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The integration of multi-omic data is pivotal for understanding complex diseases, but its high dimensionality and noise present significant challenges. Graph Neural Networks (GNNs) offer a robust framework for analyzing large-scale signaling pathways and protein-protein interaction networks, yet they face limitations in expressivity when capturing intricate biological relationships. To address this, we propose Graph Sequence Language Model (GraphSeqLM), a framework that enhances GNNs with biological sequence embeddings generated by Large Language Models (LLMs). These embeddings encode structural and biological properties of DNA, RNA, and proteins, augmenting GNNs with enriched features for analyzing sample-specific multi-omic data. By integrating topological, sequence-derived, and biological information, GraphSeqLM demonstrates superior predictive accuracy and outperforms existing methods, paving the way for more effective multi-omic data integration in precision medicine.

Code generation with large language models has shown significant promise, especially when employing retrieval-augmented generation (RAG) with few-shot examples. However, selecting effective examples that enhance generation quality remains a challenging task, particularly when the target programming language (PL) is underrepresented. In this study, we present two key findings: (1) retrieving examples whose presented algorithmic plans can be referenced for generating the desired behavior significantly improves generation accuracy, and (2) converting code into pseudocode effectively captures such algorithmic plans, enhancing retrieval quality even when the source and the target PLs are different. Based on these findings, we propose Plan-as-query Example Retrieval for few-shot prompting in Code generation (PERC), a novel framework that utilizes algorithmic plans to identify and retrieve effective examples. We validate the effectiveness of PERC through extensive experiments on the CodeContests, HumanEval and MultiPL-E benchmarks: PERC consistently outperforms the state-of-the-art RAG methods in code generation, both when the source and target programming languages match or differ, highlighting its adaptability and robustness in diverse coding environments.

Data races are critical issues in multithreaded program, leading to unpredictable, catastrophic and difficult-to-diagnose problems. Despite the extensive in-house testing, data races often escape to deployed software and manifest in production runs. Existing approaches suffer from either prohibitively high runtime overhead or incomplete detection capability. In this paper, we introduce HardRace, a data race monitor to detect races on-the-fly while with sufficiently low runtime overhead and high detection capability. HardRace firstly employs sound static analysis to determine a minimal set of essential memory accesses relevant to data races. It then leverages hardware trace instruction, i.e., Intel PTWRITE, to selectively record only these memory accesses and thread synchronization events during execution with negligible runtime overhead. Given the tracing data, HardRace performs standard data race detection algorithms to timely report potential races occurred in production runs. The experimental evaluations show that HardRace outperforms state-of-the-art tools like ProRace and Kard in terms of both runtime overhead and detection capability -- HardRace can detect all kinds of data races in read-world applications while maintaining a negligible overhead, less than 2% on average.

Despite the great success of large language models (LLMs), efficiently controlling the length of the output sequence still remains a challenge. In this paper, we propose Hansel, an efficient framework for length control in LLMs without affecting its generation ability. Hansel utilizes periodically outputted hidden special tokens to keep track of the remaining target length of the output sequence. Together with techniques to avoid abrupt termination of the output, this seemingly simple method proved to be efficient and versatile, while not harming the coherency and fluency of the generated text. The framework can be applied to any pre-trained LLMs during the finetuning stage of the model, regardless of its original positional encoding method. We demonstrate this by finetuning four different LLMs with Hansel and show that the mean absolute error of the output sequence decreases significantly in every model and dataset compared to the prompt-based length control finetuning. Moreover, the framework showed a substantially improved ability to extrapolate to target lengths unseen during finetuning, such as long dialog responses or extremely short summaries. This indicates that the model learns the general means of length control, rather than learning to match output lengths to those seen during training.

Understanding sensor data can be challenging for non-experts because of the complexity and unique semantic meanings of sensor modalities. This calls for intuitive and effective methods to present sensor information. However, creating intuitive sensor data visualizations presents three key challenges: the variability of sensor readings, gaps in domain comprehension, and the dynamic nature of sensor data. To address these issues, we develop Vivar, a novel AR system that integrates multi-modal sensor data and presents 3D volumetric content for visualization. In particular, we introduce a cross-modal embedding approach that maps sensor data into a pre-trained visual embedding space through barycentric interpolation. This allows for accurate and continuous integration of multi-modal sensor information. Vivar also incorporates sensor-aware AR scene generation using foundation models and 3D Gaussian Splatting (3DGS) without requiring domain expertise. In addition, Vivar leverages latent reuse and caching strategies to accelerate 2D and AR content generation. Our extensive experiments demonstrate that our system achieves 11$\times$ latency reduction without compromising quality. A user study involving over 485 participants, including domain experts, demonstrates Vivar's effectiveness in accuracy, consistency, and real-world applicability, paving the way for more intuitive sensor data visualization.

The rapid evolution of Internet of Things (IoT) environments has created an urgent need for secure and trustworthy distributed computing systems, particularly when dealing with heterogeneous devices and applications where centralized trust cannot be assumed. This paper proposes TrustMesh, a novel blockchain-enabled framework that addresses these challenges through a unique three-layer architecture combining permissioned blockchain technology with a novel multi-phase Practical Byzantine Fault Tolerance (PBFT) consensus protocol. The key innovation lies in TrustMesh's ability to support non-deterministic scheduling algorithms while maintaining Byzantine fault tolerance - features traditionally considered mutually exclusive in blockchain systems. The framework supports a sophisticated resource management approach that enables flexible scheduling decisions while preserving the security guarantees of blockchain-based verification. Our experimental evaluation using a real-world cold chain monitoring scenario demonstrates that TrustMesh successfully maintains Byzantine fault tolerance with fault detection latencies under 150 milliseconds, while maintaining consistent framework overhead across varying computational workloads even with network scaling. These results establish TrustMesh's effectiveness in balancing security, performance, and flexibility requirements in trustless IoT environments, advancing the state-of-the-art in secure distributed computing frameworks.

Writing effective prompts for large language models (LLM) can be unintuitive and burdensome. In response, services that optimize or suggest prompts have emerged. While such services can reduce user effort, they also introduce a risk: the prompt provider can subtly manipulate prompts to produce heavily biased LLM responses. In this work, we show that subtle synonym replacements in prompts can increase the likelihood (by a difference up to 78%) that LLMs mention a target concept (e.g., a brand, political party, nation). We substantiate our observations through a user study, showing our adversarially perturbed prompts 1) are indistinguishable from unaltered prompts by humans, 2) push LLMs to recommend target concepts more often, and 3) make users more likely to notice target concepts, all without arousing suspicion. The practicality of this attack has the potential to undermine user autonomy. Among other measures, we recommend implementing warnings against using prompts from untrusted parties.

We present CoDEx, a set of knowledge graph completion datasets extracted from Wikidata and Wikipedia that improve upon existing knowledge graph completion benchmarks in scope and level of difficulty. In terms of scope, CoDEx comprises three knowledge graphs varying in size and structure, multilingual descriptions of entities and relations, and tens of thousands of hard negative triples that are plausible but verified to be false. To characterize CoDEx, we contribute thorough empirical analyses and benchmarking experiments. First, we analyze each CoDEx dataset in terms of logical relation patterns. Next, we report baseline link prediction and triple classification results on CoDEx for five extensively tuned embedding models. Finally, we differentiate CoDEx from the popular FB15K-237 knowledge graph completion dataset by showing that CoDEx covers more diverse and interpretable content, and is a more difficult link prediction benchmark. Data, code, and pretrained models are available at //bit.ly/2EPbrJs.

A large number of real-world graphs or networks are inherently heterogeneous, involving a diversity of node types and relation types. Heterogeneous graph embedding is to embed rich structural and semantic information of a heterogeneous graph into low-dimensional node representations. Existing models usually define multiple metapaths in a heterogeneous graph to capture the composite relations and guide neighbor selection. However, these models either omit node content features, discard intermediate nodes along the metapath, or only consider one metapath. To address these three limitations, we propose a new model named Metapath Aggregated Graph Neural Network (MAGNN) to boost the final performance. Specifically, MAGNN employs three major components, i.e., the node content transformation to encapsulate input node attributes, the intra-metapath aggregation to incorporate intermediate semantic nodes, and the inter-metapath aggregation to combine messages from multiple metapaths. Extensive experiments on three real-world heterogeneous graph datasets for node classification, node clustering, and link prediction show that MAGNN achieves more accurate prediction results than state-of-the-art baselines.

The design of deep graph models still remains to be investigated and the crucial part is how to explore and exploit the knowledge from different hops of neighbors in an efficient way. In this paper, we propose a novel RNN-like deep graph neural network architecture by incorporating AdaBoost into the computation of network; and the proposed graph convolutional network called AdaGCN~(AdaBoosting Graph Convolutional Network) has the ability to efficiently extract knowledge from high-order neighbors and integrate knowledge from different hops of neighbors into the network in an AdaBoost way. We also present the architectural difference between AdaGCN and existing graph convolutional methods to show the benefits of our proposal. Finally, extensive experiments demonstrate the state-of-the-art prediction performance and the computational advantage of our approach AdaGCN.