We present a framework that combines Large Language Models with computational image analytics for non-invasive, zero-shot prediction of IDH mutation status in brain gliomas. For each subject, coregistered multi-parametric MRI scans and multi-class tumor segmentation maps were processed to extract interpretable semantic (visual) attributes and quantitative features, serialized in a standardized JSON file, and used to query GPT 4o and GPT 5 without fine-tuning. We evaluated this framework on six publicly available datasets (N = 1427) and results showcased high accuracy and balanced classification performance across heterogeneous cohorts, even in the absence of manual annotations. GPT 5 outperformed GPT 4o in context-driven phenotype interpretation. Volumetric features emerged as the most important predictors, supplemented by subtype-specific imaging markers and clinical information. Our results demonstrate the potential of integrating LLM-based reasoning with computational image analytics for precise, non-invasive tumor genotyping, advancing diagnostic strategies in neuro-oncology. The code is available at https://github.com/ATPLab-LUMS/CIM-LLM.

For complex logical data augmentation, heavy reliance on human annotation is costly, whereas direct generation with large language models yields uninterpretable and logically homogeneous examples. To address this, we present LFC-DA, a symbolic-logic-controlled pipeline: logical text is first mapped to propositional expressions, a compact rule library is compiled, and a bounded state-space search systematically discovers valid formulas that are then verbalized back into natural-language questions, ensuring both diversity and logical rigor under propositional logic. Experiments on ReClor and LogiQA show significant improvements in the logical-reasoning accuracy of pretrained models, confirming the effectiveness of LFC-DA for LLM-guided logical data augmentation.

In this study, a modular, data-free pipeline for multi-label intention recognition is proposed for agentic AI applications in transportation. Unlike traditional intent recognition systems that depend on large, annotated corpora and often struggle with fine-grained, multi-label discrimination, our approach eliminates the need for costly data collection while enhancing the accuracy of multi-label intention understanding. Specifically, the overall pipeline, named DMTC, consists of three steps: 1) using prompt engineering to guide large language models (LLMs) to generate diverse synthetic queries in different transport scenarios; 2) encoding each textual query with a Sentence-T5 model to obtain compact semantic embeddings; 3) training a lightweight classifier using a novel online focal-contrastive (OFC) loss that emphasizes hard samples and maximizes inter-class separability. The applicability of the proposed pipeline is demonstrated in an agentic AI application in the maritime transportation context. Extensive experiments show that DMTC achieves a Hamming loss of 5.35% and an AUC of 95.92%, outperforming state-of-the-art multi-label classifiers and recent end-to-end SOTA LLM-based baselines. Further analysis reveals that Sentence-T5 embeddings improve subset accuracy by at least 3.29% over alternative encoders, and integrating the OFC loss yields an additional 0.98% gain compared to standard contrastive objectives. In conclusion, our system seamlessly routes user queries to task-specific modules (e.g., ETA information, traffic risk evaluation, and other typical scenarios in the transportation domain), laying the groundwork for fully autonomous, intention-aware agents without costly manual labelling.

Generative artificial intelligence (GenAI) has become a transformative approach in bioinformatics that often enables advancements in genomics, proteomics, transcriptomics, structural biology, and drug discovery. To systematically identify and evaluate these growing developments, this review proposed six research questions (RQs), according to the preferred reporting items for systematic reviews and meta-analysis methods. The objective is to evaluate impactful GenAI strategies in methodological advancement, predictive performance, and specialization, and to identify promising approaches for advanced modeling, data-intensive discovery, and integrative biological analysis. RQ1 highlights diverse applications across multiple bioinformatics subfields (sequence analysis, molecular design, and integrative data modeling), which demonstrate superior performance over traditional methods through pattern recognition and output generation. RQ2 reveals that adapted specialized model architectures outperformed general-purpose models, an advantage attributed to targeted pretraining and context-aware strategies. RQ3 identifies significant benefits in the bioinformatics domains, focusing on molecular analysis and data integration, which improves accuracy and reduces errors in complex analysis. RQ4 indicates improvements in structural modeling, functional prediction, and synthetic data generation, validated by established benchmarks. RQ5 suggests the main constraints, such as the lack of scalability and biases in data that impact generalizability, and proposes future directions focused on robust evaluation and biologically grounded modeling. RQ6 examines that molecular datasets (such as UniProtKB and ProteinNet12), cellular datasets (such as CELLxGENE and GTEx) and textual resources (such as PubMedQA and OMIM) broadly support the training and generalization of GenAI models.

A recent advancement in Multimodal Large Language Models (MLLMs) research is the emergence of "reasoning MLLMs" that offer explicit control over their internal thinking processes (normally referred as the "thinking mode") alongside the standard "non-thinking mode". This capability allows these models to engage in a step-by-step process of internal deliberation before generating a final response. With the rapid transition to and adoption of these "dual-state" MLLMs, this work rigorously evaluated how the enhanced reasoning processes of these MLLMs impact model performance and reliability in clinical tasks. This paper evaluates the active "thinking mode" capabilities of two leading MLLMs, Seed1.5-VL and Gemini-2.5-Flash, for medical applications. We assessed their performance on four visual medical tasks using VQA-RAD and ROCOv2 datasets. Our findings reveal that the improvement from activating the thinking mode remains marginal compared to the standard non-thinking mode for the majority of the tasks. Their performance on complex medical tasks such as open-ended VQA and medical image interpretation remains suboptimal, highlighting the need for domain-specific medical data and more advanced methods for medical knowledge integration.

Under strictly controlled pre-training settings, we observe a Crossover: when unique data is limited, diffusion language models (DLMs) consistently surpass autoregressive (AR) models by training for more epochs. The crossover shifts later with more or higher-quality data, earlier with larger models, and persists across dense and sparse architectures. We attribute the gains to three compounding factors: (1) any-order modeling, (2) super-dense compute from iterative bidirectional denoising, and (3) built-in Monte Carlo augmentation; input or parameter noise improves AR under data constraint but cannot close the gap. At scale, a 1.7B DLM trained with a ~1.5T-token compute budget on 10B unique Python tokens overtakes an AR coder trained with strictly matched settings. In addition, a 1B-parameter DLM achieves > 56% accuracy on HellaSwag and > 33% on MMLU using only 1B tokens, without any special tricks, just by repeating standard pre-training data. We also show that rising validation cross-entropy does not imply degraded downstream performance in this regime.

Large Language Models (LLMs) have been widely deployed across various applications, yet their potential security and ethical risks have raised increasing concerns. Existing research employs red teaming evaluations, utilizing multi-turn jailbreaks to identify potential vulnerabilities in LLMs. However, these approaches often lack exploration of successful dialogue trajectories within the attack space, and they tend to overlook the considerable overhead associated with the attack process. To address these limitations, this paper first introduces a theoretical model based on dynamically weighted graph topology, abstracting the multi-turn attack process as a path planning problem. Based on this framework, we propose ABC, an enhanced Artificial Bee Colony algorithm for multi-turn jailbreaks, featuring a collaborative search mechanism with employed, onlooker, and scout bees. This algorithm significantly improves the efficiency of optimal attack path search while substantially reducing the average number of queries required. Empirical evaluations on three open-source and two proprietary language models demonstrate the effectiveness of our approach, achieving attack success rates above 90\% across the board, with a peak of 98\% on GPT-3.5-Turbo, and outperforming existing baselines. Furthermore, it achieves comparable success with only 26 queries on average, significantly reducing red teaming overhead and highlighting its superior efficiency.

Retrieval Augmented Generation (RAG) is emerging as a powerful technique to enhance the capabilities of Generative AI models by reducing hallucination. Thus, the increasing prominence of RAG alongside Large Language Models (LLMs) has sparked interest in comparing the performance of different LLMs in question-answering (QA) in diverse domains. This study compares the performance of four open-source LLMs, Mistral-7b-instruct, LLaMa2-7b-chat, Falcon-7b-instruct and Orca-mini-v3-7b, and OpenAI's trending GPT-3.5 over QA tasks within the computer science literature leveraging RAG support. Evaluation metrics employed in the study include accuracy and precision for binary questions and ranking by a human expert, ranking by Google's AI model Gemini, alongside cosine similarity for long-answer questions. GPT-3.5, when paired with RAG, effectively answers binary and long-answer questions, reaffirming its status as an advanced LLM. Regarding open-source LLMs, Mistral AI's Mistral-7b-instruct paired with RAG surpasses the rest in answering both binary and long-answer questions. However, among the open-source LLMs, Orca-mini-v3-7b reports the shortest average latency in generating responses, whereas LLaMa2-7b-chat by Meta reports the highest average latency. This research underscores the fact that open-source LLMs, too, can go hand in hand with proprietary models like GPT-3.5 with better infrastructure.

Department of Medicine, Division of Cardiology Bakar Computational Health Sciences Institute UCSF - UC Berkeley Joint Program in Computational Precision Health Department of Radiology, Center for Intelligent Imaging University of California, San Francisco Corresponding Author Keywords: medical imaging, video translation, deep learning, image synthesis, ultrasound Word Count: 4129 Abstract Deep learning (DL) has the potential to revolutionize image acquisition and interpretation across medicine, h owever, attention to data imbalance and missin gness is required . U ltrasound data presents a particular challenge because in addition to different views and structures, it includes several sub - modalities -- such as greyscale and color flow doppler (CFD) -- that are often imbalanced in clinical studies . Image translation can help balance datasets but is challenging for ultrasound sub - modalities to date . Here, we present a generative method for ultrasound CFD - greyscale video translation, t rained on 5 4, 975 videos and tested on 8, 3 68 . The method developed leveraged pixel - wise, adversarial, and perceptual loses and utilized two networks: one for reconstructing anatomic structures and one for denoising to achieve realistic ultrasound imaging . A verage pairwise SSIM between synthetic videos and ground truth was 0.9 1 0.0 4 . Synthetic videos performed indistinguishably from real ones in DL classification and segmentation tasks and when evaluated by b linded clinical experts: F1 score was 0.9 for real and 0.89 for synthetic videos; Dice score between real and synthetic segmentation was 0.97. Overall c linician accuracy in distinguishing real vs synthetic videos was 54 6% (42 - 61%), indicating reali stic synthetic videos . Although trained only on heart videos, the model worked well on ultrasound spanning several clinical domains (av erage SSIM 0.91 0.0 5), demonstrating foundational abilit ies .

Open-weight models provide researchers and developers with accessible foundations for diverse downstream applications. We tested the safety and security postures of eight open-weight large language models (LLMs) to identify vulnerabilities that may impact subsequent fine-tuning and deployment. Using automated adversarial testing, we measured each model's resilience against single-turn and multi-turn prompt injection and jailbreak attacks. Our findings reveal pervasive vulnerabilities across all tested models, with multi-turn attacks achieving success rates between 25.86\% and 92.78\% -- representing a $2\times$ to $10\times$ increase over single-turn baselines. These results underscore a systemic inability of current open-weight models to maintain safety guardrails across extended interactions. We assess that alignment strategies and lab priorities significantly influence resilience: capability-focused models such as Llama 3.3 and Qwen 3 demonstrate higher multi-turn susceptibility, whereas safety-oriented designs such as Google Gemma 3 exhibit more balanced performance. The analysis concludes that open-weight models, while crucial for innovation, pose tangible operational and ethical risks when deployed without layered security controls. These findings are intended to inform practitioners and developers of the potential risks and the value of professional AI security solutions to mitigate exposure. Addressing multi-turn vulnerabilities is essential to ensure the safe, reliable, and responsible deployment of open-weight LLMs in enterprise and public domains. We recommend adopting a security-first design philosophy and layered protections to ensure resilient deployments of open-weight models.