Deep Learning
HARE: an entity and relation centric evaluation framework for histopathology reports
Kim, Yunsoo, Ong, Michal W. S., Shavick, Alex, Wu, Honghan, Levine, Adam P.
Medical domain automated text generation is an active area of research and development; however, evaluating the clinical quality of generated reports remains a challenge, especially in instances where domain-specific metrics are lacking, e.g. histopathology. We propose HARE (Histopathology Automated Report Evaluation), a novel entity and relation centric framework, composed of a benchmark dataset, a named entity recognition (NER) model, a relation extraction (RE) model, and a novel metric, which prioritizes clinically relevant content by aligning critical histopathology entities and relations between reference and generated reports. To develop the HARE benchmark, we annotated 813 de-identified clinical diagnostic histopathology reports and 652 histopathology reports from The Cancer Genome Atlas (TCGA) with domain-specific entities and relations. We fine-tuned GatorTronS, a domain-adapted language model to develop HARE-NER and HARE-RE which achieved the highest overall F1-score (0.915) among the tested models. The proposed HARE metric outperformed traditional metrics including ROUGE and Meteor, as well as radiology metrics such as RadGraph-XL, with the highest correlation and the best regression to expert evaluations (higher than the second best method, GREEN, a large language model based radiology report evaluator, by Pearson $r = 0.168$, Spearman $ฯ= 0.161$, Kendall $ฯ= 0.123$, $R^2 = 0.176$, $RMSE = 0.018$). We release HARE, datasets, and the models at https://github.com/knowlab/HARE to foster advancements in histopathology report generation, providing a robust framework for improving the quality of reports.
Overhearing LLM Agents: A Survey, Taxonomy, and Roadmap
Zhu, Andrew, Callison-Burch, Chris
Imagine AI assistants that enhance conversations without interrupting them: quietly providing relevant information during a medical consultation, seamlessly preparing materials as teachers discuss lesson plans, or unobtrusively scheduling meetings as colleagues debate calendars. While modern conversational LLM agents directly assist human users with tasks through a chat interface, we study this alternative paradigm for interacting with LLM agents, which we call "overhearing agents". Rather than demanding the user's attention, overhearing agents continuously monitor ambient activity and intervene only when they can provide contextual assistance. In this paper, we present the first analysis of overhearing LLM agents as a distinct paradigm in human-AI interaction and establish a taxonomy of overhearing agent interactions and tasks grounded in a survey of works on prior LLM-powered agents and exploratory HCI studies. Based on this taxonomy, we create a list of best practices for researchers and developers building overhearing agent systems. Finally, we outline the remaining research gaps and reveal opportunities for future research in the overhearing paradigm.
How Large Language Models are Designed to Hallucinate
Ackermann, Richard, Emanuilov, Simeon
Large language models (LLMs) achieve remarkable fluency across linguistic and reasoning tasks but remain systematically prone to hallucination. Prevailing accounts attribute hallucinations to data gaps, limited context, or optimization errors. We argue instead that hallucination is a structural outcome of the transformer architecture. As coherence engines, transformers are compelled to produce fluent continuations, with self-attention simulating the relational structure of meaning but lacking the existential grounding of temporality, mood, and care that stabilizes human understanding. On this basis, we distinguish ontological hallucination, arising when continuations require disclosure of beings in world, and residual reasoning hallucination, where models mimic inference by recycling traces of human reasoning in text. We illustrate these patterns through case studies aligned with Heideggerian categories and an experiment across twelve LLMs showing how simulated "self-preservation" emerges under extended prompts. Our contribution is threefold: (1) a comparative account showing why existing explanations are insufficient; (2) a predictive taxonomy of hallucination linked to existential structures with proposed benchmarks; and (3) design directions toward "truth-constrained" architectures capable of withholding or deferring when disclosure is absent. We conclude that hallucination is not an incidental defect but a defining limit of transformer-based models, an outcome scaffolding can mask but never resolve.
Architectural change in neural networks using fuzzy vertex pooling
Ali, Shanookha, Niralda, Nitha, Mathew, Sunil
The process of pooling vertices involves the creation of a new vertex, which becomes adjacent to all the vertices that were originally adjacent to the endpoints of the vertices being pooled. After this, the endpoints of these vertices and all edges connected to them are removed. In this document, we introduce a formal framework for the concept of fuzzy vertex pooling (FVP) and provide an overview of its key properties with its applications to neural networks. The pooling model demonstrates remarkable efficiency in minimizing loss rapidly while maintaining competitive accuracy, even with fewer hidden layer neurons. However, this advantage diminishes over extended training periods or with larger datasets, where the model's performance tends to degrade. This study highlights the limitations of pooling in later stages of deep learning training, rendering it less effective for prolonged or large-scale applications. Consequently, pooling is recommended as a strategy for early-stage training in advanced deep learning models to leverage its initial efficiency.
Language Modeling with Learned Meta-Tokens
Shah, Alok N., Gupta, Khush, Ramji, Keshav, Chaudhari, Pratik
While modern Transformer-based language models (LMs) have achieved major success in multi-task generalization, they often struggle to capture long-range dependencies within their context window. This work introduces a novel approach using meta-tokens, special tokens injected during pre-training, along with a dedicated meta-attention mechanism to guide LMs to use these tokens. We pre-train a language model with a modified GPT-2 architecture equipped with meta-attention in addition to causal multi-head attention, and study the impact of these tokens on a suite of synthetic tasks. We find that data-efficient language model pre-training on fewer than 100B tokens utilizing meta-tokens and our meta-attention mechanism achieves strong performance on these tasks after fine-tuning. We suggest that these gains arise due to the meta-tokens sharpening the positional encoding. This enables them to operate as trainable, content-based landmarks, implicitly compressing preceding context and "caching" it in the meta-token. At inference-time, the meta-token points to relevant context, facilitating length generalization up to 2$\times$ its context window, even after extension with YaRN. We provide further evidence of these behaviors by visualizing model internals to study the residual stream, and assessing the compression quality by information-theoretic analysis on the rate-distortion tradeoff. Our findings suggest that pre-training LMs with meta-tokens offers a simple, data-efficient method to enhance long-context language modeling performance, while introducing new insights into the nature of their behavior towards length generalization.
Stabilizing Information Flow Entropy: Regularization for Safe and Interpretable Autonomous Driving Perception
Yang, Haobo, Zhang, Shiyan, Yang, Zhuoyi, Guo, Jilong, Yang, Jun, Zhang, Xinyu
Deep perception networks in autonomous driving traditionally rely on data-intensive training regimes and post-hoc anomaly detection, often disregarding fundamental information-theoretic constraints governing stable information processing. We reconceptualize deep neural encoders as hierarchical communication chains that incrementally compress raw sensory inputs into task-relevant latent features. Within this framework, we establish two theoretically justified design principles for robust perception: (D1) smooth variation of mutual information between consecutive layers, and (D2) monotonic decay of latent entropy with network depth. Our analysis shows that, under realistic architectural assumptions, particularly blocks comprising repeated layers of similar capacity, enforcing smooth information flow (D1) naturally encourages entropy decay (D2), thus ensuring stable compression. Guided by these insights, we propose Eloss, a novel entropy-based regularizer designed as a lightweight, plug-and-play training objective. Rather than marginal accuracy improvements, this approach represents a conceptual shift: it unifies information-theoretic stability with standard perception tasks, enabling explicit, principled detection of anomalous sensor inputs through entropy deviations. Experimental validation on large-scale 3D object detection benchmarks (KITTI and nuScenes) demonstrates that incorporating Eloss consistently achieves competitive or improved accuracy while dramatically enhancing sensitivity to anomalies, amplifying distribution-shift signals by up to two orders of magnitude. This stable information-compression perspective not only improves interpretability but also establishes a solid theoretical foundation for safer, more robust autonomous driving perception systems.
SecureFixAgent: A Hybrid LLM Agent for Automated Python Static Vulnerability Repair
Gajjar, Jugal, Subramaniakuppusamy, Kamalasankari, Puthal, Relsy, Ranaware, Kaustik
Modern software development pipelines face growing challenges in securing large codebases with extensive dependencies. Static analysis tools like Bandit are effective at vulnerability detection but suffer from high false positives and lack repair capabilities. Large Language Models (LLMs), in contrast, can suggest fixes but often hallucinate changes and lack self-validation. We present SecureFixAgent, a hybrid repair framework integrating Bandit with lightweight local LLMs (<8B parameters) in an iterative detect-repair-validate loop. To improve precision, we apply parameter-efficient LoRA-based fine-tuning on a diverse, curated dataset spanning multiple Python project domains, mitigating dataset bias and reducing unnecessary edits. SecureFixAgent uses Bandit for detection, the LLM for candidate fixes with explanations, and Bandit re-validation for verification, all executed locally to preserve privacy and reduce cloud reliance. Experiments show SecureFixAgent reduces false positives by 10.8% over static analysis, improves fix accuracy by 13.51%, and lowers false positives by 5.46% compared to pre-trained LLMs, typically converging within three iterations. Beyond metrics, developer studies rate explanation quality 4.5/5, highlighting its value for human trust and adoption. By combining verifiable security improvements with transparent rationale in a resource-efficient local framework, SecureFixAgent advances trustworthy, automated vulnerability remediation for modern pipelines.
Digging Into the Internal: Causality-Based Analysis of LLM Function Calling
Ji, Zhenlan, Wu, Daoyuan, Wang, Wenxuan, Ma, Pingchuan, Wang, Shuai, Ma, Lei
Function calling (FC) has emerged as a powerful technique for facilitating large language models (LLMs) to interact with external systems and perform structured tasks. However, the mechanisms through which it influences model behavior remain largely under-explored. Besides, we discover that in addition to the regular usage of FC, this technique can substantially enhance the compliance of LLMs with user instructions. These observations motivate us to leverage causality, a canonical analysis method, to investigate how FC works within LLMs. In particular, we conduct layer-level and token-level causal interventions to dissect FC's impact on the model's internal computational logic when responding to user queries. Our analysis confirms the substantial influence of FC and reveals several in-depth insights into its mechanisms. To further validate our findings, we conduct extensive experiments comparing the effectiveness of FC-based instructions against conventional prompting methods. We focus on enhancing LLM safety robustness, a critical LLM application scenario, and evaluate four mainstream LLMs across two benchmark datasets. The results are striking: FC shows an average performance improvement of around 135% over conventional prompting methods in detecting malicious inputs, demonstrating its promising potential to enhance LLM reliability and capability in practical applications.
HausaMovieReview: A Benchmark Dataset for Sentiment Analysis in Low-Resource African Language
Zanga, Asiya Ibrahim, Abdulrahman, Salisu Mamman, Ado, Abubakar, Bichi, Abdulkadir Abubakar, Jibril, Lukman Aliyu, Umar, Abdulmajid Babangida, Adamu, Alhassan, Muhammad, Shamsuddeen Hassan, Abubakar, Bashir Salisu
The development of Natural Language Processing (NLP) tools for low-resource languages is critically hindered by the scarcity of annotated datasets. This paper addresses this fundamental challenge by introducing HausaMovieReview, a novel benchmark dataset comprising 5,000 YouTube comments in Hausa and code-switched English. The dataset was meticulously annotated by three independent annotators, demonstrating a robust agreement with a Fleiss' Kappa score of 0.85 between annotators. We used this dataset to conduct a comparative analysis of classical models (Logistic Regression, Decision Tree, K-Nearest Neighbors) and fine-tuned transformer models (BERT and RoBERTa). Our results reveal a key finding: the Decision Tree classifier, with an accuracy and F1-score 89.72% and 89.60% respectively, significantly outperformed the deep learning models. Our findings also provide a robust baseline, demonstrating that effective feature engineering can enable classical models to achieve state-of-the-art performance in low-resource contexts, thereby laying a solid foundation for future research. Keywords: Hausa, Kannywood, Low-Resource Languages, NLP, Sentiment Analysis
Imaging Modalities-Based Classification for Lung Cancer Detection
Ahmed, Sajim, Chaudhary, Muhammad Zain, Chaudhary, Muhammad Zohaib, Abbass, Mahmoud, Sherif, Ahmed, Mamun, Mohammad Mahbubur Rahman Khan
Abstract--Lung cancer continues to be the predominant cause of cancer-related mortality globally. This review analyzes various approaches, including advanced image processing methods, focusing on their efficacy in interpreting CT scans, chest radiographs, and biological markers. Notably, we identify critical gaps in the previous surveys, including the need for robust models that can generalize across diverse populations and imaging modalities. This comprehensive synthesis aims to serve as a foundational resource for researchers and clinicians, guiding future efforts toward more accurate and efficient lung cancer detection. Key findings reveal that 3D CNN architectures integrated with CT scans achieve the most superior performances, yet challenges such as high false positives, dataset variability, and computational complexity persist across modalities.