Ulcerative Colitis (UC) is an incurable inflammatory bowel disease that leads to ulcers along the large intestine and rectum. The increase in the prevalence of UC coupled with gastrointestinal physician shortages stresses the healthcare system and limits the care UC patients receive. A colonoscopy is performed to diagnose UC and assess its severity based on the Mayo Endoscopic Score (MES). The MES ranges between zero and three, wherein zero indicates no inflammation and three indicates that the inflammation is markedly high. Artificial Intelligence (AI)-based neural network models, such as convolutional neural networks (CNNs) are capable of analyzing colonoscopies to diagnose and determine the severity of UC by modeling colonoscopy analysis as a multi-class classification problem. Prior research for AI-based UC diagnosis relies on supervised learning approaches that require large annotated datasets to train the CNNs. However, creating such datasets necessitates that domain experts invest a significant amount of time, rendering the process expensive and challenging. To address the challenge, this research employs self-supervised learning (SSL) frameworks that can efficiently train on unannotated datasets to analyze colonoscopies and, aid in diagnosing UC and its severity. A comparative analysis with supervised learning models shows that SSL frameworks, such as SwAV and SparK outperform supervised learning models on the LIMUC dataset, the largest publicly available annotated dataset of colonoscopy images for UC.
This paper introduces the Granular Ball K-Class Twin Support Vector Classifier (GB-TWKSVC), a novel multi-class classification framework that combines Twin Support Vector Machines (TWSVM) with granular ball computing. The proposed method addresses key challenges in multi-class classification by utilizing granular ball representation for improved noise robustness and TWSVM's non-parallel hyperplane architecture solves two smaller quadratic programming problems, enhancing efficiency. Our approach introduces a novel formulation that effectively handles multi-class scenarios, advancing traditional binary classification methods. Experimental evaluation on diverse benchmark datasets shows that GB-TWKSVC significantly outperforms current state-of-the-art classifiers in both accuracy and computational performance. The method's effectiveness is validated through comprehensive statistical tests and complexity analysis. Our work advances classification algorithms by providing a mathematically sound framework that addresses the scalability and robustness needs of modern machine learning applications. The results demonstrate GB-TWKSVC's broad applicability across domains including pattern recognition, fault diagnosis, and large-scale data analytics, establishing it as a valuable addition to the classification algorithm landscape.
The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types. However, comparing the performance of these models consistently has proven to be a challenge due to differences in training data and downstream tasks. To tackle this problem, we developed an architecture-agnostic benchmarking approach that, instead of evaluating the models directly, leverages entity representation vectors from each model and trains simple predictive models for each benchmarking task. This ensures that all types of models are evaluated using the same input and output types. Here we focus on gene properties collected from professionally curated bioinformatics databases. These gene properties are categorized into five major groups: genomic properties, regulatory functions, localization, biological processes, and protein properties. Overall, we define hundreds of tasks based on these databases, which include binary, multi-label, and multi-class classification tasks. We apply these benchmark tasks to evaluate expression-based models, large language models, protein language models, DNA-based models, and traditional baselines. Our findings suggest that text-based models and protein language models generally outperform expression-based models in genomic properties and regulatory functions tasks, whereas expression-based models demonstrate superior performance in localization tasks. These results should aid in the development of more informed artificial intelligence strategies for biological understanding and therapeutic discovery. To ensure the reproducibility and transparency of our findings, we have made the source code and benchmark data publicly accessible for further investigation and expansion at github.com/BiomedSciAI/gene-benchmark.
Advanced classification algorithms are being increasingly used in safety-critical applications like health-care, engineering, etc. In such applications, miss-classifications made by ML algorithms can result in substantial financial or health-related losses. To better anticipate and prepare for such losses, the algorithm user seeks an estimate for the probability that the algorithm miss-classifies a sample. We refer to this task as the risk-assessment. For a variety of models and datasets, we numerically analyze the performance of different methods in solving the risk-assessment problem. We consider two solution strategies: a) calibration techniques that calibrate the output probabilities of classification models to provide accurate probability outputs; and b) a novel approach based upon the prediction interval generation technique of conformal prediction. Our conformal prediction based approach is model and data-distribution agnostic, simple to implement, and provides reasonable results for a variety of use-cases. We compare the different methods on a broad variety of models and datasets.
Annotating data for sensitive labels (e.g., disease, smoking) poses a potential threats to individual privacy in many real-world scenarios. To cope with this problem, we propose a novel setting to protect privacy of each instance, namely learning from concealed labels for multi-class classification. Concealed labels prevent sensitive labels from appearing in the label set during the label collection stage, which specifies none and some random sampled insensitive labels as concealed labels set to annotate sensitive data. In this paper, an unbiased estimator can be established from concealed data under mild assumptions, and the learned multi-class classifier can not only classify the instance from insensitive labels accurately but also recognize the instance from the sensitive labels. Moreover, we bound the estimation error and show that the multi-class classifier achieves the optimal parametric convergence rate. Experiments demonstrate the significance and effectiveness of the proposed method for concealed labels in synthetic and real-world datasets.
In the application of brain-computer interface (BCI), being able to accurately decode brain signals is a critical task. For the multi-class classification task of brain signal ECoG, how to improve the classification accuracy is one of the current research hotspots. ECoG acquisition uses a high-density electrode array and a high sampling frequency, which makes ECoG data have a certain high similarity and data redundancy in the temporal domain, and also unique spatial pattern in spatial domain. How to effectively extract features is both exciting and challenging. Previous work found that visual-related ECoG can carry visual information via frequency and spatial domain. Based on this finding, we focused on using deep learning to design frequency and spatial feature extraction modules, and proposed a Bi-Band ECoGNet model based on deep learning. The main contributions of this paper are: 1) The Bi-BCWT (Bi-Band Channel-Wise Transform) neural network module is designed to replace the time-consume method MST, this module greatly improves the model calculation and data storage efficiency, and effectively increases the training speed; 2) The Bi-BCWT module can effectively take into account the information both in low-frequency and high-frequency domain, which is more conducive to ECoG multi-classification tasks; 3) ECoG is acquired using 2D electrode array, the newly designed 2D Spatial-Temporal feature encoder can extract the 2D spatial feature better. Experiments have shown that the unique 2D spatial data structure can effectively improve classification accuracy; 3) Compared with previous work, the Bi-Band ECoGNet model is smaller and has higher performance, with an accuracy increase of 1.24%, and the model training speed is increased by 6 times, which is more suitable for BCI applications.
Large language models (LLMs) are effective at capturing complex, valuable conceptual representations from textual data for a wide range of real-world applications. However, in fields like Intelligent Fault Diagnosis (IFD), incorporating additional sensor data-such as vibration signals, temperature readings, and operational metrics-is essential but it is challenging to capture such sensor data information within traditional text corpora. This study introduces a novel IFD approach by effectively adapting LLMs to numerical data inputs for identifying various machine faults from time-series sensor data. We propose FD-LLM, an LLM framework specifically designed for fault diagnosis by formulating the training of the LLM as a multi-class classification problem. We explore two methods for encoding vibration signals: the first method uses a string-based tokenization technique to encode vibration signals into text representations, while the second extracts statistical features from both the time and frequency domains as statistical summaries of each signal. We assess the fault diagnosis capabilities of four open-sourced LLMs based on the FD-LLM framework, and evaluate the models' adaptability and generalizability under various operational conditions and machine components, namely for traditional fault diagnosis, cross-operational conditions, and cross-machine component settings. Our results show that LLMs such as Llama3 and Llama3-instruct demonstrate strong fault detection capabilities and significant adaptability across different operational conditions, outperforming state-of-the-art deep learning (DL) approaches in many cases.
Precise breast cancer classification on histopathological images has the potential to greatly improve the diagnosis and patient outcome in oncology. The data imbalance problem largely stems from the inherent imbalance within medical image datasets, where certain tumor subtypes may appear much less frequently. This constitutes a considerable limitation in biased model predictions that can overlook critical but rare classes. In this work, we adopted EfficientNet, a state-of-the-art convolutional neural network (CNN) model that balances high accuracy with computational cost efficiency. To address data imbalance, we introduce an intensive data augmentation pipeline and cost-sensitive learning, improving representation and ensuring that the model does not overly favor majority classes. This approach provides the ability to learn effectively from rare tumor types, improving its robustness. Additionally, we fine-tuned the model using transfer learning, where weights in the beginning trained on a binary classification task were adopted to multi-class classification, improving the capability to detect complex patterns within the BreakHis dataset. Our results underscore significant improvements in the binary classification performance, achieving an exceptional recall increase for benign cases from 0.92 to 0.95, alongside an accuracy enhancement from 97.35 % to 98.23%. Our approach improved the performance of multi-class tasks from 91.27% with regular augmentation to 94.54% with intensive augmentation, reaching 95.04% with transfer learning. This framework demonstrated substantial gains in precision in the minority classes, such as Mucinous carcinoma and Papillary carcinoma, while maintaining high recall consistently across these critical subtypes, as further confirmed by confusion matrix analysis.
Accurate brain tumor classification in MRI images is critical for timely diagnosis and treatment planning. While deep learning models like ResNet-18, VGG-16 have shown high accuracy, they often come with increased complexity and computational demands. This study presents a comparative analysis of effective yet simple Convolutional Neural Network (CNN) architecture and pre-trained ResNet18, and VGG16 model for brain tumor classification using two publicly available datasets: Br35H:: Brain Tumor Detection 2020 and Brain Tumor MRI Dataset. The custom CNN architecture, despite its lower complexity, demonstrates competitive performance with the pre-trained ResNet18 and VGG16 models. In binary classification tasks, the custom CNN achieved an accuracy of 98.67% on the Br35H dataset and 99.62% on the Brain Tumor MRI Dataset. For multi-class classification, the custom CNN, with a slight architectural modification, achieved an accuracy of 98.09%, on the Brain Tumor MRI Dataset. Comparatively, ResNet18 and VGG16 maintained high performance levels, but the custom CNNs provided a more computationally efficient alternative. Additionally,the custom CNNs were evaluated using few-shot learning (0, 5, 10, 15, 20, 40, and 80 shots) to assess their robustness, achieving notable accuracy improvements with increased shots. This study highlights the potential of well-designed, less complex CNN architectures as effective and computationally efficient alternatives to deeper, pre-trained models for medical imaging tasks, including brain tumor classification. This study underscores the potential of custom CNNs in medical imaging tasks and encourages further exploration in this direction.
This paper studies the pool strategy for price-makers under imperfect information. In this occasion, market participants cannot obtain essential transmission parameters of the power system. Thus, price-makers should estimate the market results with respect to their offer curves using available historical information. The linear programming model of economic dispatch is analyzed with the theory of rim multi-parametric linear programming (rim-MPLP). The characteristics of system patterns (combinations of status flags for generating units and transmission lines) are revealed. A multi-class classification model based on support vector machine (SVM) is trained to map the offer curves to system patterns, which is then integrated into the decision framework of the price-maker. The performance of the proposed method is validated on the IEEE 30-bus system, Illinois synthetic 200-bus system, and South Carolina synthetic 500-bus system.
The human brain receives stimuli in multiple ways; among them, audio constitutes an important source of relevant stimuli for the brain regarding communication, amusement, warning, etc. In this context, the aim of this manuscript is to advance in the classification of brain responses to music of diverse genres and to sounds of different nature: speech and music. For this purpose, two different experiments have been designed to acquiere EEG signals from subjects listening to songs of different musical genres and sentences in various languages. With this, a novel scheme is proposed to characterize brain signals for their classification; this scheme is based on the construction of a feature matrix built on relations between energy measured at the different EEG channels and the usage of a bi-LSTM neural network. With the data obtained, evaluations regarding EEG-based classification between speech and music, different musical genres, and whether the subject likes the song listened to or not are carried out. The experiments unveil satisfactory performance to the proposed scheme. The results obtained for binary audio type classification attain 98.66% of success. In multi-class classification between 4 musical genres, the accuracy attained is 61.59%, and results for binary classification of musical taste rise to 96.96%.
This study evaluates metrics for tasks such as classification, regression, clustering, correlation analysis, statistical tests, segmentation, and image-to-image (I2I) translation. Metrics were compared across Python libraries, R packages, and Matlab functions to assess their consistency and highlight discrepancies. The findings underscore the need for a unified roadmap to standardize metrics, ensuring reliable and reproducible ML evaluations across platforms. This study examined a wide range of evaluation metrics across various tasks and found only some to be consistent across platforms, such as (i) Accuracy, Balanced Accuracy, Cohens Kappa, F-beta Score, MCC, Geometric Mean, AUC, and Log Loss in binary classification; (ii) Accuracy, Cohens Kappa, and F-beta Score in multi-class classification; (iii) MAE, MSE, RMSE, MAPE, Explained Variance, Median AE, MSLE, and Huber in regression; (iv) Davies-Bouldin Index and Calinski-Harabasz Index in clustering; (v) Pearson, Spearman, Kendall's Tau, Mutual Information, Distance Correlation, Percbend, Shepherd, and Partial Correlation in correlation analysis; (vi) Paired t-test, Chi-Square Test, ANOVA, Kruskal-Wallis Test, Shapiro-Wilk Test, Welchs t-test, and Bartlett's test in statistical tests; (vii) Accuracy, Precision, and Recall in 2D segmentation; (viii) Accuracy in 3D segmentation; (ix) MAE, MSE, RMSE, and R-Squared in 2D-I2I translation; and (x) MAE, MSE, and RMSE in 3D-I2I translation. Given observation of discrepancies in a number of metrics (e.g. precision, recall and F1 score in binary classification, WCSS in clustering, multiple statistical tests, and IoU in segmentation, amongst multiple metrics), this study concludes that ML evaluation metrics require standardization and recommends that future research use consistent metrics for different tasks to effectively compare ML techniques and solutions.
Diabetic retinopathy is a leading cause of blindness around the world and demands precise AI-based diagnostic tools. Traditional loss functions in multi-class classification, such as Categorical Cross-Entropy (CCE), are very common but break down with class imbalance, especially in cases with inherently challenging or overlapping classes, which leads to biased and less sensitive models. Since a heavy imbalance exists in the number of examples for higher severity stage 4 diabetic retinopathy, etc., classes compared to those very early stages like class 0, achieving class balance is key. For this purpose, we propose the Adaptive Hybrid Focal-Entropy Loss which combines the ideas of focal loss and entropy loss with adaptive weighting in order to focus on minority classes and highlight the challenging samples. The state-of-the art models applied for diabetic retinopathy detection with AHFE revealed good performance improvements, indicating the top performances of ResNet50 at 99.79%, DenseNet121 at 98.86%, Xception at 98.92%, MobileNetV2 at 97.84%, and InceptionV3 at 93.62% accuracy. This sheds light into how AHFE promotes enhancement in AI-driven diagnostics for complex and imbalanced medical datasets.
The paper "Is Complexity an Illusion?" (Bennett, 2024) provides a formalism for complexity, learning, inference, and generalization, and introduces a formal definition for a "policy". This reply shows that correct policies do not exist for a simple task of supervised multi-class classification, via mathematical proof and exhaustive search. Implications of this result are discussed, as well as possible responses and amendments to the theory.
Just Recognizable Difference (JRD) represents the minimum visual difference that is detectable by machine vision, which can be exploited to promote machine vision oriented visual signal processing. In this paper, we propose a Deep Transformer based JRD (DT-JRD) prediction model for Video Coding for Machines (VCM), where the accurately predicted JRD can be used reduce the coding bit rate while maintaining the accuracy of machine tasks. Firstly, we model the JRD prediction as a multi-class classification and propose a DT-JRD prediction model that integrates an improved embedding, a content and distortion feature extraction, a multi-class classification and a novel learning strategy. Secondly, inspired by the perception property that machine vision exhibits a similar response to distortions near JRD, we propose an asymptotic JRD loss by using Gaussian Distribution-based Soft Labels (GDSL), which significantly extends the number of training labels and relaxes classification boundaries. Finally, we propose a DT-JRD based VCM to reduce the coding bits while maintaining the accuracy of object detection. Extensive experimental results demonstrate that the mean absolute error of the predicted JRD by the DT-JRD is 5.574, outperforming the state-of-the-art JRD prediction model by 13.1%. Coding experiments shows that comparing with the VVC, the DT-JRD based VCM achieves an average of 29.58% bit rate reduction while maintaining the object detection accuracy.
Global variable importance measures are commonly used to interpret the results of machine learning models. Local variable importance techniques assess how variables contribute to individual observations. Current methods typically fail to accurately reflect locally dependent relationships between variables and instead focus on marginal importance values. Additionally, they are not natively adapted for multi-class classification problems. We propose a new model-agnostic method for calculating local variable importance, CLIQUE, that captures locally dependent relationships, improves over permutation-based methods, and can be directly applied to multi-category classification problems. Simulated and real-world examples show that CLIQUE emphasizes locally dependent information and properly reduces bias in regions where variables do not affect the response.
Fine-grained classification of whole slide images (WSIs) is essential in precision oncology, enabling precise cancer diagnosis and personalized treatment strategies. The core of this task involves distinguishing subtle morphological variations within the same broad category of gigapixel-resolution images, which presents a significant challenge. While the multi-instance learning (MIL) paradigm alleviates the computational burden of WSIs, existing MIL methods often overlook hierarchical label correlations, treating fine-grained classification as a flat multi-class classification task. To overcome these limitations, we introduce a novel hierarchical multi-instance learning (HMIL) framework. By facilitating on the hierarchical alignment of inherent relationships between different hierarchy of labels at instance and bag level, our approach provides a more structured and informative learning process. Specifically, HMIL incorporates a class-wise attention mechanism that aligns hierarchical information at both the instance and bag levels. Furthermore, we introduce supervised contrastive learning to enhance the discriminative capability for fine-grained classification and a curriculum-based dynamic weighting module to adaptively balance the hierarchical feature during training. Extensive experiments on our large-scale cytology cervical cancer (CCC) dataset and two public histology datasets, BRACS and PANDA, demonstrate the state-of-the-art class-wise and overall performance of our HMIL framework. Our source code is available at https://github.com/ChengJin-git/HMIL.
Large Language Models (LLMs) face significant challenges at inference time due to their high computational demands. To address this, we present Performance-Guided Knowledge Distillation (PGKD), a cost-effective and high-throughput solution for production text classification applications. PGKD utilizes teacher-student Knowledge Distillation to distill the knowledge of LLMs into smaller, task-specific models. PGKD establishes an active learning routine between the student model and the LLM; the LLM continuously generates new training data leveraging hard-negative mining, student model validation performance, and early-stopping protocols to inform the data generation. By employing a cyclical, performance-aware approach tailored for highly multi-class, sparsely annotated datasets prevalent in industrial text classification, PGKD effectively addresses training challenges and outperforms traditional BERT-base models and other knowledge distillation methods on several multi-class classification datasets. Additionally, cost and latency benchmarking reveals that models fine-tuned with PGKD are up to 130X faster and 25X less expensive than LLMs for inference on the same classification task. While PGKD is showcased for text classification tasks, its versatile framework can be extended to any LLM distillation task, including language generation, making it a powerful tool for optimizing performance across a wide range of AI applications.
Recurrent Neural Networks (RNNs) have achieved great success in the prediction of sequential data. However, their theoretical studies are still lagging behind because of their complex interconnected structures. In this paper, we establish a new generalization error bound for vanilla RNNs, and provide a unified framework to calculate the Rademacher complexity that can be applied to a variety of loss functions. When the ramp loss is used, we show that our bound is tighter than the existing bounds based on the same assumptions on the Frobenius and spectral norms of the weight matrices and a few mild conditions. Our numerical results show that our new generalization bound is the tightest among all existing bounds in three public datasets. Our bound improves the second tightest one by an average percentage of 13.80% and 3.01% when the $\tanh$ and ReLU activation functions are used, respectively. Moreover, we derive a sharp estimation error bound for RNN-based estimators obtained through empirical risk minimization (ERM) in multi-class classification problems when the loss function satisfies a Bernstein condition.
Traditional decision trees are limited by axis-orthogonal splits, which can perform poorly when true decision boundaries are oblique. While oblique decision tree methods address this limitation, they often face high computational costs, difficulties with multi-class classification, and a lack of effective feature selection. In this paper, we introduce LDATree and FoLDTree, two novel frameworks that integrate Uncorrelated Linear Discriminant Analysis (ULDA) and Forward ULDA into a decision tree structure. These methods enable efficient oblique splits, handle missing values, support feature selection, and provide both class labels and probabilities as model outputs. Through evaluations on simulated and real-world datasets, LDATree and FoLDTree consistently outperform axis-orthogonal and other oblique decision tree methods, achieving accuracy levels comparable to the random forest. The results highlight the potential of these frameworks as robust alternatives to traditional single-tree methods.