Goto

Collaborating Authors

 Generative AI


Deep Generative Models of Evolution: SNP-level Population Adaptation by Genomic Linkage Incorporation

arXiv.org Artificial Intelligence

The investigation of allele frequency trajectories in populations evolving under controlled environmental pressures has become a popular approach to study evolutionary processes on the molecular level. Statistical models based on well-defined evolutionary concepts can be used to validate different hypotheses about empirical observations. Despite their popularity, classic statistical models like the Wright-Fisher model suffer from simplified assumptions such as the independence of selected loci along a chromosome and uncertainty about the parameters. Deep generative neural networks offer a powerful alternative known for the integration of multivariate dependencies and noise reduction. Due to their high data demands and challenging interpretability they have, so far, not been widely considered in the area of population genomics. To address the challenges in the area of Evolve and Resequencing experiments (E&R) based on pooled sequencing (Pool-Seq) data, we introduce a deep generative neural network that aims to model a concept of evolution based on empirical observations over time. The proposed model estimates the distribution of allele frequency trajectories by embedding the observations from single nucleotide polymorphisms (SNPs) with information from neighboring loci. Evaluation on simulated E&R experiments demonstrates the model's ability to capture the distribution of allele frequency trajectories and illustrates the representational power of deep generative models on the example of linkage disequilibrium (LD) estimation. Inspecting the internally learned representations enables estimating pairwise LD, which is typically inaccessible in Pool-Seq data. Our model provides competitive LD estimation in Pool-Seq data high degree of LD when compared to existing methods.


A Survey on Generative Model Unlearning: Fundamentals, Taxonomy, Evaluation, and Future Direction

arXiv.org Artificial Intelligence

With the rapid advancement of generative models, associated privacy concerns have attracted growing attention. To address this, researchers have begun adapting machine unlearning techniques from traditional classification models to generative settings. Although notable progress has been made in this area, a unified framework for systematically organizing and integrating existing work is still lacking. The substantial differences among current studies in terms of unlearning objectives and evaluation protocols hinder the objective and fair comparison of various approaches. While some studies focus on specific types of generative models, they often overlook the commonalities and systematic characteristics inherent in Generative Model Unlearning (GenMU). To bridge this gap, we provide a comprehensive review of current research on GenMU and propose a unified analytical framework for categorizing unlearning objectives, methodological strategies, and evaluation metrics. In addition, we explore the connections between GenMU and related techniques, including model editing, reinforcement learning from human feedback, and controllable generation. We further highlight the potential practical value of unlearning techniques in real-world applications. Finally, we identify key challenges and outline future research directions aimed at laying a solid foundation for further advancements in this field. We consistently maintain the related open-source materials at https://github.com/caxLee/Generative-model-unlearning-survey.


MazeEval: A Benchmark for Testing Sequential Decision-Making in Language Models

arXiv.org Artificial Intelligence

As Large Language Models (LLMs) increasingly power autonomous agents in robotics and embodied AI, understanding their spatial reasoning capabilities becomes crucial for ensuring reliable real-world deployment. Despite advances in language understanding, current research lacks evaluation of how LLMs perform spatial navigation without visual cues, a fundamental requirement for agents operating with limited sensory information. This paper addresses this gap by introducing MazeEval, a benchmark designed to isolate and evaluate pure spatial reasoning in LLMs through coordinate-based maze navigation tasks. Our methodology employs a function-calling interface where models navigate mazes of varying complexity ($5\times 5$ to $15\times 15$ grids) using only coordinate feedback and distance-to-wall information, excluding visual input to test fundamental spatial cognition. We evaluate eight state-of-the-art LLMs across identical mazes in both English and Icelandic to assess cross-linguistic transfer of spatial abilities. Our findings reveal striking disparities: while OpenAI's O3 achieves perfect navigation for mazes up to size $30\times 30$, other models exhibit catastrophic failure beyond $9\times 9$ mazes, with 100% of failures attributed to excessive looping behavior where models revisit a cell at least 10 times. We document a significant performance degradation in Icelandic, with models solving mazes 3-4 sizes smaller than in English, suggesting spatial reasoning in LLMs emerges from linguistic patterns rather than language-agnostic mechanisms. These results have important implications for global deployment of LLM-powered autonomous systems, showing spatial intelligence remains fundamentally constrained by training data availability and highlighting the need for architectural innovations to achieve reliable navigation across linguistic contexts.


$K^4$: Online Log Anomaly Detection Via Unsupervised Typicality Learning

arXiv.org Artificial Intelligence

--Log anomaly detection (LogAD) is crucial for identifying failures and threats in large-scale computing and cyberin-frastructure systems. However, most existing LogAD approaches suffer from key limitations: they depend on slow and error-prone log parsing, employ tightly coupled end-to-end pipelines, often require supervision for improved detection performance, and rely on flawed single-pass evaluation protocols that fail to reflect the temporal dynamics of real-world online detection. These issues significantly hinder scalability, adaptability, and the practical deployment of solutions. These descriptors inform lightweight, modular detectors, including KDE, GMM, OCSVM, and a new adaptation of DeepSVDD, which enables efficient and accurate anomaly scoring without relying on structured formats or log representation retraining. T o support realistic deployment scenarios, we also propose a principled chunk-based evaluation protocol that mimics online log ingestion, alleviates the performance overestimation and dataset undercoverage issues of prior single-pass evaluations, and enables reproducible benchmarking across datasets with varying anomaly densities. Using this setup, we conduct over 125,000 experiments across three real-world datasets (HDFS, BGL, Thunderbird), six pre-trained embedding models, four detectors, and multiple training and log sampling configurations. Logs are essential artifacts in computing systems, recording the operational behavior of applications, kernels, and user activities. This work was supported in part by the NSF research grant #2137603, #2112606, #2117439, and #2320952. These authors contributed equally to this work. With the recent surge in language models and generative AI, a growing body of work [4]-[9] has begun leveraging AI techniques to capture semantic patterns in log sequences, aiming to enable more effective LogAD.


AgentMesh: A Cooperative Multi-Agent Generative AI Framework for Software Development Automation

arXiv.org Artificial Intelligence

Software development is a complex, multi-phase process traditionally requiring collaboration among individuals with diverse expertise. We propose AgentMesh, a Python-based framework that uses multiple cooperating LLM-powered agents to automate software development tasks. In AgentMesh, specialized agents - a Planner, Coder, Debugger, and Reviewer - work in concert to transform a high-level requirement into fully realized code. The Planner agent first decomposes user requests into concrete subtasks; the Coder agent implements each subtask in code; the Debugger agent tests and fixes the code; and the Reviewer agent validates the final output for correctness and quality. We describe the architecture and design of these agents and their communication, and provide implementation details including prompt strategies and workflow orchestration. A case study illustrates AgentMesh handling a non-trivial development request via sequential task planning, code generation, iterative debugging, and final code review. We discuss how dividing responsibilities among cooperative agents leverages the strengths of large language models while mitigating single-agent limitations. Finally, we examine current limitations - such as error propagation and context scaling - and outline future work toward more robust, scalable multi-agent AI systems for software engineering automation.


Zero-shot Performance of Generative AI in Brazilian Portuguese Medical Exam

arXiv.org Artificial Intelligence

Artificial intelligence (AI) has shown the potential to revolutionize healthcare by improving diagnostic accuracy, optimizing workflows, and personalizing treatment plans. Large Language Models (LLMs) and Multimodal Large Language Models (MLLMs) have achieved notable advancements in natural language processing and medical applications. However, the evaluation of these models has focused predominantly on the English language, leading to potential biases in their performance across different languages. This study investigates the capability of six LLMs (GPT-4.0 Turbo, LLaMA-3-8B, LLaMA-3-70B, Mixtral 8x7B Instruct, Titan Text G1-Express, and Command R+) and four MLLMs (Claude-3.5-Sonnet, Claude-3-Opus, Claude-3-Sonnet, and Claude-3-Haiku) to answer questions written in Brazilian spoken portuguese from the medical residency entrance exam of the Hospital das Clรญnicas da Faculdade de Medicina da Universidade de Sรฃo Paulo (HCFMUSP) - the largest health complex in South America. The performance of the models was benchmarked against human candidates, analyzing accuracy, processing time, and coherence of the generated explanations. The results show that while some models, particularly Claude-3.5-Sonnet and Claude-3-Opus, achieved accuracy levels comparable to human candidates, performance gaps persist, particularly in multimodal questions requiring image interpretation. Furthermore, the study highlights language disparities, emphasizing the need for further fine-tuning and data set augmentation for non-English medical AI applications. Our findings reinforce the importance of evaluating generative AI in various linguistic and clinical settings to ensure a fair and reliable deployment in healthcare. Future research should explore improved training methodologies, improved multimodal reasoning, and real-world clinical integration of AI-driven medical assistance.


Enhancing Materials Discovery with Valence Constrained Design in Generative Modeling

arXiv.org Artificial Intelligence

Diffusion-based deep generative models have emerged as powerful tools for inverse materials design. Yet, many existing approaches overlook essential chemical constraints such as oxidation state balance, which can lead to chemically invalid structures. Here we introduce CrysVCD (Crystal generator with Valence-Constrained Design), a modular framework that integrates chemical rules directly into the generative process. CrysVCD first employs a transformer-based elemental language model to generate valence-balanced compositions, followed by a diffusion model to generate crystal structures. The valence constraint enables orders-of-magnitude more efficient chemical valence checking, compared to pure data-driven approaches with post-screening. When fine-tuned on stability metrics, CrysVCD achieves 85% thermodynamic stability and 68% phonon stability. Moreover, CrysVCD supports conditional generation of functional materials, enabling discovery of candidates such as high thermal conductivity semiconductors and high-$ฮบ$ dielectric compounds. Designed as a general-purpose plugin, CrysVCD can be integrated into diverse generative pipeline to promote chemical validity, offering a reliable, scientifically grounded path for materials discovery.


Large Language Model Agent for Structural Drawing Generation Using ReAct Prompt Engineering and Retrieval Augmented Generation

arXiv.org Artificial Intelligence

Structural drawings are widely used in many fields, e.g., mechanical engineering, civil engineering, etc. In civil engineering, structural drawings serve as the main communication tool between architects, engineers, and builders to avoid conflicts, act as legal documentation, and provide a reference for future maintenance or evaluation needs. They are often organized using key elements such as title/subtitle blocks, scales, plan views, elevation view, sections, and detailed sections, which are annotated with standardized symbols and line types for interpretation by engineers and contractors. Despite advances in software capabilities, the task of generating a structural drawing remains labor-intensive and time-consuming for structural engineers. Here we introduce a novel generative AI-based method for generating structural drawings employing a large language model (LLM) agent. The method incorporates a retrieval-augmented generation (RAG) technique using externally-sourced facts to enhance the accuracy and reliability of the language model. This method is capable of understanding varied natural language descriptions, processing these to extract necessary information, and generating code to produce the desired structural drawing in AutoCAD. The approach developed, demonstrated and evaluated herein enables the efficient and direct conversion of a structural drawing's natural language description into an AutoCAD drawing, significantly reducing the workload compared to current working process associated with manual drawing production, facilitating the typical iterative process of engineers for expressing design ideas in a simplified way.


Unlimited Editions: Documenting Human Style in AI Art Generation

arXiv.org Artificial Intelligence

As AI art generation becomes increasingly sophisticated, HCI research has focused primarily on questions of detection, authenticity, and automation. This paper argues that such approaches fundamentally misunderstand how artistic value emerges from the concerns that drive human image production. Through examination of historical precedents, we demonstrate that artistic style is not only visual appearance but the resolution of creative struggle, as artists wrestle with influence and technical constraints to develop unique ways of seeing. Current AI systems flatten these human choices into reproducible patterns without preserving their provenance. We propose that HCI's role lies not only in perfecting visual output, but in developing means to document the origins and evolution of artistic style as it appears within generated visual traces. This reframing suggests new technical directions for HCI research in generative AI, focused on automatic documentation of stylistic lineage and creative choice rather than simple reproduction of aesthetic effects.


Assessing the Reliability of LLMs Annotations in the Context of Demographic Bias and Model Explanation

arXiv.org Artificial Intelligence

Understanding the sources of variability in annotations is crucial for developing fair NLP systems, especially for tasks like sexism detection where demographic bias is a concern. This study investigates the extent to which annotator demographic features influence labeling decisions compared to text content. Using a Generalized Linear Mixed Model, we quantify this inf luence, finding that while statistically present, demographic factors account for a minor fraction ( 8%) of the observed variance, with tweet content being the dominant factor. We then assess the reliability of Generative AI (GenAI) models as annotators, specifically evaluating if guiding them with demographic personas improves alignment with human judgments. Our results indicate that simplistic persona prompting often fails to enhance, and sometimes degrades, performance compared to baseline models. Furthermore, explainable AI (XAI) techniques reveal that model predictions rely heavily on content-specific tokens related to sexism, rather than correlates of demographic characteristics. We argue that focusing on content-driven explanations and robust annotation protocols offers a more reliable path towards fairness than potentially persona simulation.