quality research.

Seeking answers to questions within long scientific research articles is a crucial area of study that aids readers in quickly addressing their inquiries. However, existing question-answering (QA) datasets based on scientific papers are limited in scale and focus solely on textual content. We introduce SPIQA (Scientific Paper Image Question Answering), the first large-scale QA dataset specifically designed to interpret complex figures and tables within the context of scientific research articles across various domains of computer science. Leveraging the breadth of expertise and ability of multimodal large language models (MLLMs) to understand figures, we employ automatic and manual curation to create the dataset. We craft an information-seeking task on interleaved images and text that involves multiple images covering a wide variety of plots, charts, tables, schematic diagrams, and result visualizations.

In recent years, there has been a growing concern and emphasis on conducting research beyond academic or scientific research communities, benefiting society at large. A well-known approach to measuring the impact of research on society is enumerating its policy citation(s). Despite the importance of research in informing policy, there is no concrete evidence to suggest the research's relevance in cited policy documents. This is concerning because it may increase the possibility of evidence used in policy being manipulated by individual, social, or political biases that may lead to inappropriate, fragmented, or archaic research evidence in policy. Therefore, it is crucial to identify the degree of relevance between research articles and citing policy documents. In this paper, we examined the scale of contextual relevance of youth-focused research in the referenced US policy documents using natural language processing techniques, state-of-the-art pre-trained Large Language Models (LLMs), and statistical analysis. Our experiments and analysis concluded that youth-related research articles that get US policy citations are mostly relevant to the citing policy documents.

While the Water-Gas Shift (WGS) reaction plays a crucial role in hydrogen production for fuel cells, finding suitable catalysts to achieve high yields for low-temperature WGS reactions remains a persistent challenge. Artificial Intelligence (AI) has shown promise in accelerating catalyst design by exploring vast candidate spaces, however, two key gaps limit its effectiveness. First, AI models primarily train on numerical data, which fail to capture essential text-based information, such as catalyst synthesis methods. Second, the cross-disciplinary nature of catalyst design requires seamless collaboration between AI, theory, experiments, and numerical simulations, often leading to communication barriers. To address these gaps, we present AceWGS, a Large Language Models (LLMs)-aided framework to streamline WGS catalyst design. AceWGS interacts with researchers through natural language, answering queries based on four features: (i) answering general queries, (ii) extracting information about the database comprising WGS-related journal articles, (iii) comprehending the context described in these articles, and (iv) identifying catalyst candidates using our proposed AI inverse model. We presented a practical case study demonstrating how AceWGS can accelerate the catalyst design process. AceWGS, built with open-source tools, offers an adjustable framework that researchers can readily adapt for a range of AI-accelerated catalyst design applications, supporting seamless integration across cross-disciplinary studies.

Context: Machine Learning (ML) significantly impacts Software Engineering (SE), but studies mainly focus on practitioners, neglecting researchers. This overlooks practices and challenges in teaching, researching, or reviewing ML applications in SE. Objective: This study aims to contribute to the knowledge, about the synergy between ML and SE from the perspective of SE researchers, by providing insights into the practices followed when researching, teaching, and reviewing SE studies that apply ML. Method: We analyzed SE researchers familiar with ML or who authored SE articles using ML, along with the articles themselves. We examined practices, SE tasks addressed with ML, challenges faced, and reviewers' and educators' perspectives using grounded theory coding and qualitative analysis. Results: We found diverse practices focusing on data collection, model training, and evaluation. Some recommended practices (e.g., hyperparameter tuning) appeared in less than 20\% of literature. Common challenges involve data handling, model evaluation (incl. non-functional properties), and involving human expertise in evaluation. Hands-on activities are common in education, though traditional methods persist. Conclusion: Despite accepted practices in applying ML to SE, significant gaps remain. By enhancing guidelines, adopting diverse teaching methods, and emphasizing underrepresented practices, the SE community can bridge these gaps and advance the field.

In the digital age, the amount of scholarly articles is growing exponentially. In the Open Research Knowledge Graph's question-answering facility ASK, for example, more than 80 million research articles have already been indexed. Finding the most relevant information from vast collections of scholarly data can be daunting for researchers, students, and academics. To tackle this challenge, search engines and digital libraries often rely on advanced search techniques, one of the most effective being faceted search. Faceted search is an advanced search method that allows users to filter and refine search results based on multiple predefined attributes, known as facets.

Large Language Models (LLMs) excel in data synthesis but can be inaccurate in domain-specific tasks, which retrieval-augmented generation (RAG) systems address by leveraging user-provided data. However, RAGs require optimization in both retrieval and generation stages, which can affect output quality. In this paper, we present LLM-Ref, a writing assistant tool that aids researchers in writing articles from multiple source documents with enhanced reference synthesis and handling capabilities. Unlike traditional RAG systems that use chunking and indexing, our tool retrieves and generates content directly from text paragraphs. This method facilitates direct reference extraction from the generated outputs, a feature unique to our tool. Additionally, our tool employs iterative response generation, effectively managing lengthy contexts within the language model's constraints. Compared to baseline RAG-based systems, our approach achieves a $3.25\times$ to $6.26\times$ increase in Ragas score, a comprehensive metric that provides a holistic view of a RAG system's ability to produce accurate, relevant, and contextually appropriate responses. This improvement shows our method enhances the accuracy and contextual relevance of writing assistance tools.