Identifying druggable genes is essential for developing effective pharmaceuticals. With the availability of extensive, high-quality data, computational methods have become a significant asset. Protein Interaction Network (PIN) is valuable but challenging to implement due to its high dimensionality and sparsity. Previous methods relied on indirect integration, leading to resolution loss. This study proposes GAN-TAT, a framework utilizing an advanced graph embedding technology, ImGAGN, to directly integrate PIN for druggable gene inference work. Tested on three Pharos datasets, GAN-TAT achieved the highest AUC-ROC score of 0.951 on Tclin. Further evaluation shows that GAN-TAT's predictions are supported by clinical evidence, highlighting its potential practical applications in pharmacogenomics. This research represents a methodological attempt with the direct utilization of PIN, expanding potential new solutions for developing drug targets.

AI is demanding an evergrowing portion of environmental resources. Despite their potential impact on AI environmental sustainability, the role that programming languages play in AI (in)efficiency is to date still unknown. With this study, we aim to understand the impact that programming languages can have on AI environmental sustainability. To achieve our goal, we conduct a controlled empirical experiment by considering five programming languages (C++, Java, Python, MATLAB, and R), seven AI algorithms (KNN, SVC, AdaBoost, decision tree, logistic regression, naive bayses, and random forest), three popular datasets, and the training and inference phases. The collected results show that programming languages have a considerable impact on AI environmental sustainability. Compiled and semi-compiled languages (C++, Java) consistently consume less than interpreted languages (Python, MATLAB, R), which require up to 54x more energy. Some languages are cumulatively more efficient in training, while others in inference. Which programming language consumes the most highly depends on the algorithm considered. Ultimately, algorithm implementation might be the most determining factor in Green AI, regardless of the language used. As conclusion, while making AI more environmentally sustainable is paramount, a trade-off between energy efficiency and implementation ease should always be considered. Green AI can be achieved without the need of completely disrupting the development practices and technologies currently in place.

This study proposes a debiasing method for smooth nonparametric estimators. While machine learning techniques such as random forests and neural networks have demonstrated strong predictive performance, their theoretical properties remain relatively underexplored. Specifically, many modern algorithms lack assurances of pointwise asymptotic normality and uniform convergence, which are critical for statistical inference and robustness under covariate shift and have been well-established for classical methods like Nadaraya-Watson regression. To address this, we introduce a model-free debiasing method that guarantees these properties for smooth estimators derived from any nonparametric regression approach. By adding a correction term that estimates the conditional expected residual of the original estimator, or equivalently, its estimation error, we obtain a debiased estimator with proven pointwise asymptotic normality, and uniform convergence. These properties enable statistical inference and enhance robustness to covariate shift, making the method broadly applicable to a wide range of nonparametric regression problems.

Graph Neural Networks (GNNs) have demonstrated remarkable efficacy in tackling a wide array of graph-related tasks across diverse domains. However, a significant challenge lies in their propensity to generate biased predictions, particularly with respect to sensitive node attributes such as age and gender. These biases, inherent in many machine learning models, are amplified in GNNs due to the message-passing mechanism, which allows nodes to influence each other, rendering the task of making fair predictions notably challenging. This issue is particularly pertinent in critical domains where model fairness holds paramount importance. In this paper, we propose a novel generative Fairness-Aware Subgraph Diffusion (FASD) method for unbiased GNN learning. The method initiates by strategically sampling small subgraphs from the original large input graph, and then proceeds to conduct subgraph debiasing via generative fairness-aware graph diffusion processes based on stochastic differential equations (SDEs). To effectively diffuse unfairness in the input data, we introduce additional adversary bias perturbations to the subgraphs during the forward diffusion process, and train score-based models to predict these applied perturbations, enabling them to learn the underlying dynamics of the biases present in the data. Subsequently, the trained score-based models are utilized to further debias the original subgraph samples through the reverse diffusion process. Finally, FASD induces fair node predictions on the input graph by performing standard GNN learning on the debiased subgraphs. Experimental results demonstrate the superior performance of the proposed method over state-of-the-art Fair GNN baselines across multiple benchmark datasets.

The rapid advancement of foundation modelslarge-scale neural networks trained on diverse, extensive datasetshas revolutionized artificial intelligence, enabling unprecedented advancements across domains such as natural language processing, computer vision, and scientific discovery. However, the substantial parameter count of these models, often reaching billions or trillions, poses significant challenges in adapting them to specific downstream tasks. Low-Rank Adaptation (LoRA) has emerged as a highly promising approach for mitigating these challenges, offering a parameter-efficient mechanism to fine-tune foundation models with minimal computational overhead. This survey provides the first comprehensive review of LoRA techniques beyond large Language Models to general foundation models, including recent techniques foundations, emerging frontiers and applications of low-rank adaptation across multiple domains. Finally, this survey discusses key challenges and future research directions in theoretical understanding, scalability, and robustness. This survey serves as a valuable resource for researchers and practitioners working with efficient foundation model adaptation.

Deep learning's preponderance across scientific domains has reshaped high-stakes decision-making, making it essential to follow rigorous operational frameworks that include both Right-to-Privacy (RTP) and Right-to-Explanation (RTE). This paper examines the complexities of combining these two requirements. For RTP, we focus on `Differential privacy' (DP), which is considered the current \textit{gold standard} for privacy-preserving machine learning due to its strong quantitative guarantee of privacy. For RTE, we focus on post-hoc explainers: they are the \textit{go-to} option for model auditing as they operate independently of model training. We formally investigate DP models and various commonly-used post-hoc explainers: how to evaluate these explainers subject to RTP, and analyze the intrinsic interactions between DP models and these explainers. Furthermore, our work throws light on how RTP and RTE can be effectively combined in high-stakes applications. Our study concludes by outlining an industrial software pipeline, with the example of a wildly used use-case, that respects both RTP and RTE requirements.

Given that AI systems are set to play a pivotal role in future decision-making processes, their trustworthiness and reliability are of critical concern. Due to their scale and complexity, modern AI systems resist direct interpretation, and alternative ways are needed to establish trust in those systems, and determine how well they align with human values. We argue that good measures of the information processing similarities between AI and humans, may be able to achieve these same ends. While Representational alignment (RA) approaches measure similarity between the internal states of two systems, the associated data can be expensive and difficult to collect for human systems. In contrast, Behavioural alignment (BA) comparisons are cheaper and easier, but questions remain as to their sensitivity and reliability. We propose two new behavioural alignment metrics misclassification agreement which measures the similarity between the errors of two systems on the same instances, and class-level error similarity which measures the similarity between the error distributions of two systems. We show that our metrics correlate well with RA metrics, and provide complementary information to another BA metric, within a range of domains, and set the scene for a new approach to value alignment.

This article considers the impact of different thresholding methods to the Nearest Shrunken Centroid algorithm, which is popularly referred as the Prediction Analysis of Microarrays (PAM) for high-dimensional classification. PAM uses soft thresholding to achieve high computational efficiency and high classification accuracy but in the price of retaining too many features. When applied to microarray human cancers, PAM selected 2611 features on average from 10 multi-class datasets. Such a large number of features make it difficult to perform follow up study. One reason behind this problem is the soft thresholding, which is known to produce biased parameter estimate in regression analysis. In this article, we extend the PAM algorithm with two other thresholding methods, hard and order thresholding, and a deep search algorithm to achieve better thresholding parameter estimate. The modified algorithms are extensively tested and compared to the original one based on real data and Monte Carlo studies. In general, the modification not only gave better cancer status prediction accuracy, but also resulted in more parsimonious models with significantly smaller number of features.

High-dimensional sparse matrix data frequently arise in various applications. A notable example is the weighted word-word co-occurrence count data, which summarizes the weighted frequency of word pairs appearing within the same context window. This type of data typically contains highly skewed non-negative values with an abundance of zeros. Another example is the co-occurrence of item-item or user-item pairs in e-commerce, which also generates high-dimensional data. The objective is to utilize this data to predict the relevance between items or users. In this paper, we assume that items or users can be represented by unknown dense vectors. The model treats the co-occurrence counts as arising from zero-inflated Gamma random variables and employs cosine similarity between the unknown vectors to summarize item-item relevance. The unknown values are estimated using the shared parameter alternating zero-inflated Gamma regression models (SA-ZIG). Both canonical link and log link models are considered. Two parameter updating schemes are proposed, along with an algorithm to estimate the unknown parameters. Convergence analysis is presented analytically. Numerical studies demonstrate that the SA-ZIG using Fisher scoring without learning rate adjustment may fail to fi nd the maximum likelihood estimate. However, the SA-ZIG with learning rate adjustment performs satisfactorily in our simulation studies.

In this article, we present a model for analyzing the cooccurrence count data derived from practical fields such as user-item or item-item data from online shopping platform, cooccurring word-word pairs in sequences of texts. Such data contain important information for developing recommender systems or studying relevance of items or words from non-numerical sources. Different from traditional regression models, there are no observations for covariates. Additionally, the cooccurrence matrix is typically of so high dimension that it does not fit into a computer's memory for modeling. We extract numerical data by defining windows of cooccurrence using weighted count on the continuous scale. Positive probability mass is allowed for zero observations. We present Shared parameter Alternating Tweedie (SA-Tweedie) model and an algorithm to estimate the parameters. We introduce a learning rate adjustment used along with the Fisher scoring method in the inner loop to help the algorithm stay on track of optimizing direction. Gradient descent with Adam update was also considered as an alternative method for the estimation. Simulation studies and an application showed that our algorithm with Fisher scoring and learning rate adjustment outperforms the other two methods. Pseudo-likelihood approach with alternating parameter update was also studied. Numerical studies showed that the pseudo-likelihood approach is not suitable in our shared parameter alternating regression models with unobserved covariates.