Link prediction (LP) is an important problem in network science and machine learning research. The state-of-the-art LP methods are usually evaluated in a uniform setup, ignoring several factors associated with the data and application specific needs. We identify a number of such factors, such as, network-type, problem-type, geodesic distance between the end nodes and its distribution over the classes, nature and applicability of LP methods, class imbalance and its impact on early retrieval, evaluation metric, etc., and present an experimental setup which allows us to evaluate LP methods in a rigorous and controlled manner. We perform extensive experiments with a variety of LP methods over real network datasets in this controlled setup, and gather valuable insights on the interactions of these factors with the performance of LP through an array of carefully designed hypotheses. Following the insights, we provide recommendations to be followed as best practice for evaluating LP methods.

In real-world applications, machine learning models must reliably detect Out-of-Distribution (OoD) samples to prevent unsafe decisions. Current OoD detection methods often rely on analyzing the logits or the embeddings of the penultimate layer of a neural network. However, little work has been conducted on the exploitation of the rich information encoded in intermediate layers. To address this, we analyze the discriminative power of intermediate layers and show that they can positively be used for OoD detection. Therefore, we propose to regularize intermediate layers with an energy-based contrastive loss, and by grouping multiple layers in a single aggregated response. We demonstrate that intermediate layer activations improves OoD detection performance by running a comprehensive evaluation across multiple datasets.

As synthetic data becomes increasingly popular in machine learning tasks, numerous methods--without formal differential privacy guarantees--use synthetic data for training. These methods often claim, either explicitly or implicitly, to protect the privacy of the original training data. In this work, we explore four different training paradigms: coreset selection, dataset distillation, data-free knowledge distillation, and synthetic data generated from diffusion models. While all these methods utilize synthetic data for training, they lead to vastly different conclusions regarding privacy preservation. We caution that empirical approaches to preserving data privacy require careful and rigorous evaluation; otherwise, they risk providing a false sense of privacy. Synthetic data is increasingly utilized for training machine learning (ML) models, especially in situations where real-world data is scarce, sensitive, costly to obtain, or subject to regulations such as GDPR (GDPR.eu). Synthetic data is particularly beneficial in scenarios where data distributions are atypical, such as in federated learning with non-IID data (Zhang et al., 2023c), long-tailed learning (Shin et al., 2023), and continual learning (Meng et al., 2024). It enables the creation of diverse datasets that include edge cases or rare events that may be underrepresented in real-world data. Consequently, training models with synthetic data has proven beneficial for enhancing model robustness and adaptability across a wide range of real-world scenarios. Many empirical methods--without formal differential privacy guarantees--rely on synthetic data for training, such as coreset selection (Feldman, 2020), dataset distillation (Wang et al., 2018), data-free knowledge distillation (Yin et al., 2020), and synthetic data generated from diffusion models (Yuan et al., 2024). This proxy data can be directly sampled from private sources (Guo et al., 2022; Mirzasoleiman et al., 2020) or out-of-distribution sources (Wang et al., 2023), iteratively optimized (Zhang et al., 2023d; Zhao et al., 2020), or generated using GANs (Karras et al., 2019) and diffusion models (Rombach et al., 2022). Since the model may never encounter any private training data and the synthetic images are often visually distinct from the original private data, these methods often claim to preserve privacy while still maintaining satisfactory performance. In this work, we aim to address the following question: Does training with synthetic data truly protect privacy? To rigorously measure the privacy leakage of empirical methods trained on synthetic data, we use membership inference attacks (Shokri et al., 2017) as a privacy auditing tool.

The rapid growth of mobile applications has escalated Android malware threats. Although there are numerous detection methods, they often struggle with evolving attacks, dataset biases, and limited explainability. Large Language Models (LLMs) offer a promising alternative with their zero-shot inference and reasoning capabilities. However, applying LLMs to Android malware detection presents two key challenges: (1)the extensive support code in Android applications, often spanning thousands of classes, exceeds LLMs' context limits and obscures malicious behavior within benign functionality; (2)the structural complexity and interdependencies of Android applications surpass LLMs' sequence-based reasoning, fragmenting code analysis and hindering malicious intent inference. To address these challenges, we propose LAMD, a practical context-driven framework to enable LLM-based Android malware detection. LAMD integrates key context extraction to isolate security-critical code regions and construct program structures, then applies tier-wise code reasoning to analyze application behavior progressively, from low-level instructions to high-level semantics, providing final prediction and explanation. A well-designed factual consistency verification mechanism is equipped to mitigate LLM hallucinations from the first tier. Evaluation in real-world settings demonstrates LAMD's effectiveness over conventional detectors, establishing a feasible basis for LLM-driven malware analysis in dynamic threat landscapes.

Gene expression classification is a pivotal yet challenging task in bioinformatics, primarily due to the high dimensionality of genomic data and the risk of overfitting. To bridge this gap, we propose BOLIMES, a novel feature selection algorithm designed to enhance gene expression classification by systematically refining the feature subset. Unlike conventional methods that rely solely on statistical ranking or classifier-specific selection, we integrate the robustness of Boruta with the interpretability of LIME, ensuring that only the most relevant and influential genes are retained. BOLIMES first employs Boruta to filter out non-informative genes by comparing each feature against its randomized counterpart, thus preserving valuable information. It then uses LIME to rank the remaining genes based on their local importance to the classifier. Finally, an iterative classification evaluation determines the optimal feature subset by selecting the number of genes that maximizes predictive accuracy. By combining exhaustive feature selection with interpretability-driven refinement, our solution effectively balances dimensionality reduction with high classification performance, offering a powerful solution for high-dimensional gene expression analysis.

Tensor Networks have emerged as a prominent alternative to neural networks for addressing Machine Learning challenges in foundational sciences, paving the way for their applications to real-life problems. This paper introduces tn4ml, a novel library designed to seamlessly integrate Tensor Networks into optimization pipelines for Machine Learning tasks. Inspired by existing Machine Learning frameworks, the library offers a user-friendly structure with modules for data embedding, objective function definition, and model training using diverse optimization strategies. We demonstrate its versatility through two examples: supervised learning on tabular data and unsupervised learning on an image dataset. Additionally, we analyze how customizing the parts of the Machine Learning pipeline for Tensor Networks influences performance metrics.

Reliably labelling data typically requires annotations from multiple human workers. However, humans are far from being perfect. Hence, it is a common practice to aggregate labels gathered from multiple annotators to make a more confident estimate of the true label. Among many aggregation methods, the simple and well known Majority Vote (MV) selects the class label polling the highest number of votes. However, despite its importance, the optimality of MV's label aggregation has not been extensively studied. We address this gap in our work by characterising the conditions under which MV achieves the theoretically optimal lower bound on label estimation error. Our results capture the tolerable limits on annotation noise under which MV can optimally recover labels for a given class distribution. This certificate of optimality provides a more principled approach to model selection for label aggregation as an alternative to otherwise inefficient practices that sometimes include higher experts, gold labels, etc., that are all marred by the same human uncertainty despite huge time and monetary costs. Experiments on both synthetic and real world data corroborate our theoretical findings.

In this paper, we investigate the problem of unsupervised anomaly detection using the k-Nearest Neighbor method. The k-Nearest Neighbor Anomaly Detection (kNNAD) is a simple yet effective approach for identifying anomalies across various domains and fields. A critical challenge in anomaly detection, including kNNAD, is appropriately quantifying the reliability of detected anomalies. To address this, we formulate kNNAD as a statistical hypothesis test and quantify the probability of false detection using $p$-values. The main technical challenge lies in performing both anomaly detection and statistical testing on the same data, which hinders correct $p$-value calculation within the conventional statistical testing framework. To resolve this issue, we introduce a statistical hypothesis testing framework called Selective Inference (SI) and propose a method named Statistically Significant NNAD (Stat-kNNAD). By leveraging SI, the Stat-kNNAD method ensures that detected anomalies are statistically significant with theoretical guarantees. The proposed Stat-kNNAD method is applicable to anomaly detection in both the original feature space and latent feature spaces derived from deep learning models. Through numerical experiments on synthetic data and applications to industrial product anomaly detection, we demonstrate the validity and effectiveness of the Stat-kNNAD method.

Smart contracts are essential to decentralized finance (DeFi) and blockchain ecosystems but are increasingly vulnerable to exploits due to coding errors and complex attack vectors. Traditional static analysis tools and existing vulnerability detection methods often fail to address these challenges comprehensively, leading to high false-positive rates and an inability to detect dynamic vulnerabilities. This paper introduces SmartLLM, a novel approach leveraging fine-tuned LLaMA 3.1 models with Retrieval-Augmented Generation (RAG) to enhance the accuracy and efficiency of smart contract auditing. By integrating domain-specific knowledge from ERC standards and employing advanced techniques such as QLoRA for efficient fine-tuning, SmartLLM achieves superior performance compared to static analysis tools like Mythril and Slither, as well as zero-shot large language model (LLM) prompting methods such as GPT-3.5 and GPT-4. Experimental results demonstrate a perfect recall of 100% and an accuracy score of 70%, highlighting the model's robustness in identifying vulnerabilities, including reentrancy and access control issues. This research advances smart contract security by offering a scalable and effective auditing solution, supporting the secure adoption of decentralized applications.

The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a motif), the task is to identify diverse protein structures (scaffolds) that include the motif and maintain its geometry. Significant recent progress on motif-scaffolding has been made due to computational evaluation with reliable protein structure prediction and fixed-backbone sequence design methods [1-17]. However, significant variability in evaluation strategies across publications has hindered comparability of results, challenged reproducibility, and impeded robust progress. In response we introduce MotifBench, comprising (1) a precisely specified pipeline and evaluation metrics, (2) a collection of 30 benchmark problems, and (3) an implementation of this benchmark and leaderboard at github.com/blt2114/MotifBench. The MotifBench test cases are more difficult compared to earlier benchmarks (e.g. A motif-scaffolding method takes a motif as input and returns a set of putatively compatible scaffolds as output. This section details how motifs and scaffolds in MotifBench are specified, proposes metrics by which a scaffold set is evaluated, and describes how these metrics are computed. Appendix A describes considerations upon which these specifications and metrics were chosen. Motif specification (inputs): A motif is specified by the coordinates of the backbone atoms of several residues and (in some cases) the amino acid types of a subset of those residues.