Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including spurious gene correlations, sample correlations, and batch effects. To address these complexities, we introduce a robust method for high-dimensional graph inference from multiple independent studies. We base our approach on the premise that each dataset is essentially a noisy linear mixture of gene loadings that follow a multivariate $t$-distribution with a sparse precision matrix, which is shared across studies. This allows us to show that we can identify the co-expression matrix up to a scaling factor among other model parameters. Our method employs an Expectation-Maximization procedure for parameter estimation. Empirical evaluation on synthetic and gene expression data demonstrates our method's improved ability to learn the underlying graph structure compared to baseline methods.

Objective: realtime monitoring of invasive ventilation (iV) in intensive care units (ICUs) plays a crucial role in ensuring prompt interventions and better patient outcomes. However, conventional methods often overlook valuable insights embedded within clinical notes, relying solely on tabular data. In this study, we propose an innovative approach to enhance iV risk monitoring by incorporating clinical notes into the monitoring pipeline through using language models for text summarization. Results: We achieve superior performance in all metrics reported by the state-of-the-art in iV risk monitoring, namely: an AUROC of 0.86, an AUC-PR of 0.35, and an AUCt of up to 0.86. We also demonstrate that our methodology allows for more lead time in flagging iV for certain time buckets. Conclusion: Our study underscores the potential of integrating clinical notes and language models into realtime iV risk monitoring, paving the way for improved patient care and informed clinical decision-making in ICU settings.

We consider the problem of a training data proof, where a data creator or owner wants to demonstrate to a third party that some machine learning model was trained on their data. Training data proofs play a key role in recent lawsuits against foundation models trained on web-scale data. Many prior works suggest to instantiate training data proofs using membership inference attacks. We argue that this approach is fundamentally unsound: to provide convincing evidence, the data creator needs to demonstrate that their attack has a low false positive rate, i.e., that the attack's output is unlikely under the null hypothesis that the model was not trained on the target data. Yet, sampling from this null hypothesis is impossible, as we do not know the exact contents of the training set, nor can we (efficiently) retrain a large foundation model. We conclude by offering two paths forward, by showing that data extraction attacks and membership inference on special canary data can be used to create sound training data proofs.

OCR errors are common in digitised historical archives significantly affecting their usability and value. Generative Language Models (LMs) have shown potential for correcting these errors using the context provided by the corrupted text and the broader socio-cultural context, a process called Context Leveraging OCR Correction (CLOCR-C). However, getting sufficient training data for fine-tuning such models can prove challenging. This paper shows that fine-tuning a language model on synthetic data using an LM and using a character level Markov corruption process can significantly improve the ability to correct OCR errors. Models trained on synthetic data reduce the character error rate by 55% and word error rate by 32% over the base LM and outperform models trained on real data. Key findings include; training on under-corrupted data is better than over-corrupted data; non-uniform character level corruption is better than uniform corruption; More tokens-per-observation outperforms more observations for a fixed token budget. The outputs for this paper are a set of 8 heuristics for training effective CLOCR-C models, a dataset of 11,000 synthetic 19th century newspaper articles and scrambledtext a python library for creating synthetic corrupted data.

Class imbalance in binary classification tasks remains a significant challenge in machine learning, often resulting in poor performance on minority classes. This study comprehensively evaluates three widely-used strategies for handling class imbalance: Synthetic Minority Over-sampling Technique (SMOTE), Class Weights tuning, and Decision Threshold Calibration. We compare these methods against a baseline scenario of no-intervention across 15 diverse machine learning models and 30 datasets from various domains, conducting a total of 9,000 experiments. Performance was primarily assessed using the F1-score, although our study also tracked results on additional 9 metrics including F2-score, precision, recall, Brier-score, PR-AUC, and AUC. Our results indicate that all three strategies generally outperform the baseline, with Decision Threshold Calibration emerging as the most consistently effective technique. However, we observed substantial variability in the best-performing method across datasets, highlighting the importance of testing multiple approaches for specific problems. This study provides valuable insights for practitioners dealing with imbalanced datasets and emphasizes the need for dataset-specific analysis in evaluating class imbalance handling techniques.

Partial Label Learning (PLL) is a typical weakly supervised learning task, which assumes each training instance is annotated with a set of candidate labels containing the ground-truth label. Recent PLL methods adopt identification-based disambiguation to alleviate the influence of false positive labels and achieve promising performance. However, they require all classes in the test set to have appeared in the training set, ignoring the fact that new classes will keep emerging in real applications. To address this issue, in this paper, we focus on the problem of Partial Label Learning with Augmented Class (PLLAC), where one or more augmented classes are not visible in the training stage but appear in the inference stage. Specifically, we propose an unbiased risk estimator with theoretical guarantees for PLLAC, which estimates the distribution of augmented classes by differentiating the distribution of known classes from unlabeled data and can be equipped with arbitrary PLL loss functions. Besides, we provide a theoretical analysis of the estimation error bound of the estimator, which guarantees the convergence of the empirical risk minimizer to the true risk minimizer as the number of training data tends to infinity. Furthermore, we add a risk-penalty regularization term in the optimization objective to alleviate the influence of the over-fitting issue caused by negative empirical risk. Extensive experiments on benchmark, UCI and real-world datasets demonstrate the effectiveness of the proposed approach.

Accurately predicting passenger travel choices under train delays can provide interpretable insights into the redistribution of passenger flow, offering crucial decision support for emergency response and service recovery. However, the diversity of travel choices due to passenger heterogeneity and the sparsity of delay events leads to issues of data sparsity and sample imbalance in the travel choices dataset under metro delays. It is challenging to model this problem using traditional machine learning approaches, which typically rely on large, balanced datasets. Given the strengths of large language models (LLMs) in text processing, understanding, and their capabilities in small-sample and even zero-shot learning, this paper proposes a novel Passenger Travel Choice prediction framework under metro delays with the Large Language Model (DelayPTC-LLM). The well-designed prompting engineering is developed to guide the LLM in making and rationalizing predictions about travel choices, taking into account passenger heterogeneity and features of the delay events. Utilizing real-world data from Shenzhen Metro, including Automated Fare Collection (AFC) data and detailed delay logs, a comparative analysis of DelayPTC-LLM with traditional prediction models demonstrates the superior capability of LLMs in handling complex, sparse datasets commonly encountered under disruption of transportation systems. The results validate the advantages of DelayPTC-LLM in terms of predictive accuracy and its potential to provide actionable insights for big traffic data.

Creation of synthetic data models has represented a significant advancement across diverse scientific fields, but this technology also brings important privacy considerations for users. This work focuses on enhancing a non-parametric copula-based synthetic data generation model, DPNPC, by incorporating Differential Privacy through an Enhanced Fourier Perturbation method. The model generates synthetic data for mixed tabular databases while preserving privacy. We compare DPNPC with three other models (PrivBayes, DP-Copula, and DP-Histogram) across three public datasets, evaluating privacy, utility, and execution time. DPNPC outperforms others in modeling multivariate dependencies, maintaining privacy for small $\epsilon$ values, and reducing training times. However, limitations include the need to assess the model's performance with different encoding methods and consider additional privacy attacks. Future research should address these areas to enhance privacy-preserving synthetic data generation.

The early detection and nuanced subtype classification of non-small cell lung cancer (NSCLC), a predominant cause of cancer mortality worldwide, is a critical and complex issue. In this paper, we introduce an innovative integration of multi-modal data, synthesizing fused medical imaging (CT and PET scans) with clinical health records and genomic data. This unique fusion methodology leverages advanced machine learning models, notably MedClip and BEiT, for sophisticated image feature extraction, setting a new standard in computational oncology. Our research surpasses existing approaches, as evidenced by a substantial enhancement in NSCLC detection and classification precision. The results showcase notable improvements across key performance metrics, including accuracy, precision, recall, and F1-score. Specifically, our leading multi-modal classifier model records an impressive accuracy of 94.04%. We believe that our approach has the potential to transform NSCLC diagnostics, facilitating earlier detection and more effective treatment planning and, ultimately, leading to superior patient outcomes in lung cancer care.

One of the most important challenges in the financial and cryptocurrency field is accurately predicting cryptocurrency price trends. Leveraging artificial intelligence (AI) is beneficial in addressing this challenge. Cryptocurrency markets, marked by substantial growth and volatility, attract investors and scholars keen on deciphering and forecasting cryptocurrency price movements. The vast and diverse array of data available for such predictions increases the complexity of the task. In our study, we introduce a novel approach termed hard and soft information fusion (HSIF) to enhance the accuracy of cryptocurrency price movement forecasts. The hard information component of our approach encompasses historical price records alongside technical indicators. Complementing this, the soft data component extracts from X (formerly Twitter), encompassing news headlines and tweets about the cryptocurrency. To use this data, we use the Bidirectional Encoder Representations from Transformers (BERT)-based sentiment analysis method, financial BERT (FinBERT), which performs best. Finally, our model feeds on the information set including processed hard and soft data. We employ the bidirectional long short-term memory (BiLSTM) model because processing information in both forward and backward directions can capture long-term dependencies in sequential information. Our empirical findings emphasize the superiority of the HSIF approach over models dependent on single-source data by testing on Bitcoin-related data. By fusing hard and soft information on Bitcoin dataset, our model has about 96.8\% accuracy in predicting price movement. Incorporating information enables our model to grasp the influence of social sentiment on price fluctuations, thereby supplementing the technical analysis-based predictions derived from hard information.