Many machine learning models have been proposed to classify phenotypes from gene expression data. In addition to their good performance, these models can potentially provide some understanding of phenotypes by extracting explanations for their decisions. These explanations often take the form of a list of genes ranked in order of importance for the predictions, the highest-ranked genes being interpreted as linked to the phenotype. We discuss the biological and the methodological limitations of such explanations. Experiments are performed on several datasets gathering cancer and healthy tissue samples from the TCGA, GTEx and TARGET databases. A collection of machine learning models including logistic regression, multilayer perceptron, and graph neural network are trained to classify samples according to their cancer type. Gene rankings are obtained from explainability methods adapted to these models, and compared to the ones from classical statistical feature selection methods such as mutual information, DESeq2, and EdgeR. Interestingly, on simple tasks, we observe that the information learned by black-box neural networks is related to the notion of differential expression. In all cases, a small set containing the best-ranked genes is sufficient to achieve a good classification. However, these genes differ significantly between the methods and similar classification performance can be achieved with numerous lower ranked genes. In conclusion, although these methods enable the identification of biomarkers characteristic of certain pathologies, our results question the completeness of the selected gene sets and thus of explainability by the identification of the underlying biological processes.

Models based on vision transformer architectures are considered state-of-the-art when it comes to image classification tasks. However, they require extensive computational resources both for training and deployment. The problem is exacerbated as the amount and complexity of the data increases. Quantum-based vision transformer models could potentially alleviate this issue by reducing the training and operating time while maintaining the same predictive power. Although current quantum computers are not yet able to perform high-dimensional tasks yet, they do offer one of the most efficient solutions for the future. In this work, we construct several variations of a quantum hybrid vision transformer for a classification problem in high energy physics (distinguishing photons and electrons in the electromagnetic calorimeter). We test them against classical vision transformer architectures. Our findings indicate that the hybrid models can achieve comparable performance to their classical analogues with a similar number of parameters.

Image classifiers often rely on convolutional neural networks (CNN) for their tasks, which are inherently more heavyweight than multilayer perceptrons (MLPs), which can be problematic in real-time applications. Additionally, many image classification models work on both RGB and grayscale datasets. Classifiers that operate solely on grayscale images are much less common. Grayscale image classification has diverse applications, including but not limited to medical image classification and synthetic aperture radar (SAR) automatic target recognition (ATR). Thus, we present a novel grayscale (single channel) image classification approach using a vectorized view of images. We exploit the lightweightness of MLPs by viewing images as a vector and reducing our problem setting to the grayscale image classification setting. We find that using a single graph convolutional layer batch-wise increases accuracy and reduces variance in the performance of our model. Moreover, we develop a customized accelerator on FPGA for the proposed model with several optimizations to improve its performance. Our experimental results on benchmark grayscale image datasets demonstrate the effectiveness of the proposed model, achieving vastly lower latency (up to 16$\times$ less) and competitive or leading performance compared to other state-of-the-art image classification models on various domain-specific grayscale image classification datasets.

Predicting and understanding the changes in cognitive performance, especially after a longitudinal intervention, is a fundamental goal in neuroscience. Longitudinal brain stimulation-based interventions like transcranial direct current stimulation (tDCS) induce short-term changes in the resting membrane potential and influence cognitive processes. However, very little research has been conducted on predicting these changes in cognitive performance post-intervention. In this research, we intend to address this gap in the literature by employing different EEG-based functional connectivity analyses and machine learning algorithms to predict changes in cognitive performance in a complex multitasking task. Forty subjects were divided into experimental and active-control conditions. On Day 1, all subjects executed a multitasking task with simultaneous 32-channel EEG being acquired. From Day 2 to Day 7, subjects in the experimental condition undertook 15 minutes of 2mA anodal tDCS stimulation during task training. Subjects in the active-control condition undertook 15 minutes of sham stimulation during task training. On Day 10, all subjects again executed the multitasking task with EEG acquisition. Source-level functional connectivity metrics, namely phase lag index and directed transfer function, were extracted from the EEG data on Day 1 and Day 10. Various machine learning models were employed to predict changes in cognitive performance. Results revealed that the multi-layer perceptron and directed transfer function recorded a cross-validation training RMSE of 5.11% and a test RMSE of 4.97%. We discuss the implications of our results in developing real-time cognitive state assessors for accurately predicting cognitive performance in dynamic and complex tasks post-tDCS intervention

Executive functioning is a cognitive process that enables humans to plan, organize, and regulate their behavior in a goal-directed manner. Understanding and classifying the changes in executive functioning after longitudinal interventions (like transcranial direct current stimulation (tDCS)) has not been explored in the literature. This study employs functional connectivity and machine learning algorithms to classify executive functioning performance post-tDCS. Fifty subjects were divided into experimental and placebo control groups. EEG data was collected while subjects performed an executive functioning task on Day 1. The experimental group received tDCS during task training from Day 2 to Day 8, while the control group received sham tDCS. On Day 10, subjects repeated the tasks specified on Day 1. Different functional connectivity metrics were extracted from EEG data and eventually used for classifying executive functioning performance using different machine learning algorithms. Results revealed that a novel combination of partial directed coherence and multi-layer perceptron (along with recursive feature elimination) resulted in a high classification accuracy of 95.44%. We discuss the implications of our results in developing real-time neurofeedback systems for assessing and enhancing executive functioning performance post-tDCS administration.

We present BlockFusion, a diffusion-based model that generates 3D scenes as unit blocks and seamlessly incorporates new blocks to extend the scene. BlockFusion is trained using datasets of 3D blocks that are randomly cropped from complete 3D scene meshes. Through per-block fitting, all training blocks are converted into the hybrid neural fields: with a tri-plane containing the geometry features, followed by a Multi-layer Perceptron (MLP) for decoding the signed distance values. A variational auto-encoder is employed to compress the tri-planes into the latent tri-plane space, on which the denoising diffusion process is performed. Diffusion applied to the latent representations allows for high-quality and diverse 3D scene generation. To expand a scene during generation, one needs only to append empty blocks to overlap with the current scene and extrapolate existing latent tri-planes to populate new blocks. The extrapolation is done by conditioning the generation process with the feature samples from the overlapping tri-planes during the denoising iterations. Latent tri-plane extrapolation produces semantically and geometrically meaningful transitions that harmoniously blend with the existing scene. A 2D layout conditioning mechanism is used to control the placement and arrangement of scene elements. Experimental results indicate that BlockFusion is capable of generating diverse, geometrically consistent and unbounded large 3D scenes with unprecedented high-quality shapes in both indoor and outdoor scenarios.

Recent advances in solving ordinary differential equations (ODEs) with neural networks have been remarkable. Neural networks excel at serving as trial functions and approximating solutions within functional spaces, aided by gradient backpropagation algorithms. However, challenges remain in solving complex ODEs, including high-order and nonlinear cases, emphasizing the need for improved efficiency and effectiveness. Traditional methods have typically relied on established knowledge integration to improve problem-solving efficiency. In contrast, this study takes a different approach by introducing a new neural network architecture for constructing trial functions, known as ratio net. This architecture draws inspiration from rational fraction polynomial approximation functions, specifically the Pade approximant. Through empirical trials, it demonstrated that the proposed method exhibits higher efficiency compared to existing approaches, including polynomial-based and multilayer perceptron (MLP) neural network-based methods. The ratio net holds promise for advancing the efficiency and effectiveness of solving differential equations.

We present an approach to outsourcing of training neural networks while preserving data confidentiality from malicious parties. We use fully homomorphic encryption to build a unified training approach that works on encrypted data and learns quantized neural network models. The data can be horizontally or vertically split between multiple parties, enabling collaboration on confidential data. We train logistic regression and multi-layer perceptrons on several datasets.

Diabetes, especially T2DM, continues to be a significant health problem. One of the major concerns associated with diabetes is the development of its complications. Diabetic nephropathy, one of the chronic complication of diabetes, adversely affects the kidneys, leading to kidney damage. Diagnosing diabetic nephropathy involves considering various criteria, one of which is the presence of a pathologically significant quantity of albumin in urine, known as albuminuria. Thus, early prediction of albuminuria in diabetic patients holds the potential for timely preventive measures. This study aimed to develop a supervised learning model to predict the risk of developing albuminuria in T2DM patients. The selected supervised learning algorithms included Na\"ive Bayes, Support Vector Machine (SVM), decision tree, random forest, AdaBoost, XGBoost, and Multi-Layer Perceptron (MLP). Our private dataset, comprising 184 entries of diabetes complications risk factors, was used to train the algorithms. It consisted of 10 attributes as features and 1 attribute as the target (albuminuria). Upon conducting the experiments, the MLP demonstrated superior performance compared to the other algorithms. It achieved accuracy and f1-score values as high as 0.74 and 0.75, respectively, making it suitable for screening purposes in predicting albuminuria in T2DM. Nonetheless, further studies are warranted to enhance the model's performance.

This study introduces CCNETS (Causal Learning with Causal Cooperative Nets), a novel generative model-based classifier designed to tackle the challenge of generating data for imbalanced datasets in pattern recognition. CCNETS is uniquely crafted to emulate brain-like information processing and comprises three main components: Explainer, Producer, and Reasoner. Each component is designed to mimic specific brain functions, which aids in generating high-quality datasets and enhancing classification performance. The model is particularly focused on addressing the common and significant challenge of handling imbalanced datasets in machine learning. CCNETS's effectiveness is demonstrated through its application to a "fraud dataset," where normal transactions significantly outnumber fraudulent ones (99.83% vs. 0.17%). Traditional methods often struggle with such imbalances, leading to skewed performance metrics. However, CCNETS exhibits superior classification ability, as evidenced by its performance metrics. Specifically, it achieved an F1-score of 0.7992, outperforming traditional models like Autoencoders and Multi-layer Perceptrons (MLP) in the same context. This performance indicates CCNETS's proficiency in more accurately distinguishing between normal and fraudulent patterns. The innovative structure of CCNETS enhances the coherence between generative and classification models, helping to overcome the limitations of pattern recognition that rely solely on generative models. This study emphasizes CCNETS's potential in diverse applications, especially where quality data generation and pattern recognition are key. It proves effective in machine learning, particularly for imbalanced datasets. CCNETS overcomes current challenges in these datasets and advances machine learning with brain-inspired approaches.