Deep Learning
GuessingGame: Measuring the Informativeness of Open-Ended Questions in Large Language Models
Hutson, Dylan, Vennemeyer, Daniel, Deshmukh, Aneesh, Zhan, Justin, Jiang, Tianyu
We introduce GuessingGame, a protocol for evaluating large language models (LLMs) as strategic question-askers in open-ended, open-domain settings. A Guesser LLM identifies a hidden object by posing free-form questions to an Oracle without predefined choices or candidate lists. To measure question quality, we propose two information gain (IG) metrics: a Bayesian method that tracks belief updates over semantic concepts using LLM-scored relevance, and an entropy-based method that filters candidates via ConceptNet. Both metrics are model-agnostic and support post hoc analysis. Across 858 games with multiple models and prompting strategies, higher IG strongly predicts efficiency: a one-standard-deviation IG increase reduces expected game length by 43\%. Prompting constraints guided by IG, such as enforcing question diversity, enable weaker models to significantly improve performance. These results show that question-asking in LLMs is both measurable and improvable, and crucial for interactive reasoning.
What Does Your Benchmark Really Measure? A Framework for Robust Inference of AI Capabilities
Evaluations of generative models on benchmark data are now ubiquitous, and their outcomes critically shape public and scientific expectations of AI's capabilities. Yet growing skepticism surrounds their reliability. How can we know that a reported accuracy genuinely reflects a model's true performance? Evaluations are often presented as simple measurements, but in reality they are inferences: to treat benchmark scores as evidence of capability is already to assume a theory of what capability is and how it manifests in a test. We make this step explicit by proposing a principled framework for evaluation as inference: begin from a theory of capability, and then derive methods for estimating it. This perspective, familiar in fields such as psychometrics, has not yet become commonplace in AI evaluation. As a proof of concept, we address a central challenge that undermines reliability: sensitivity to perturbations. After formulating a model of ability, we introduce methods that infer ability while accounting for uncertainty from sensitivity and finite samples, including an adaptive algorithm that significantly reduces sample complexity. Together, these contributions lay the groundwork for more reliable and trustworthy estimates of AI capabilities as measured through benchmarks.
Reverse Engineering User Stories from Code using Large Language Models
Ouf, Mohamed, Li, Haoyu, Zhang, Michael, Guizani, Mariam
User stories are essential in agile development, yet often missing or outdated in legacy and poorly documented systems. We investigate whether large language models (LLMs) can automatically recover user stories directly from source code and how prompt design impacts output quality. Using 1,750 annotated C++ snippets of varying complexity, we evaluate five state-of-the-art LLMs across six prompting strategies. Results show that all models achieve, on average, an F1 score of 0.8 for code up to 200 NLOC. Our findings show that a single illustrative example enables the smallest model (8B) to match the performance of a much larger 70B model. In contrast, structured reasoning via Chain-of-Thought offers only marginal gains, primarily for larger models.
A Foundation Chemical Language Model for Comprehensive Fragment-Based Drug Discovery
Ho, Alexander, Lee, Sukyeong, Tsai, Francis T. F.
We introduce FragAtlas-62M, a specialized foundation model trained on the largest fragment dataset to date. Built on the complete ZINC-22 fragment subset comprising over 62 million molecules, it achieves unprecedented coverage of fragment chemical space. Our GPT-2 based model (42.7M parameters) generates 99.90% chemically valid fragments. Validation across 12 descriptors and three fingerprint methods shows generated fragments closely match the training distribution (all effect sizes < 0.4). The model retains 53.6% of known ZINC fragments while producing 22% novel structures with practical relevance. We release FragAtlas-62M with training code, preprocessed data, documentation, and model weights to accelerate adoption.
Nano Bio-Agents (NBA): Small Language Model Agents for Genomics
Hong, George, Banos, Daniel Trejo
We investigate the application of Small Language Models (<10 billion parameters) for genomics question answering via agentic framework to address hallucination issues and computational cost challenges. The Nano Bio-Agent (NBA) framework we implemented incorporates task decomposition, tool orchestration, and API access into well-established systems such as NCBI and AlphaGenome. Results show that SLMs combined with such agentic framework can achieve comparable and in many cases superior performance versus existing approaches utilising larger models, with our best model-agent combination achieving 98% accuracy on the GeneTuring benchmark. Notably, small 3-10B parameter models consistently achieve 85-97% accuracy while requiring much lower computational resources than conventional approaches. This demonstrates promising potential for efficiency gains, cost savings, and democratization of ML-powered genomics tools while retaining highly robust and accurate performance.
Uncertainty in Semantic Language Modeling with PIXELS
Radu, Stefania, Zullich, Marco, Valdenegro-Toro, Matias
Pixel-based language models aim to solve the vocabulary bottleneck problem in language modeling, but the challenge of uncertainty quantification remains open. The novelty of this work consists of analysing uncertainty and confidence in pixel-based language models across 18 languages and 7 scripts, all part of 3 semantically challenging tasks. This is achieved through several methods such as Monte Carlo Dropout, Transformer Attention, and Ensemble Learning. The results suggest that pixel-based models underestimate uncertainty when reconstructing patches. The uncertainty is also influenced by the script, with Latin languages displaying lower uncertainty. The findings on ensemble learning show better performance when applying hyperparameter tuning during the named entity recognition and question-answering tasks across 16 languages.
Semantic-Aware Fuzzing: An Empirical Framework for LLM-Guided, Reasoning-Driven Input Mutation
Lu, Mengdi, Ding, Steven, Alaca, Furkan, Charland, Philippe
Security vulnerabilities in Internet-of-Things devices, mobile platforms, and autonomous systems remain critical. Traditional mutation-based fuzzers -- while effectively explore code paths -- primarily perform byte- or bit-level edits without semantic reasoning. Coverage-guided tools such as AFL++ use dictionaries, grammars, and splicing heuristics to impose shallow structural constraints, leaving deeper protocol logic, inter-field dependencies, and domain-specific semantics unaddressed. Conversely, reasoning-capable large language models (LLMs) can leverage pretraining knowledge to understand input formats, respect complex constraints, and propose targeted mutations, much like an experienced reverse engineer or testing expert. However, lacking ground truth for "correct" mutation reasoning makes supervised fine-tuning impractical, motivating explorations of off-the-shelf LLMs via prompt-based few-shot learning. To bridge this gap, we present an open-source microservices framework that integrates reasoning LLMs with AFL++ on Google's FuzzBench, tackling asynchronous execution and divergent hardware demands (GPU- vs. CPU-intensive) of LLMs and fuzzers. We evaluate four research questions: (R1) How can reasoning LLMs be integrated into the fuzzing mutation loop? (R2) Do few-shot prompts yield higher-quality mutations than zero-shot? (R3) Can prompt engineering with off-the-shelf models improve fuzzing directly? and (R4) Which open-source reasoning LLMs perform best under prompt-only conditions? Experiments with Llama3.3, Deepseek-r1-Distill-Llama-70B, QwQ-32B, and Gemma3 highlight Deepseek as the most promising. Mutation effectiveness depends more on prompt complexity and model choice than shot count. Response latency and throughput bottlenecks remain key obstacles, offering directions for future work.
AIRwaves at CheckThat! 2025: Retrieving Scientific Sources for Implicit Claims on Social Media with Dual Encoders and Neural Re-Ranking
Ashbaugh, Cem, Baumgรคrtner, Leon, Gress, Tim, Sidorov, Nikita, Werner, Daniel
Linking implicit scientific claims made on social media to their original publications is crucial for evidence-based fact-checking and scholarly discourse, yet it is hindered by lexical sparsity, very short queries, and domain-specific language. Team AIRwaves ranked second in Subtask 4b of the CLEF-2025 CheckThat! Lab with an evidence-retrieval approach that markedly outperforms the competition baseline. The optimized sparse-retrieval baseline(BM25) achieves MRR@5 = 0.5025 on the gold label blind test set. To surpass this baseline, a two-stage retrieval pipeline is introduced: (i) a first stage that uses a dual encoder based on E5-large, fine-tuned using in-batch and mined hard negatives and enhanced through chunked tokenization and rich document metadata; and (ii) a neural re-ranking stage using a SciBERT cross-encoder. Replacing purely lexical matching with neural representations lifts performance to MRR@5 = 0.6174, and the complete pipeline further improves to MRR@5 = 0.6828. The findings demonstrate that coupling dense retrieval with neural re-rankers delivers a powerful and efficient solution for tweet-to-study matching and provides a practical blueprint for future evidence-retrieval pipelines.
STARQA: A Question Answering Dataset for Complex Analytical Reasoning over Structured Databases
Maddela, Mounica, Xie, Lingjue, Preotiuc-Pietro, Daniel, Mausam, null
Semantic parsing methods for converting text to SQL queries enable question answering over structured data and can greatly benefit analysts who routinely perform complex analytics on vast data stored in specialized relational databases. Although several benchmarks measure the abilities of text to SQL, the complexity of their questions is inherently limited by the level of expressiveness in query languages and none focus explicitly on questions involving complex analytical reasoning which require operations such as calculations over aggregate analytics, time series analysis or scenario understanding. In this paper, we introduce STARQA, the first public human-created dataset of complex analytical reasoning questions and answers on three specialized-domain databases. In addition to generating SQL directly using LLMs, we evaluate a novel approach (Text2SQLCode) that decomposes the task into a combination of SQL and Python: SQL is responsible for data fetching, and Python more naturally performs reasoning. Our results demonstrate that identifying and combining the abilities of SQL and Python is beneficial compared to using SQL alone, yet the dataset still remains quite challenging for the existing state-of-the-art LLMs.
Generative AI as a catalyst for democratic Innovation: Enhancing citizen engagement in participatory budgeting
Sousa, Italo Alberto do Nascimento, Machado, Jorge, Vaz, Jose Carlos
This research examines the role of Generative Artificial Intelligence (AI) in enhancing citizen engagement in participatory budgeting. In response to challenges like declining civic participation and increased societal polarization, the study explores how online political participation can strengthen democracy and promote social equity. By integrating Generative AI into public consultation platforms, the research aims to improve citizen proposal formulation and foster effective dialogue between citizens and government. It assesses the capacities governments need to implement AI-enhanced participatory tools, considering technological dependencies and vulnerabilities. Analyzing technological structures, actors, interests, and strategies, the study contributes to understanding how technological advancements can reshape participatory institutions to better facilitate citizen involvement. Ultimately, the research highlights how Generative AI can transform participatory institutions, promoting inclusive, democratic engagement and empowering citizens.