In binary classification tasks, accurate representation of probabilistic predictions is essential for various real-world applications such as predicting payment defaults or assessing medical risks. The model must then be well-calibrated to ensure alignment between predicted probabilities and actual outcomes. However, when score heterogeneity deviates from the underlying data probability distribution, traditional calibration metrics lose reliability, failing to align score distribution with actual probabilities. In this study, we highlight approaches that prioritize optimizing the alignment between predicted scores and true probability distributions over minimizing traditional performance or calibration metrics. When employing tree-based models such as Random Forest and XGBoost, our analysis emphasizes the flexibility these models offer in tuning hyperparameters to minimize the Kullback-Leibler (KL) divergence between predicted and true distributions. Through extensive empirical analysis across 10 UCI datasets and simulations, we demonstrate that optimizing tree-based models based on KL divergence yields superior alignment between predicted scores and actual probabilities without significant performance loss. In real-world scenarios, the reference probability is determined a priori as a Beta distribution estimated through maximum likelihood. Conversely, minimizing traditional calibration metrics may lead to suboptimal results, characterized by notable performance declines and inferior KL values. Our findings reveal limitations in traditional calibration metrics, which could undermine the reliability of predictive models for critical decision-making.
In cognitive neuroscience and brain-computer interface research, accurately predicting imagined stimuli is crucial. This study investigates the effectiveness of Domain Adaptation (DA) in enhancing imagery prediction using primarily visual data from fMRI scans of 18 subjects. Initially, we train a baseline model on visual stimuli to predict imagined stimuli, utilizing data from 14 brain regions. We then develop several models to improve imagery prediction, comparing different DA methods. Our results demonstrate that DA significantly enhances imagery prediction in binary classification on our dataset, as well as in multiclass classification on a publicly available dataset. We then conduct a DA-enhanced searchlight analysis, followed by permutation-based statistical tests to identify brain regions where imagery decoding is consistently above chance across subjects. Our DA-enhanced searchlight predicts imagery contents in a highly distributed set of brain regions, including the visual cortex and the frontoparietal cortex, thereby outperforming standard cross-domain classification methods. The complete code and data for this paper have been made openly available for the use of the scientific community.
Non-local operations play a crucial role in computer vision enabling the capture of long-range dependencies through weighted sums of features across the input, surpassing the constraints of traditional convolution operations that focus solely on local neighborhoods. Non-local operations typically require computing pairwise relationships between all elements in a set, leading to quadratic complexity in terms of time and memory. Due to the high computational and memory demands, scaling non-local neural networks to large-scale problems can be challenging. This article introduces a hybrid quantum-classical scalable non-local neural network, referred to as Quantum Non-Local Neural Network (QNL-Net), to enhance pattern recognition. The proposed QNL-Net relies on inherent quantum parallelism to allow the simultaneous processing of a large number of input features enabling more efficient computations in quantum-enhanced feature space and involving pairwise relationships through quantum entanglement. We benchmark our proposed QNL-Net with other quantum counterparts to binary classification with datasets MNIST and CIFAR-10. The simulation findings showcase our QNL-Net achieves cutting-edge accuracy levels in binary image classification among quantum classifiers while utilizing fewer qubits.
Feature selection poses a challenge in small-sample high-dimensional datasets, where the number of features exceeds the number of observations, as seen in microarray, gene expression, and medical datasets. There isn't a universally optimal feature selection method applicable to any data distribution, and as a result, the literature consistently endeavors to address this issue. One recent approach in feature selection is termed frequency-based feature selection. However, existing methods in this domain tend to overlook feature values, focusing solely on the distribution in the response variable. In response, this paper introduces the Distance-based Mutual Congestion (DMC) as a filter method that considers both the feature values and the distribution of observations in the response variable. DMC sorts the features of datasets, and the top 5% are retained and clustered by KMeans to mitigate multicollinearity. This is achieved by randomly selecting one feature from each cluster. The selected features form the feature space, and the search space for the Genetic Algorithm with Adaptive Rates (GAwAR) will be approximated using this feature space. GAwAR approximates the combination of the top 10 features that maximizes prediction accuracy within a wrapper scheme. To prevent premature convergence, GAwAR adaptively updates the crossover and mutation rates. The hybrid DMC-GAwAR is applicable to binary classification datasets, and experimental results demonstrate its superiority over some recent works. The implementation and corresponding data are available at https://github.com/hnematzadeh/DMC-GAwAR
Volumetric neuroimaging examinations like structural Magnetic Resonance Imaging (sMRI) are routinely applied to support the clinical diagnosis of dementia like Alzheimer's Disease (AD). Neuroradiologists examine 3D sMRI to detect and monitor abnormalities in brain morphology due to AD, like global and/or local brain atrophy and shape alteration of characteristic structures. There is a strong research interest in developing diagnostic systems based on Deep Learning (DL) models to analyse sMRI for AD. However, anatomical information extracted from an sMRI examination needs to be interpreted together with patient's age to distinguish AD patterns from the regular alteration due to a normal ageing process. In this context, part-prototype neural networks integrate the computational advantages of DL in an interpretable-by-design architecture and showed promising results in medical imaging applications. We present PIMPNet, the first interpretable multimodal model for 3D images and demographics applied to the binary classification of AD from 3D sMRI and patient's age. Despite age prototypes do not improve predictive performance compared to the single modality model, this lays the foundation for future work in the direction of the model's design and multimodal prototype training process
We present OxonFair, a new open source toolkit for enforcing fairness in binary classification. Compared to existing toolkits: (i) We support NLP and Computer Vision classification as well as standard tabular problems. (ii) We support enforcing fairness on validation data, making us robust to a wide range of overfitting challenges. (iii) Our approach can optimize any measure based on True Positives, False Positive, False Negatives, and True Negatives. This makes it easily extensible and much more expressive than existing toolkits. It supports all 9 and all 10 of the decision-based group metrics of two popular review articles. (iv) We jointly optimize a performance objective alongside fairness constraints. This minimizes degradation while enforcing fairness, and even improves the performance of inadequately tuned unfair baselines. OxonFair is compatible with standard ML toolkits, including sklearn, Autogluon, and PyTorch and is available at https://github.com/oxfordinternetinstitute/oxonfair
Euphemisms are a form of figurative language relatively understudied in natural language processing. This research extends the current computational work on potentially euphemistic terms (PETs) to Turkish. We introduce the Turkish PET dataset, the first available of its kind in the field. By creating a list of euphemisms in Turkish, collecting example contexts, and annotating them, we provide both euphemistic and non-euphemistic examples of PETs in Turkish. We describe the dataset and methodologies, and also experiment with transformer-based models on Turkish euphemism detection by using our dataset for binary classification. We compare performances across models using F1, accuracy, and precision as evaluation metrics.
This study addresses a binary classification task to determine whether a text sequence, either a sentence or paragraph, is subjective or objective. The task spans five languages: Arabic, Bulgarian, English, German, and Italian, along with a multilingual category. Our approach involved several key techniques. Initially, we preprocessed the data through parts of speech (POS) tagging, identification of question marks, and application of attention masks. We fine-tuned the sentiment-based Transformer model 'MarieAngeA13/Sentiment-Analysis-BERT' on our dataset. Given the imbalance with more objective data, we implemented a custom classifier that assigned greater weight to objective data. Additionally, we translated non-English data into English to maintain consistency across the dataset. Our model achieved notable results, scoring top marks for the multilingual dataset (Macro F1=0.7121) and German (Macro F1=0.7908). It ranked second for Arabic (Macro F1=0.4908) and Bulgarian (Macro F1=0.7169), third for Italian (Macro F1=0.7430), and ninth for English (Macro F1=0.6893).
We study the problem of assessing the robustness of counterfactual explanations for deep learning models. We focus on $\textit{plausible model shifts}$ altering model parameters and propose a novel framework to reason about the robustness property in this setting. To motivate our solution, we begin by showing for the first time that computing the robustness of counterfactuals with respect to plausible model shifts is NP-complete. As this (practically) rules out the existence of scalable algorithms for exactly computing robustness, we propose a novel probabilistic approach which is able to provide tight estimates of robustness with strong guarantees while preserving scalability. Remarkably, and differently from existing solutions targeting plausible model shifts, our approach does not impose requirements on the network to be analyzed, thus enabling robustness analysis on a wider range of architectures. Experiments on four binary classification datasets indicate that our method improves the state of the art in generating robust explanations, outperforming existing methods on a range of metrics.
To address overfitting and enhance model generalization in gastroenterological polyp size assessment, our study introduces Feature-Selection Gates (FSG) or Hard-Attention Gates (HAG) alongside Gradient Routing (GR) for dynamic feature selection. This technique aims to boost Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs) by promoting sparse connectivity, thereby reducing overfitting and enhancing generalization. HAG achieves this through sparsification with learnable weights, serving as a regularization strategy. GR further refines this process by optimizing HAG parameters via dual forward passes, independently from the main model, to improve feature re-weighting. Our evaluation spanned multiple datasets, including CIFAR-100 for a broad impact assessment and specialized endoscopic datasets (REAL-Colon, Misawa, and SUN) focusing on polyp size estimation, covering over 200 polyps in more than 370,000 frames. The findings indicate that our HAG-enhanced networks substantially enhance performance in both binary and triclass classification tasks related to polyp sizing. Specifically, CNNs experienced an F1 Score improvement to 87.8% in binary classification, while in triclass classification, the ViT-T model reached an F1 Score of 76.5%, outperforming traditional CNNs and ViT-T models. To facilitate further research, we are releasing our codebase, which includes implementations for CNNs, multistream CNNs, ViT, and HAG-augmented variants. This resource aims to standardize the use of endoscopic datasets, providing public training-validation-testing splits for reliable and comparable research in gastroenterological polyp size estimation. The codebase is available at github.com/cosmoimd/feature-selection-gates.
Electronic health records (EHRs) contain vast amounts of complex data, but harmonizing and processing this information remains a challenging and costly task requiring significant clinical expertise. While large language models (LLMs) have shown promise in various healthcare applications, their potential for abstracting medical concepts from EHRs remains largely unexplored. We introduce EHRmonize, a framework leveraging LLMs to abstract medical concepts from EHR data. Our study uses medication data from two real-world EHR databases to evaluate five LLMs on two free-text extraction and six binary classification tasks across various prompting strategies. GPT-4o's with 10-shot prompting achieved the highest performance in all tasks, accompanied by Claude-3.5-Sonnet in a subset of tasks. GPT-4o achieved an accuracy of 97% in identifying generic route names, 82% for generic drug names, and 100% in performing binary classification of antibiotics. While EHRmonize significantly enhances efficiency, reducing annotation time by an estimated 60%, we emphasize that clinician oversight remains essential. Our framework, available as a Python package, offers a promising tool to assist clinicians in EHR data abstraction, potentially accelerating healthcare research and improving data harmonization processes.
This study presents an innovative method for Alzheimer's disease diagnosis using 3D MRI designed to enhance the explainability of model decisions. Our approach adopts a soft attention mechanism, enabling 2D CNNs to extract volumetric representations. At the same time, the importance of each slice in decision-making is learned, allowing the generation of a voxel-level attention map to produce an explainable MRI. To test our method and ensure the reproducibility of our results, we chose a standardized collection of MRI data from the Alzheimer's Disease Neuroimaging Initiative (ADNI). On this dataset, our method significantly outperforms state-of-the-art methods in (i) distinguishing AD from cognitive normal (CN) with an accuracy of 0.856 and Matthew's correlation coefficient (MCC) of 0.712, representing improvements of 2.4% and 5.3% respectively over the second-best, and (ii) in the prognostic task of discerning stable from progressive mild cognitive impairment (MCI) with an accuracy of 0.725 and MCC of 0.443, showing improvements of 10.2% and 20.5% respectively over the second-best. We achieved this prognostic result by adopting a double transfer learning strategy, which enhanced sensitivity to morphological changes and facilitated early-stage AD detection. With voxel-level precision, our method identified which specific areas are being paid attention to, identifying these predominant brain regions: the hippocampus, the amygdala, the parahippocampal, and the inferior lateral ventricles. All these areas are clinically associated with AD development. Furthermore, our approach consistently found the same AD-related areas across different cross-validation folds, proving its robustness and precision in highlighting areas that align closely with known pathological markers of the disease.
Pairwise difference learning (PDL) has recently been introduced as a new meta-learning technique for regression. Instead of learning a mapping from instances to outcomes in the standard way, the key idea is to learn a function that takes two instances as input and predicts the difference between the respective outcomes. Given a function of this kind, predictions for a query instance are derived from every training example and then averaged. This paper extends PDL toward the task of classification and proposes a meta-learning technique for inducing a PDL classifier by solving a suitably defined (binary) classification problem on a paired version of the original training data. We analyze the performance of the PDL classifier in a large-scale empirical study and find that it outperforms state-of-the-art methods in terms of prediction performance. Last but not least, we provide an easy-to-use and publicly available implementation of PDL in a Python package.
In this paper we demonstrate the possibility of a trend reversal in binary classification tasks between the dataset and a classification score obtained from a trained model. This trend reversal occurs for certain choices of the regularization parameter for model training, namely, if the parameter is contained in what we call the pathological regularization regime. For ridge regression, we give necessary and sufficient algebraic conditions on the dataset for the existence of a pathological regularization regime. Moreover, our results provide a data science practitioner with a hands-on tool to avoid hyperparameter choices suffering from trend reversal. We furthermore present numerical results on pathological regularization regimes for logistic regression. Finally, we draw connections to datasets exhibiting Simpson's paradox, providing a natural source of pathological datasets.
In recent progress, mathematical verifiers have achieved success in mathematical reasoning tasks by validating the correctness of solutions generated by policy models. However, existing verifiers are trained with binary classification labels, which are not informative enough for the model to accurately assess the solutions. To mitigate the aforementioned insufficiency of binary labels, we introduce step-wise natural language feedback as rationale labels, that is, the correctness of each step and the detailed explanations. In this paper, we propose Math-Minos, a natural language feedback-enhanced verifier by constructing automatically generated training data and a two-stage training paradigm for effective training and efficient inference. Our experiments reveal that a small set of natural language feedback can significantly boost the performance of the verifier in both verification and reinforcement learning. We have released the code and data for further exploration.
In-context learning is a key paradigm in large language models (LLMs) that enables them to generalize to new tasks and domains by simply prompting these models with a few exemplars without explicit parameter updates. Many attempts have been made to understand in-context learning in LLMs as a function of model scale, pretraining data, and other factors. In this work, we propose a new mechanism to probe and understand in-context learning from the lens of decision boundaries for in-context binary classification. Decision boundaries are straightforward to visualize and provide important information about the qualitative behavior of the inductive biases of standard classifiers. To our surprise, we find that the decision boundaries learned by current LLMs in simple binary classification tasks are often irregular and non-smooth, regardless of linear separability in the underlying task. This paper investigates the factors influencing these decision boundaries and explores methods to enhance their generalizability. We assess various approaches, including training-free and fine-tuning methods for LLMs, the impact of model architecture, and the effectiveness of active prompting techniques for smoothing decision boundaries in a data-efficient manner. Our findings provide a deeper understanding of in-context learning dynamics and offer practical improvements for enhancing robustness and generalizability of in-context learning.
Internet memes, channels for humor, social commentary, and cultural expression, are increasingly used to spread toxic messages. Studies on the computational analyses of toxic memes have significantly grown over the past five years, and the only three surveys on computational toxic meme analysis cover only work published until 2022, leading to inconsistent terminology and unexplored trends. Our work fills this gap by surveying content-based computational perspectives on toxic memes, and reviewing key developments until early 2024. Employing the PRISMA methodology, we systematically extend the previously considered papers, achieving a threefold result. First, we survey 119 new papers, analyzing 158 computational works focused on content-based toxic meme analysis. We identify over 30 datasets used in toxic meme analysis and examine their labeling systems. Second, after observing the existence of unclear definitions of meme toxicity in computational works, we introduce a new taxonomy for categorizing meme toxicity types. We also note an expansion in computational tasks beyond the simple binary classification of memes as toxic or non-toxic, indicating a shift towards achieving a nuanced comprehension of toxicity. Third, we identify three content-based dimensions of meme toxicity under automatic study: target, intent, and conveyance tactics. We develop a framework illustrating the relationships between these dimensions and meme toxicities. The survey analyzes key challenges and recent trends, such as enhanced cross-modal reasoning, integrating expert and cultural knowledge, the demand for automatic toxicity explanations, and handling meme toxicity in low-resource languages. Also, it notes the rising use of Large Language Models (LLMs) and generative AI for detecting and generating toxic memes. Finally, it proposes pathways for advancing toxic meme detection and interpretation.
We introduce a novel method for acquiring boundary representations (B-Reps) of 3D CAD models which involves a two-step process: it first applies a spatial partitioning, referred to as the ``split``, followed by a ``fit`` operation to derive a single primitive within each partition. Specifically, our partitioning aims to produce the classical Voronoi diagram of the set of ground-truth (GT) B-Rep primitives. In contrast to prior B-Rep constructions which were bottom-up, either via direct primitive fitting or point clustering, our Split-and-Fit approach is top-down and structure-aware, since a Voronoi partition explicitly reveals both the number of and the connections between the primitives. We design a neural network to predict the Voronoi diagram from an input point cloud or distance field via a binary classification. We show that our network, coined NVD-Net for neural Voronoi diagrams, can effectively learn Voronoi partitions for CAD models from training data and exhibits superior generalization capabilities. Extensive experiments and evaluation demonstrate that the resulting B-Reps, consisting of parametric surfaces, curves, and vertices, are more plausible than those obtained by existing alternatives, with significant improvements in reconstruction quality. Code will be released on https://github.com/yilinliu77/NVDNet.
This paper presents LogiCode, a novel framework that leverages Large Language Models (LLMs) for identifying logical anomalies in industrial settings, moving beyond traditional focus on structural inconsistencies. By harnessing LLMs for logical reasoning, LogiCode autonomously generates Python codes to pinpoint anomalies such as incorrect component quantities or missing elements, marking a significant leap forward in anomaly detection technologies. A custom dataset "LOCO-Annotations" and a benchmark "LogiBench" are introduced to evaluate the LogiCode's performance across various metrics including binary classification accuracy, code generation success rate, and precision in reasoning. Findings demonstrate LogiCode's enhanced interpretability, significantly improving the accuracy of logical anomaly detection and offering detailed explanations for identified anomalies. This represents a notable shift towards more intelligent, LLM-driven approaches in industrial anomaly detection, promising substantial impacts on industry-specific applications.
PROTACs are a promising therapeutic modality that harnesses the cell's built-in degradation machinery to degrade specific proteins. Despite their potential, developing new PROTACs is challenging and requires significant domain expertise, time, and cost. Meanwhile, machine learning has transformed drug design and development. In this work, we present a strategy for curating open-source PROTAC data and an open-source deep learning tool for predicting the degradation activity of novel PROTAC molecules. The curated dataset incorporates important information such as $pDC_{50}$, $D_{max}$, E3 ligase type, POI amino acid sequence, and experimental cell type. Our model architecture leverages learned embeddings from pretrained machine learning models, in particular for encoding protein sequences and cell type information. We assessed the quality of the curated data and the generalization ability of our model architecture against new PROTACs and targets via three tailored studies, which we recommend other researchers to use in evaluating their degradation activity models. In each study, three models predict protein degradation in a majority vote setting, reaching a top test accuracy of 80.8% and 0.865 ROC AUC, and a test accuracy of 62.3% and 0.604 ROC AUC when generalizing to novel protein targets. Our results are not only comparable to state-of-the-art models for protein degradation prediction, but also part of an open-source implementation which is easily reproducible and less computationally complex than existing approaches.