Glioblastoma (GBM) is one of the most aggressive and lethal human cancers. Intra-tumoral genetic heterogeneity poses a significant challenge for treatment. Biopsy is invasive, which motivates the development of non-invasive, MRI-based machine learning (ML) models to quantify intra-tumoral genetic heterogeneity for each patient. This capability holds great promise for enabling better therapeutic selection to improve patient outcomes. We proposed a novel Weakly Supervised Ordinal Support Vector Machine (WSO-SVM) to predict regional genetic alteration status within each GBM tumor using MRI. WSO-SVM was applied to a unique dataset of 318 image-localized biopsies with spatially matched multiparametric MRI from 74 GBM patients. The model was trained to predict the regional genetic alteration of three GBM driver genes (EGFR, PDGFRA, and PTEN) based on features extracted from the corresponding region of five MRI contrast images. For comparison, a variety of existing ML algorithms were also applied. The classification accuracy of each gene was compared between the different algorithms. The SHapley Additive exPlanations (SHAP) method was further applied to compute contribution scores of different contrast images. Finally, the trained WSO-SVM was used to generate prediction maps within the tumoral area of each patient to help visualize the intra-tumoral genetic heterogeneity. This study demonstrated the feasibility of using MRI and WSO-SVM to enable non-invasive prediction of intra-tumoral regional genetic alteration for each GBM patient, which can inform future adaptive therapies for individualized oncology.

Synthetic data has made tremendous strides in various commercial settings including finance, healthcare, and virtual reality. We present a broad overview of prototypical applications of synthetic data in the financial sector and in particular provide richer details for a few select ones. These cover a wide variety of data modalities including tabular, time-series, event-series, and unstructured arising from both markets and retail financial applications. Since finance is a highly regulated industry, synthetic data is a potential approach for dealing with issues related to privacy, fairness, and explainability. Various metrics are utilized in evaluating the quality and effectiveness of our approaches in these applications. We conclude with open directions in synthetic data in the context of the financial domain.

The tasks of designing messenger RNAs and non-coding RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we formulate these problems as continuous optimization and develop a general framework for this optimization based on a new concept of "expected partition function". The basic idea is to start with a distribution over all possible candidate sequences, and extend the objective function from a sequence to a distribution. We then use gradient descent-based optimization methods to improve the extended objective function, and the distribution will gradually shrink towards a one-hot sequence (i.e., a single sequence). We consider two important case studies within this framework, the mRNA design problem optimizing for partition function (i.e., ensemble free energy) and the non-coding RNA design problem optimizing for conditional (i.e., Boltzmann) probability. In both cases, our approach demonstrate promising preliminary results.

Design patterns provide a systematic way to convey solutions to recurring modeling challenges. This paper introduces design patterns for hybrid modeling, an approach that combines modeling based on first principles with data-driven modeling techniques. While both approaches have complementary advantages there are often multiple ways to combine them into a hybrid model, and the appropriate solution will depend on the problem at hand. In this paper, we provide four base patterns that can serve as blueprints for combining data-driven components with domain knowledge into a hybrid approach. In addition, we also present two composition patterns that govern the combination of the base patterns into more complex hybrid models. Each design pattern is illustrated by typical use cases from application areas such as climate modeling, engineering, and physics.

Recent papers have demonstrated the possibility of energy-based text generation by adapting gradient-based sampling algorithms, a paradigm of MCMC algorithms that promises fast convergence. However, as we show in this paper, previous attempts on this approach to text generation all fail to sample correctly from the target language model distributions. To address this limitation, we consider the problem of designing text samplers that are faithful, meaning that they have the target text distribution as its limiting distribution. We propose several faithful gradient-based sampling algorithms to sample from the target energy-based text distribution correctly, and study their theoretical properties. Through experiments on various forms of text generation, we demonstrate that faithful samplers are able to generate more fluent text while adhering to the control objectives better.

Graph outlier detection is a prominent task of research and application in the realm of graph neural networks. It identifies the outlier nodes that exhibit deviation from the majority in the graph. One of the fundamental challenges confronting supervised graph outlier detection algorithms is the prevalent issue of class imbalance, where the scarcity of outlier instances compared to normal instances often results in suboptimal performance. Conventional methods mitigate the imbalance by reweighting instances in the estimation of the loss function, assigning higher weights to outliers and lower weights to inliers. Nonetheless, these strategies are prone to overfitting and underfitting, respectively. Recently, generative models, especially diffusion models, have demonstrated their efficacy in synthesizing high-fidelity images. Despite their extraordinary generation quality, their potential in data augmentation for supervised graph outlier detection remains largely underexplored. To bridge this gap, we introduce GODM, a novel data augmentation for mitigating class imbalance in supervised Graph Outlier detection with latent Diffusion Models. Specifically, our proposed method consists of three key components: (1) Variantioanl Encoder maps the heterogeneous information inherent within the graph data into a unified latent space. (2) Graph Generator synthesizes graph data that are statistically similar to real outliers from latent space, and (3) Latent Diffusion Model learns the latent space distribution of real organic data by iterative denoising. Extensive experiments conducted on multiple datasets substantiate the effectiveness and efficiency of GODM. The case study further demonstrated the generation quality of our synthetic data. To foster accessibility and reproducibility, we encapsulate GODM into a plug-and-play package and release it at the Python Package Index (PyPI).

This paper introduces AIJack, an open-source library designed to assess security and privacy risks associated with the training and deployment of machine learning models. Amid the growing interest in big data and AI, advancements in machine learning research and business are accelerating. However, recent studies reveal potential threats, such as the theft of training data and the manipulation of models by malicious attackers. Therefore, a comprehensive understanding of machine learning's security and privacy vulnerabilities is crucial for the safe integration of machine learning into real-world products. AIJack aims to address this need by providing a library with various attack and defense methods through a unified API. The library is publicly available on GitHub (https://github.com/Koukyosyumei/AIJack).

This research explores the effectiveness of various Machine Learning (ML) models used to predicting solar radiation at the Central Campus of the State Technical University of Quevedo (UTEQ). The data was obtained from a pyranometer, strategically located in a high area of the campus. This instrument continuously recorded solar irradiance data since 2020, offering a comprehensive dataset encompassing various weather conditions and temporal variations. After a correlation analysis, temperature and the time of day were identified as the relevant meteorological variables that influenced the solar irradiance. Different machine learning algorithms such as Linear Regression, K-Nearest Neighbors, Decision Tree, and Gradient Boosting were compared using the evaluation metrics Mean Squared Error (MSE), Root Mean Squared Error (RMSE), Mean Absolute Error (MAE), and the Coefficient of Determination ($R^2$). The study revealed that Gradient Boosting Regressor exhibited superior performance, closely followed by the Random Forest Regressor. These models effectively captured the non-linear patterns in solar radiation, as evidenced by their low MSE and high $R^2$ values. With the aim of assess the performance of our ML models, we developed a web-based tool for the Solar Radiation Forecasting in the UTEQ available at http://https://solarradiationforecastinguteq.streamlit.app/. The results obtained demonstrate the effectiveness of our ML models in solar radiation prediction and contribute a practical utility in real-time solar radiation forecasting, aiding in efficient solar energy management.

Predicting in-hospital mortality for intensive care unit (ICU) patients is key to final clinical outcomes. AI has shown advantaged accuracy but suffers from the lack of explainability. To address this issue, this paper proposes an eXplainable Multimodal Mortality Predictor (X-MMP) approaching an efficient, explainable AI solution for predicting in-hospital mortality via multimodal ICU data. We employ multimodal learning in our framework, which can receive heterogeneous inputs from clinical data and make decisions. Furthermore, we introduce an explainable method, namely Layer-Wise Propagation to Transformer, as a proper extension of the LRP method to Transformers, producing explanations over multimodal inputs and revealing the salient features attributed to prediction. Moreover, the contribution of each modality to clinical outcomes can be visualized, assisting clinicians in understanding the reasoning behind decision-making. We construct a multimodal dataset based on MIMIC-III and MIMIC-III Waveform Database Matched Subset. Comprehensive experiments on benchmark datasets demonstrate that our proposed framework can achieve reasonable interpretation with competitive prediction accuracy. In particular, our framework can be easily transferred to other clinical tasks, which facilitates the discovery of crucial factors in healthcare research.

Predicting the outcome of antiretroviral therapies for HIV-1 is a pressing clinical challenge, especially when the treatment regimen includes drugs for which limited effectiveness data is available. This scarcity of data can arise either due to the introduction of a new drug to the market or due to limited use in clinical settings. To tackle this issue, we introduce a novel joint fusion model, which combines features from a Fully Connected (FC) Neural Network and a Graph Neural Network (GNN). The FC network employs tabular data with a feature vector made up of viral mutations identified in the most recent genotypic resistance test, along with the drugs used in therapy. Conversely, the GNN leverages knowledge derived from Stanford drug-resistance mutation tables, which serve as benchmark references for deducing in-vivo treatment efficacy based on the viral genetic sequence, to build informative graphs. We evaluated these models' robustness against Out-of-Distribution drugs in the test set, with a specific focus on the GNN's role in handling such scenarios. Our comprehensive analysis demonstrates that the proposed model consistently outperforms the FC model, especially when considering Out-of-Distribution drugs. These results underscore the advantage of integrating Stanford scores in the model, thereby enhancing its generalizability and robustness, but also extending its utility in real-world applications with limited data availability. This research highlights the potential of our approach to inform antiretroviral therapy outcome prediction and contribute to more informed clinical decisions.