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Investigating Graph Neural Networks and Classical Feature-Extraction Techniques in Activity-Cliff and Molecular Property Prediction

arXiv.org Machine Learning

Molecular featurisation refers to the transformation of molecular data into numerical feature vectors. It is one of the key research areas in molecular machine learning and computational drug discovery. Recently, message-passing graph neural networks (GNNs) have emerged as a novel method to learn differentiable features directly from molecular graphs. While such techniques hold great promise, further investigations are needed to clarify if and when they indeed manage to definitively outcompete classical molecular featurisations such as extended-connectivity fingerprints (ECFPs) and physicochemical-descriptor vectors (PDVs). We systematically explore and further develop classical and graph-based molecular featurisation methods for two important tasks: molecular property prediction, in particular, quantitative structure-activity relationship (QSAR) prediction, and the largely unexplored challenge of activity-cliff (AC) prediction. We first give a technical description and critical analysis of PDVs, ECFPs and message-passing GNNs, with a focus on graph isomorphism networks (GINs). We then conduct a rigorous computational study to compare the performance of PDVs, ECFPs and GINs for QSAR and AC-prediction. Following this, we mathematically describe and computationally evaluate a novel twin neural network model for AC-prediction. We further introduce an operation called substructure pooling for the vectorisation of structural fingerprints as a natural counterpart to graph pooling in GNN architectures. We go on to propose Sort & Slice, a simple substructure-pooling technique for ECFPs that robustly outperforms hash-based folding at molecular property prediction. Finally, we outline two ideas for future research: (i) a graph-based self-supervised learning strategy to make classical molecular featurisations trainable, and (ii) trainable substructure-pooling via differentiable self-attention.


Locally Adaptive One-Class Classifier Fusion with Dynamic $\ell$p-Norm Constraints for Robust Anomaly Detection

arXiv.org Machine Learning

This paper presents a novel approach to one-class classifier fusion through locally adaptive learning with dynamic $\ell$p-norm constraints. We introduce a framework that dynamically adjusts fusion weights based on local data characteristics, addressing fundamental challenges in ensemble-based anomaly detection. Our method incorporates an interior-point optimization technique that significantly improves computational efficiency compared to traditional Frank-Wolfe approaches, achieving up to 19-fold speed improvements in complex scenarios. The framework is extensively evaluated on standard UCI benchmark datasets and specialized temporal sequence datasets, demonstrating superior performance across diverse anomaly types. Statistical validation through Skillings-Mack tests confirms our method's significant advantages over existing approaches, with consistent top rankings in both pure and non-pure learning scenarios. The framework's ability to adapt to local data patterns while maintaining computational efficiency makes it particularly valuable for real-time applications where rapid and accurate anomaly detection is crucial.


STRisk: A Socio-Technical Approach to Assess Hacking Breaches Risk

arXiv.org Artificial Intelligence

Data breaches have begun to take on new dimensions and their prediction is becoming of great importance to organizations. Prior work has addressed this issue mainly from a technical perspective and neglected other interfering aspects such as the social media dimension. To fill this gap, we propose STRisk which is a predictive system where we expand the scope of the prediction task by bringing into play the social media dimension. We study over 3800 US organizations including both victim and non-victim organizations. For each organization, we design a profile composed of a variety of externally measured technical indicators and social factors. In addition, to account for unreported incidents, we consider the non-victim sample to be noisy and propose a noise correction approach to correct mislabeled organizations. We then build several machine learning models to predict whether an organization is exposed to experience a hacking breach. By exploiting both technical and social features, we achieve a Area Under Curve (AUC) score exceeding 98%, which is 12% higher than the AUC achieved using only technical features. Furthermore, our feature importance analysis reveals that open ports and expired certificates are the best technical predictors, while spreadability and agreeability are the best social predictors.


A Context-Based Numerical Format Prediction for a Text-To-Speech System

arXiv.org Artificial Intelligence

Many of the existing TTS systems cannot accurately synthesize text containing a variety of numerical formats, resulting in reduced intelligibility of the synthesized speech. This research aims to develop a numerical format classifier that can classify six types of numeric contexts. Experiments were carried out using the proposed context-based feature extraction technique, which is focused on extracting keywords, punctuation marks, and symbols as the features of the numbers. Support Vector Machine, K-Nearest Neighbors Linear Discriminant Analysis, and Decision Tree were used as classifiers. We have used the 10-fold cross-validation technique to determine the classification accuracy in terms of recall and precision. It can be found that the proposed solution is better than the existing feature extraction technique with improvement to the classification accuracy by 30% to 37%. The use of the number format classification can increase the intelligibility of the TTS systems.


SNN-Based Online Learning of Concepts and Action Laws in an Open World

arXiv.org Artificial Intelligence

We present the architecture of a fully autonomous, bio-inspired cognitive agent built around a spiking neural network (SNN) implementing the agent's semantic memory. The agent explores its universe and learns concepts of objects/situations and of its own actions in a one-shot manner. While object/situation concepts are unary, action concepts are triples made up of an initial situation, a motor activity, and an outcome. They embody the agent's knowledge of its universe's actions laws. Both kinds of concepts have different degrees of generality. To make decisions the agent queries its semantic memory for the expected outcomes of envisaged actions and chooses the action to take on the basis of these predictions. Our experiments show that the agent handles new situations by appealing to previously learned general concepts and rapidly modifies its concepts to adapt to environment changes.


CLIP Unreasonable Potential in Single-Shot Face Recognition

arXiv.org Artificial Intelligence

Face recognition is a core task in computer vision designed to identify and authenticate individuals by analyzing facial patterns and features. This field intersects with artificial intelligence image processing and machine learning with applications in security authentication and personalization. Traditional approaches in facial recognition focus on capturing facial features like the eyes, nose and mouth and matching these against a database to verify identities. However challenges such as high false positive rates have persisted often due to the similarity among individuals facial features. Recently Contrastive Language Image Pretraining (CLIP) a model developed by OpenAI has shown promising advancements by linking natural language processing with vision tasks allowing it to generalize across modalities. Using CLIP's vision language correspondence and single-shot finetuning the model can achieve lower false positive rates upon deployment without the need of mass facial features extraction. This integration demonstrating CLIP's potential to address persistent issues in face recognition model performance without complicating our training paradigm.


Improving Low-Fidelity Models of Li-ion Batteries via Hybrid Sparse Identification of Nonlinear Dynamics

arXiv.org Artificial Intelligence

Accurate modeling of lithium ion (li-ion) batteries is essential for enhancing the safety, and efficiency of electric vehicles and renewable energy systems. This paper presents a data-inspired approach for improving the fidelity of reduced-order li-ion battery models. The proposed method combines a Genetic Algorithm with Sequentially Thresholded Ridge Regression (GA-STRidge) to identify and compensate for discrepancies between a low-fidelity model (LFM) and data generated either from testing or a high-fidelity model (HFM). The hybrid model, combining physics-based and data-driven methods, is tested across different driving cycles to demonstrate the ability to significantly reduce the voltage prediction error compared to the baseline LFM, while preserving computational efficiency. The model robustness is also evaluated under various operating conditions, showing low prediction errors and high Pearson correlation coefficients for terminal voltage in unseen environments.


Machine Learning Approaches on Crop Pattern Recognition a Comparative Analysis

arXiv.org Artificial Intelligence

Monitoring agricultural activities is important to ensure food security. Remote sensing plays a significant role for large-scale continuous monitoring of cultivation activities. Time series remote sensing data were used for the generation of the cropping pattern. Classification algorithms are used to classify crop patterns and mapped agriculture land used. Some conventional classification methods including support vector machine (SVM) and decision trees were applied for crop pattern recognition. However, in this paper, we are proposing Deep Neural Network (DNN) based classification to improve the performance of crop pattern recognition and make a comparative analysis with two (2) other machine learning approaches including Naive Bayes and Random Forest.


Integrating Secondary Structures Information into Triangular Spatial Relationships (TSR) for Advanced Protein Classification

arXiv.org Artificial Intelligence

Protein structures represent the key to deciphering biological functions. The more detailed form of similarity among these proteins is sometimes overlooked by the conventional structural comparison methods. In contrast, further advanced methods, such as Triangular Spatial Relationship (TSR), have been demonstrated to make finer differentiations. Still, the classical implementation of TSR does not provide for the integration of secondary structure information, which is important for a more detailed understanding of the folding pattern of a protein. To overcome these limitations, we developed the SSE-TSR approach. The proposed method integrates secondary structure elements (SSEs) into TSR-based protein representations. This allows an enriched representation of protein structures by considering 18 different combinations of helix, strand, and coil arrangements. Our results show that using SSEs improves the accuracy and reliability of protein classification to varying degrees. We worked with two large protein datasets of 9.2K and 7.8K samples, respectively. We applied the SSE-TSR approach and used a neural network model for classification. Interestingly, introducing SSEs improved performance statistics for Dataset 1, with accuracy moving from 96.0% to 98.3%. For Dataset 2, where the performance statistics were already good, further small improvements were found with the introduction of SSE, giving an accuracy of 99.5% compared to 99.4%. These results show that SSE integration can dramatically improve TSR key discrimination, with significant benefits in datasets with low initial accuracies and only incremental gains in those with high baseline performance. Thus, SSE-TSR is a powerful bioinformatics tool that improves protein classification and understanding of protein function and interaction.


A Flexible Large Language Models Guardrail Development Methodology Applied to Off-Topic Prompt Detection

arXiv.org Artificial Intelligence

Large Language Models are prone to off-topic misuse, where users may prompt these models to perform tasks beyond their intended scope. Current guardrails, which often rely on curated examples or custom classifiers, suffer from high false-positive rates, limited adaptability, and the impracticality of requiring real-world data that is not available in pre-production. In this paper, we introduce a flexible, data-free guardrail development methodology that addresses these challenges. By thoroughly defining the problem space qualitatively and passing this to an LLM to generate diverse prompts, we construct a synthetic dataset to benchmark and train off-topic guardrails that outperform heuristic approaches. Additionally, by framing the task as classifying whether the user prompt is relevant with respect to the system prompt, our guardrails effectively generalize to other misuse categories, including jailbreak and harmful prompts. Lastly, we further contribute to the field by open-sourcing both the synthetic dataset and the off-topic guardrail models, providing valuable resources for developing guardrails in pre-production environments and supporting future research and development in LLM safety.