In order to emulate the local connectivity constraints of the retina, we would like neighboring pixels in 2D image-space tomap toneighboring pixels in1D vector-space.

Latent diffusion models such as Stable Diffusion achieve state-of-the-art results on text-to-image generation tasks. However, the extent to which these models have a semantic understanding of the images they generate is not well understood. In this work, we investigate whether the internal representations used by these models during text-to-image generation contain semantic information that is meaningful to humans. To do so, we perform probing on Stable Diffusion with simple regression layers that predict semantic attributes for objects and evaluate these predictions against human annotations. Surprisingly, we find that this success can actually be attributed to the text encoding occurring in CLIP rather than the reverse diffusion process. We demonstrate that groups of specific semantic attributes have markedly different decoding accuracy than the average, and are thus represented to different degrees. Finally, we show that attributes become more difficult to disambiguate from one another during the inverse diffusion process, further demonstrating the strongest semantic representation of object attributes in CLIP. We conclude that the separately trained CLIP vision-language model is what determines the human-like semantic representation, and that the diffusion process instead takes the role of a visual decoder.

Automatic medical report generation supports clinical diagnosis, reduces the workload of radiologists, and holds the promise of improving diagnosis consistency. However, existing evaluation metrics primarily assess the accuracy of key medical information coverage in generated reports compared to human-written reports, while overlooking crucial details such as the location and certainty of reported abnormalities. These limitations hinder the comprehensive assessment of the reliability of generated reports and pose risks in their selection for clinical use. Therefore, we propose a Granular Explainable Multi-Agent Score (GEMA-Score) in this paper, which conducts both objective quantification and subjective evaluation through a large language model-based multi-agent workflow. Our GEMA-Score parses structured reports and employs NER-F1 calculations through interactive exchanges of information among agents to assess disease diagnosis, location, severity, and uncertainty. Additionally, an LLM-based scoring agent evaluates completeness, readability, and clinical terminology while providing explanatory feedback. Extensive experiments validate that GEMA-Score achieves the highest correlation with human expert evaluations on a public dataset, demonstrating its effectiveness in clinical scoring (Kendall coefficient = 0.70 for Rexval dataset and Kendall coefficient = 0.54 for RadEvalX dataset).

Foundational models have emerged as powerful tools for addressing various tasks in clinical settings. However, their potential development to breast ultrasound analysis remains untapped. In this paper, we present BUSGen, the first foundational generative model specifically designed for breast ultrasound image analysis. Pretrained on over 3.5 million breast ultrasound images, BUSGen has acquired extensive knowledge of breast structures, pathological features, and clinical variations. With few-shot adaptation, BUSGen can generate repositories of realistic and informative task-specific data, facilitating the development of models for a wide range of downstream tasks. Extensive experiments highlight BUSGen's exceptional adaptability, significantly exceeding real-data-trained foundational models in breast cancer screening, diagnosis, and prognosis. In breast cancer early diagnosis, our approach outperformed all board-certified radiologists (n=9), achieving an average sensitivity improvement of 16.5% (P-value<0.0001). Additionally, we characterized the scaling effect of using generated data which was as effective as the collected real-world data for training diagnostic models. Moreover, extensive experiments demonstrated that our approach improved the generalization ability of downstream models. Importantly, BUSGen protected patient privacy by enabling fully de-identified data sharing, making progress forward in secure medical data utilization. An online demo of BUSGen is available at https://aibus.bio.

Predicting missing facts for temporal knowledge graphs (TKGs) is a fundamental task, called temporal knowledge graph completion (TKGC). One key challenge in this task is the imbalance in data distribution, where facts are unevenly spread across entities and timestamps. This imbalance can lead to poor completion performance or long-tail entities and timestamps, and unstable training due to the introduction of false negative samples. Unfortunately, few previous studies have investigated how to mitigate these effects. Moreover, for the first time, we found that existing methods suffer from model preferences, revealing that entities with specific properties (e.g., recently active) are favored by different models. Such preferences will lead to error accumulation and further exacerbate the effects of imbalanced data distribution, but are overlooked by previous studies. To alleviate the impacts of imbalanced data and model preferences, we introduce Booster, the first data augmentation strategy for TKGs. The unique requirements here lie in generating new samples that fit the complex semantic and temporal patterns within TKGs, and identifying hard-learning samples specific to models. Therefore, we propose a hierarchical scoring algorithm based on triadic closures within TKGs. By incorporating both global semantic patterns and local time-aware structures, the algorithm enables pattern-aware validation for new samples. Meanwhile, we propose a two-stage training approach to identify samples that deviate from the model's preferred patterns. With a well-designed frequency-based filtering strategy, this approach also helps to avoid the misleading of false negatives. Experiments justify that Booster can seamlessly adapt to existing TKGC models and achieve up to an 8.7% performance improvement.

This study was part of my dissertation for my master degree and compares the power consumption using the default floating point (32bit) and Nvidia mixed precision (16bit and 32bit) while training a classification ML model. A custom PC with specific hardware was built to perform the experiments, and different ML hyper-parameters, such as batch size, neurons, and epochs, were chosen to build Deep Neural Networks (DNN). Additionally, various software was used during the experiments to collect the power consumption data in Watts from the Graphics Processing Unit (GPU), Central Processing Unit (CPU), Random Access Memory (RAM) and manually from a wattmeter connected to the wall. A benchmarking test with default hyper parameter values for the DNN was used as a reference, while the experiments used a combination of different settings. The results were recorded in Excel, and descriptive statistics were chosen to calculate the mean between the groups and compare them using graphs and tables. The outcome was positive when using mixed precision combined with specific hyper-parameters. Compared to the benchmarking, the optimisation for the classification reduced the power consumption between 7 and 11 Watts. Similarly, the carbon footprint is reduced because the calculation uses the same power consumption data. Still, a consideration is required when configuring hyper-parameters because it can negatively affect hardware performance. However, this research required inferential statistics, specifically ANOVA and T-test, to compare the relationship between the means. Furthermore, tests indicated no statistical significance of the relationship between the benchmarking and experiments. However, a more extensive implementation with a cluster of GPUs can increase the sample size significantly, as it is an essential factor and can change the outcome of the statistical analysis.

Supervised learning-based software vulnerability detectors often fall short due to the inadequate availability of labelled training data. In contrast, Large Language Models (LLMs) such as GPT-4, are not trained on labelled data, but when prompted to detect vulnerabilities, LLM prediction accuracy is only marginally better than random guessing. In this paper, we explore a different approach by reframing vulnerability detection as one of anomaly detection. Since the vast majority of code does not contain vulnerabilities and LLMs are trained on massive amounts of such code, vulnerable code can be viewed as an anomaly from the LLM's predicted code distribution, freeing the model from the need for labelled data to provide a learnable representation of vulnerable code. Leveraging this perspective, we demonstrate that LLMs trained for code generation exhibit a significant gap in prediction accuracy when prompted to reconstruct vulnerable versus non-vulnerable code. Using this insight, we implement ANVIL, a detector that identifies software vulnerabilities at line-level granularity. Our experiments explore the discriminating power of different anomaly scoring methods, as well as the sensitivity of ANVIL to context size. We also study the effectiveness of ANVIL on various LLM families, and conduct leakage experiments on vulnerabilities that were discovered after the knowledge cutoff of our evaluated LLMs. On a collection of vulnerabilities from the Magma benchmark, ANVIL outperforms state-of-the-art line-level vulnerability detectors, LineVul and LineVD, which have been trained with labelled data, despite ANVIL having never been trained with labelled vulnerabilities. Specifically, our approach achieves $1.62\times$ to $2.18\times$ better Top-5 accuracies and $1.02\times$ to $1.29\times$ times better ROC scores on line-level vulnerability detection tasks.

The American Statistical Association (ASA) statement on statistical significance and P-values \cite{wasserstein2016asa} cautioned statisticians against making scientific decisions solely on the basis of traditional P-values. The statement delineated key issues with P-values, including a lack of transparency, an inability to quantify evidence in support of the null hypothesis, and an inability to measure the size of an effect or the importance of a result. In this article, we demonstrate that the interval null hypothesis framework (instead of the point null hypothesis framework), when used in tandem with Bayes factor-based tests, is instrumental in circumnavigating the key issues of P-values. Further, we note that specifying prior densities for Bayes factors is challenging and has been a reason for criticism of Bayesian hypothesis testing in existing literature. We address this by adapting Bayes factors directly based on common test statistics. We demonstrate, through numerical experiments and real data examples, that the proposed Bayesian interval hypothesis testing procedures can be calibrated to ensure frequentist error control while retaining their inherent interpretability. Finally, we illustrate the improved flexibility and applicability of the proposed methods by providing coherent frameworks for competitive landscape analysis and end-to-end Bayesian hypothesis tests in the context of reporting clinical trial outcomes.