arXiv subjects

Jonathan Pan

Publications and source records attributed to Jonathan Pan.

At least 19 recordsLinked to original sources

arXiv2026

SciCodePile: A 128GB Corpus and Executable Benchmark for Challenging Scientific Code Generation

Large language models (LLMs) excel at general-purpose code generation, yet how well they handle scientific code remains an open question. Existing datasets and benchmarks are limited in scale, domain coverage, or executable verification, leaving the true gap between current LLMs and reliable scientific code generators inadequately assessed. To address these limitations, we present SciCodePile, the largest scientific code corpus to date, constructed from 37,737 public repositories and collectively comprising 128GB of code that spans multiple computational science disciplines. From this corpus, we further curate an executable benchmark of 200 tasks, each equipped with a sandboxed execution environment and an automated test harness for functional verification. We evaluate 15 LLMs from both open-source and closed-source families on three tasks: prefix-to-suffix completion, fill-in-the-middle infilling, and executable code generation. Results show that scientific code generation remains highly challenging: The best CodeBLEU reaches only 38.13 and 38.37 on the two completion tasks, while the strongest model achieves just 12.30\% Pass@1 on the executable benchmark, underscoring how far current models remain from reliable scientific code generation. To demonstrate the training utility of SciCodePile, we further show that continued pretraining on our corpus improves CodeBLEU by $\times$2.84 on scientific code completion, and instruction tuning on our data improves Pass@1 by $\times$4.79 on the executable benchmark. All code and data are available at https://huggingface.co/SciCodePile.

cs.SE↗

arXiv2026

MSAIC-Net: A Multi-Scale Attention and Imbalance-Aware Contrastive Network for ECG-Based Myocardial Substrate Abnormality Detection

Myocardial substrate abnormalities, such as myocardial scar and myocardial infarction (MI), are associated with adverse cardiovascular outcomes. Electrocardiography (ECG) provides a low-cost and widely available tool for detecting these abnormalities, but ECG-based detection remains challenging due to heterogeneous lead-dependent manifestations, high-dimensional multi-lead signals, class imbalance, and the limited interpretability of deep learning models. We propose a multi-scale attention-enhanced convolutional network (MSAIC-Net) for ECG-based myocardial substrate abnormality detection. MSAIC-Net employs parallel atrous convolutional branches to extract ECG features across multiple temporal receptive fields. %, enabling the model to capture both local and longer-range temporal patterns. Channel attention is then used to adaptively reweight informative lead-wise and feature-channel representations. To address class imbalance and improve feature separability, we introduce a novel imbalance-aware supervised contrastive learning strategy that encourages samples from the same class to form compact representations while increasing separation between abnormal and normal samples. Lead-wise permutation importance is further incorporated to quantify the contribution of each ECG lead and improve model interpretability. The proposed method was evaluated on two complementary datasets: a low-data institutional cohort from the University of Virginia (UVA) Health System for myocardial scar classification and the large-scale public PTB-XL dataset from PhysioNet for MI identification. Experimental results show that MSAIC-Net outperforms baseline models, with particularly pronounced improvements in the low-data UVA cohort. Overall, the proposed framework provides an effective and interpretable approach for ECG-based detection of myocardial substrate abnormalities.

cs.LG↗

arXiv2026

The Cognitive Circuit Breaker: A Systems Engineering Framework for Intrinsic AI Reliability

As Large Language Models (LLMs) are increasingly deployed in mission-critical software systems, detecting hallucinations and ``faked truthfulness'' has become a paramount engineering challenge. Current reliability architectures rely heavily on post-generation, black-box mechanisms, such as Retrieval-Augmented Generation (RAG) cross-checking or LLM-as-a-judge evaluators. These extrinsic methods introduce unacceptable latency, high computational overhead, and reliance on secondary external API calls, frequently violating standard software engineering Service Level Agreements (SLAs). In this paper, we propose the Cognitive Circuit Breaker, a novel systems engineering framework that provides intrinsic reliability monitoring with minimal latency overhead. By extracting hidden states during a model's forward pass, we calculate the ``Cognitive Dissonance Delta'' -- the mathematical gap between an LLM's outward semantic confidence (softmax probabilities) and its internal latent certainty (derived via linear probes). We demonstrate statistically significant detection of cognitive dissonance, highlight architecture-dependent Out-of-Distribution (OOD) generalization, and show that this framework adds negligible computational overhead to the active inference pipeline.

cs.SE↗

arXiv2026

SMT-AD: a scalable quantum-inspired anomaly detection approach

Quantum-inspired tensor networks algorithms have shown to be effective and efficient models for machine learning tasks, including anomaly detection. Here, we propose a highly parallelizable quantum-inspired approach which we call SMT-AD from Superposition of Multiresolution Tensors for Anomaly Detection. It is based upon the superposition of bond-dimension-1 matrix product operators to transform the input data with Fourier-assisted feature embedding, where the number of learnable parameters grows linearly with feature size, embedding resolutions, and the number of additional components in the matrix product operators structure. We demonstrate successful anomaly detection when applied to standard datasets, including credit card transactions, and find that, even with minimal configurations, it achieves competitive performance against established anomaly detection baselines. Furthermore, it provides a straightforward way to reduce the weight of the model and even improve the performance by highlighting the most relevant input features.

cs.LG↗

arXiv2026

Curriculum-Guided Myocardial Scar Segmentation for Ischemic and Non-ischemic Cardiomyopathy

Identification and quantification of myocardial scar is important for diagnosis and prognosis of cardiovascular diseases. However, reliable scar segmentation from Late Gadolinium Enhancement Cardiac Magnetic Resonance (LGE-CMR) images remains a challenge due to variations in contrast enhancement across patients, suboptimal imaging conditions such as post contrast washout, and inconsistencies in ground truth annotations on diffuse scars caused by inter observer variability. In this work, we propose a curriculum learning-based framework designed to improve segmentation performance under these challenging conditions. The method introduces a progressive training strategy that guides the model from high-confidence, clearly defined scar regions to low confidence or visually ambiguous samples with limited scar burden. By structuring the learning process in this manner, the network develops robustness to uncertain labels and subtle scar appearances that are often underrepresented in conventional training pipelines. Experimental results show that the proposed approach enhances segmentation accuracy and consistency, particularly for cases with minimal or diffuse scar, outperforming standard training baselines. This strategy provides a principled way to leverage imperfect data for improved myocardial scar quantification in clinical applications. Our code is publicly available on GitHub.

cs.CV↗

arXiv2026

Multi-Trait Subspace Steering to Reveal the Dark Side of Human-AI Interaction

Recent incidents have highlighted alarming cases where human-AI interactions led to negative psychological outcomes, including mental health crises and even user harm. As LLMs serve as sources of guidance, emotional support, and even informal therapy, these risks are poised to escalate. However, studying the mechanisms underlying harmful human-AI interactions presents significant methodological challenges, where organic harmful interactions typically develop over sustained engagement, requiring extensive conversational context that are difficult to simulate in controlled settings. To address this gap, we developed a Multi-Trait Subspace Steering (MultiTraitsss) framework that leverages established crisis-associated traits and novel subspace steering framework to generate Dark models that exhibits cumulative harmful behavioral patterns. Single-turn and multi-turn evaluations show that our dark models consistently produce harmful interaction and outcomes. Using our Dark models, we propose protective measure to reduce harmful outcomes in Human-AI interactions.

cs.AI↗

arXiv2026

The Quantum Sieve Tracer: A Hybrid Framework for Layer-Wise Activation Tracing in Large Language Models

Mechanistic interpretability aims to reverse-engineer the internal computations of Large Language Models (LLMs), yet separating sparse semantic signals from high-dimensional polysemantic noise remains a significant challenge. This paper introduces the Quantum Sieve Tracer, a hybrid quantum-classical framework designed to characterize factual recall circuits. We implement a modular pipeline that first localizes critical layers using classical causal tracing, then maps specific attention head activations into an exponentially large quantum Hilbert space. Using open-weight models (Meta Llama-3.2-1B and Alibaba Qwen2.5-1.5B-Instruct), we perform a two-stage analysis that reveals a fundamental architectural divergence. While Qwen's layer 7 circuit functions as a classic Recall Hub, we discover that Llama's layer 9 acts as an Interference Suppression circuit, where ablating the identified heads paradoxically improves factual recall. Our results demonstrate that quantum kernels can distinguish between these constructive (recall) and reductive (suppression) mechanisms, offering a high-resolution tool for analyzing the fine-grained topology of attention.

quant-ph↗

arXiv2026

Conversational Context Classification: A Representation Engineering Approach

The increasing prevalence of Large Language Models (LLMs) demands effective safeguards for their operation, particularly concerning their tendency to generate out-of-context responses. A key challenge is accurately detecting when LLMs stray from expected conversational norms, manifesting as topic shifts, factual inaccuracies, or outright hallucinations. Traditional anomaly detection struggles to directly apply within contextual semantics. This paper outlines our experiment in exploring the use of Representation Engineering (RepE) and One-Class Support Vector Machine (OCSVM) to identify subspaces within the internal states of LLMs that represent a specific context. By training OCSVM on in-context examples, we establish a robust boundary within the LLM's hidden state latent space. We evaluate out study with two open source LLMs - Llama and Qwen models in specific contextual domain. Our approach entailed identifying the optimal layers within the LLM's internal state subspaces that strongly associates with the context of interest. Our evaluation results showed promising results in identifying the subspace for a specific context. Aside from being useful in detecting in or out of context conversation threads, this research work contributes to the study of better interpreting LLMs.

cs.CL↗

arXiv2026

Automated Post-Incident Policy Gap Analysis via Threat-Informed Evidence Mapping using Large Language Models

Cybersecurity post-incident reviews are essential for identifying control failures and improving organisational resilience, yet they remain labour-intensive, time-consuming, and heavily reliant on expert judgment. This paper investigates whether Large Language Models (LLMs) can augment post-incident review workflows by autonomously analysing system evidence and identifying security policy gaps. We present a threat-informed, agentic framework that ingests log data, maps observed behaviours to the MITRE ATT&CK framework, and evaluates organisational security policies for adequacy and compliance. Using a simulated brute-force attack scenario against a Windows OpenSSH service (MITRE ATT&CK T1110), the system leverages GPT-4o for reasoning, LangGraph for multi-agent workflow orchestration, and LlamaIndex for traceable policy retrieval. Experimental results indicate that the LLM-based pipeline can interpret log-derived evidence, identify insufficient or missing policy controls, and generate actionable remediation recommendations with explicit evidence-to-policy traceability. Unlike prior work that treats log analysis and policy validation as isolated tasks, this study integrates both into a unified end-to-end proof-of-concept post-incident review framework. The findings suggest that LLM-assisted analysis has the potential to improve the efficiency, consistency, and auditability of post-incident evaluations, while highlighting the continued need for human oversight in high-stakes cybersecurity decision-making.

cs.CR↗

arXiv2025

Automating Security Audit Using Large Language Model based Agent: An Exploration Experiment

In the current rapidly changing digital environment, businesses are under constant stress to ensure that their systems are secured. Security audits help to maintain a strong security posture by ensuring that policies are in place, controls are implemented, gaps are identified for cybersecurity risks mitigation. However, audits are usually manual, requiring much time and costs. This paper looks at the possibility of developing a framework to leverage Large Language Models (LLMs) as an autonomous agent to execute part of the security audit, namely with the field audit. password policy compliance for Windows operating system. Through the conduct of an exploration experiment of using GPT-4 with Langchain, the agent executed the audit tasks by accurately flagging password policy violations and appeared to be more efficient than traditional manual audits. Despite its potential limitations in operational consistency in complex and dynamic environment, the framework suggests possibilities to extend further to real-time threat monitoring and compliance checks.

cs.CR↗

arXiv2025

Probing Latent Subspaces in LLM for AI Security: Identifying and Manipulating Adversarial States

Large Language Models (LLMs) have demonstrated remarkable capabilities across various tasks, yet they remain vulnerable to adversarial manipulations such as jailbreaking via prompt injection attacks. These attacks bypass safety mechanisms to generate restricted or harmful content. In this study, we investigated the underlying latent subspaces of safe and jailbroken states by extracting hidden activations from a LLM. Inspired by attractor dynamics in neuroscience, we hypothesized that LLM activations settle into semi stable states that can be identified and perturbed to induce state transitions. Using dimensionality reduction techniques, we projected activations from safe and jailbroken responses to reveal latent subspaces in lower dimensional spaces. We then derived a perturbation vector that when applied to safe representations, shifted the model towards a jailbreak state. Our results demonstrate that this causal intervention results in statistically significant jailbreak responses in a subset of prompts. Next, we probed how these perturbations propagate through the model's layers, testing whether the induced state change remains localized or cascades throughout the network. Our findings indicate that targeted perturbations induced distinct shifts in activations and model responses. Our approach paves the way for potential proactive defenses, shifting from traditional guardrail based methods to preemptive, model agnostic techniques that neutralize adversarial states at the representation level.

cs.LG↗

arXiv2025

Prompt Inject Detection with Generative Explanation as an Investigative Tool

Large Language Models (LLMs) are vulnerable to adversarial prompt based injects. These injects could jailbreak or exploit vulnerabilities within these models with explicit prompt requests leading to undesired responses. In the context of investigating prompt injects, the challenge is the sheer volume of input prompts involved that are likely to be largely benign. This investigative challenge is further complicated by the semantics and subjectivity of the input prompts involved in the LLM conversation with its user and the context of the environment to which the conversation is being carried out. Hence, the challenge for AI security investigators would be two-fold. The first is to identify adversarial prompt injects and then to assess whether the input prompt is contextually benign or adversarial. For the first step, this could be done using existing AI security solutions like guardrails to detect and protect the LLMs. Guardrails have been developed using a variety of approaches. A popular approach is to use signature based. Another popular approach to develop AI models to classify such prompts include the use of NLP based models like a language model. However, in the context of conducting an AI security investigation of prompt injects, these guardrails lack the ability to aid investigators in triaging or assessing the identified input prompts. In this applied research exploration, we explore the use of a text generation capabilities of LLM to detect prompt injects and generate explanation for its detections to aid AI security investigators in assessing and triaging of such prompt inject detections. The practical benefit of such a tool is to ease the task of conducting investigation into prompt injects.

cs.CR↗

arXiv2024

Audio Simulation for Sound Source Localization in Virtual Evironment

Non-line-of-sight localization in signal-deprived environments is a challenging yet pertinent problem. Acoustic methods in such predominantly indoor scenarios encounter difficulty due to the reverberant nature. In this study, we aim to locate sound sources to specific locations within a virtual environment by leveraging physically grounded sound propagation simulations and machine learning methods. This process attempts to overcome the issue of data insufficiency to localize sound sources to their location of occurrence especially in post-event localization. We achieve 0.786+/- 0.0136 F1-score using an audio transformer spectrogram approach.

cs.LG↗

arXiv2024

Enhancing Reasoning Capacity of SLM using Cognitive Enhancement

Large Language Models (LLMs) have been applied to automate cyber security activities and processes including cyber investigation and digital forensics. However, the use of such models for cyber investigation and digital forensics should address accountability and security considerations. Accountability ensures models have the means to provide explainable reasonings and outcomes. This information can be extracted through explicit prompt requests. For security considerations, it is crucial to address privacy and confidentiality of the involved data during data processing as well. One approach to deal with this consideration is to have the data processed locally using a local instance of the model. Due to limitations of locally available resources, namely memory and GPU capacities, a Smaller Large Language Model (SLM) will typically be used. These SLMs have significantly fewer parameters compared to the LLMs. However, such size reductions have notable performance reduction, especially when tasked to provide reasoning explanations. In this paper, we aim to mitigate performance reduction through the integration of cognitive strategies that humans use for problem-solving. We term this as cognitive enhancement through prompts. Our experiments showed significant improvement gains of the SLMs' performances when such enhancements were applied. We believe that our exploration study paves the way for further investigation into the use of cognitive enhancement to optimize SLM for cyber security applications.

cs.CR↗

arXiv2023

RAGLog: Log Anomaly Detection using Retrieval Augmented Generation

The ability to detect log anomalies from system logs is a vital activity needed to ensure cyber resiliency of systems. It is applied for fault identification or facilitate cyber investigation and digital forensics. However, as logs belonging to different systems and components differ significantly, the challenge to perform such analysis is humanly challenging from the volume, variety and velocity of logs. This is further complicated by the lack or unavailability of anomalous log entries to develop trained machine learning or artificial intelligence models for such purposes. In this research work, we explore the use of a Retrieval Augmented Large Language Model that leverages a vector database to detect anomalies from logs. We used a Question and Answer configuration pipeline. To the best of our knowledge, our experiment which we called RAGLog is a novel one and the experimental results show much promise.

cs.CR↗

arXiv2023

A Review on the effectiveness of Dimensional Reduction with Computational Forensics: An Application on Malware Analysis

The Android operating system is pervasively adopted as the operating system platform of choice for smart devices. However, the strong adoption has also resulted in exponential growth in the number of Android based malicious software or malware. To deal with such cyber threats as part of cyber investigation and digital forensics, computational techniques in the form of machine learning algorithms are applied for such malware identification, detection and forensics analysis. However, such Computational Forensics modelling techniques are constrained the volume, velocity, variety and veracity of the malware landscape. This in turn would affect its identification and detection effectiveness. Such consequence would inherently induce the question of sustainability with such solution approach. One approach to optimise effectiveness is to apply dimensional reduction techniques like Principal Component Analysis with the intent to enhance algorithmic performance. In this paper, we evaluate the effectiveness of the application of Principle Component Analysis on Computational Forensics task of detecting Android based malware. We applied our research hypothesis to three different datasets with different machine learning algorithms. Our research result showed that the dimensionally reduced dataset would result in a measure of degradation in accuracy performance.

cs.CR↗

arXiv2022

Deep Set Classifier for Financial Forensics: An application to detect money laundering

Financial forensics has an important role in the field of finance to detect and investigate the occurrence of finance related crimes like money laundering. However, as with other forms of criminal activities, the forensics analysis of such activities is a complex undertaking with attempts by the adversaries to constantly upgrade their ability to evade detection. Also, the extent of the volume and complexity of financial activities or transactions further complicates the task of performing financial forensics. Machine Learning or Artificial Intelligence algorithms could be used to deal with such complexities. However, the challenge of limitedly available labeled datasets especially with fraudulent activities limits the means to develop efficient algorithms. Additionally, the complexity of defining precise search patterns of evasive fraudulent transactions further complicates this challenge. In this paper, we developed a novel deep set classifier algorithm based on meta learning and applied it to deal with the complexity deriving patterns of interest with sample of limitedly labelled transactions to detect fraudulent cryptocurrency money laundering transactions. We a unique approach to train our model with progressive provision of samples and the test result exceeds leading research algorithms.

cs.CR↗

arXiv2022

AI based Log Analyser: A Practical Approach

The analysis of logs is a vital activity undertaken for fault or cyber incident detection, investigation and technical forensics analysis for system and cyber resilience. The potential application of AI algorithms for Log analysis could augment such complex and laborious tasks. However, such solution has its constraints the heterogeneity of log sources and limited to no labels for training a classifier. When such labels become available, the need for the classifier to be updated. This practice-based research seeks to address these challenges with the use of Transformer construct to train a new model with only normal log entries. Log augmentation through multiple forms of perturbation is applied as a form of self-supervised training for feature learning. The model is further finetuned using a form of reinforcement learning with a limited set of label samples to mimic real-world situation with the availability of labels. The experimental results of our model construct show promise with comparative evaluation measurements paving the way for future practical applications.

cs.LG↗