41 accepted papers
Large Language Models (LLMs) have shown remarkable capabilities in solving various programming tasks, such as code generation. However, their potential for code optimization, particularly in performance enhancement, remains largely unexplored. This paper investigates the capabilities of LLMs in opti…
Multi-objective molecular optimization is a fundamental yet inherently challenging task in drug discovery, as it requires simultaneously optimizing multiple, often conflicting, molecular properties. Although recent deep learning methods have shown promise, they often lack objective-specific special
Current research on distributed multi-modal learning typically assumes that clients can access complete information across all modalities, which may not hold in practice. In this paper, we explore patchwork learning, in which the modalities available to different clients vary, and the objective is t…
Precise property prediction of organic materials is pivotal for next-generation electronic and energy devices. In density functional theory (DFT), the electron density (ED) serves as the fundamental determinant of material properties. Yet, establishing it as an input modality for material property p…
Activation sparsity offers a compelling route to accelerate large language model (LLM) inference by selectively suppressing hidden activations, yet existing approaches exhibit severe accuracy degradation at high sparsity. We show that this failure stems from representational instability: *activation…
Scientific images often require accurate numerical representations and correct object attributes. However, current faithfulness metrics are primarily tailored toward photorealistic, real-life imagery, rendering them ill-suited for scientific image evaluation. To address this gap, we introduce a nove
Whole-Slide Images (WSIs) are widely used for estimating the prognosis of cancer patients. Current studies generally follow a cancer-specific learning paradigm. However, the available training samples for one cancer type are usually scarce in pathology. Consequently, the model often struggles to lea
Fine-tuning large-scale Vision-Language Models (VLMs) is crucial for specialized tasks, but their performance is often undermined by the label noise prevalent in real-world datasets. Traditional approaches to learning with noisy labels typically rely on a self-referential loop, using a model's own p
Identifying suitable reaction conditions is critical for chemical synthesis, as they directly affect yield, selectivity, and transformation feasibility. While recent methods have shown promising results, most approaches either encode reactants and products independently or rely on rule-based reactio
Multi-step retrosynthetic planning aims to decompose target molecules into available starting materials by iteratively invoking single-step prediction models within a search algorithm. The success of retrosynthetic planning depends on the joint guidance of single-step reasoning and global search acr
Drug-target interaction prediction (DTI) is essential in various applications including drug discovery and clinical application. There are two perspectives of input data widely used in DTI prediction: Intrinsic data represents how drugs or targets are constructed, and extrinsic data represents how d…
Drug repurposing plays a critical role in accelerating treatment discovery, especially for complex and rare diseases. Biomedical knowledge graphs (KGs), which encode rich clinical associations, have been widely adopted to support this task. However, existing methods largely overlook common-sense bio
Generating cell-level descriptions for Jupyter Notebooks, which is a major resource consisting of codes, tables, and descriptions, has been attracting increasing research attention. However, existing methods for Jupyter Notebooks mostly focus on generating descriptions from code snippets or table ou…
Identifying drug-drug interactions (DDIs) is critical for ensuring drug safety and advancing drug development, a topic that has garnered significant research interest. While existing methods have made considerable progress, approaches relying solely on known DDIs face a key challenge when applied to…
In time-series classification, interpretable models can bring additional insights but be outperformed by deep models since human-understandable features have limited expressivity and flexibility. In this work, we present InterpGN, a framework that integrates an interpretable model and a deep neural…
Inductive Knowledge Graph Completion (KGC) aims to infer missing facts between newly emerged entities within knowledge graphs (KGs), posing a significant challenge. While recent studies have shown promising results in inferring such entities through knowledge subgraph reasoning, they suffer from (i)…
Knowledge graph completion (KGC) aims to alleviate the inherent incompleteness of knowledge graphs (KGs), a crucial task for numerous applications such as recommendation systems and drug repurposing. The success of knowledge graph embedding (KGE) models provokes the question about the explainability…
Large Language Models (LLMs) have demonstrated remarkable proficiency in generating code. However, the misuse of LLM-generated (synthetic) code has raised concerns in both educational and industrial contexts, underscoring the urgent need for synthetic code detectors. Existing methods for detecting s…
In time-series analysis, many recent works seek to provide a unified view and representation for time-series across multiple domains, leading to the development of foundation models for time-series data. Despite diverse modeling techniques, existing models are black boxes and fail to provide insight…
Code Clone Detection, which aims to retrieve functionally similar programs from large code bases, has been attracting increasing attention. Modern software often involves a diverse range of programming languages. However, current code clone detection methods are generally limited to only a few popul…
Large language models (LLMs) are primarily evaluated by overall performance on various text understanding and generation tasks. However, such a paradigm fails to comprehensively differentiate the fine-grained language and cognitive skills, rendering the lack of sufficient interpretation to LLMs’ cap…
Automatically generating human-readable text describing the functionality of a program is the intent of source code summarization. Although neural language models achieve significant performance in this field, they are limited by their inability to access external knowledge. To address this limitati…
"The emergence of Vision Language Models (VLMs) is a significant advancement in integrating computer vision with Large Language Models (LLMs) to produce detailed text descriptions based on visual inputs, yet it introduces new security vulnerabilities. Unlike prior work that centered on single modali…
Graph Transformers, which incorporate self-attention and positional encoding, have recently emerged as a powerful architecture for various graph learning tasks. Despite their impressive performance, the complex non-convex interactions across layers and the recursive graph structure have made it chal…
Automatically generating function summaries for binaries is an extremely valuable but challenging task, since it involves translating the execution behavior and semantics of the low-level language (assembly code) into human-readable natural language. However, most current works on understanding asse…
Learning an effective global model on private and decentralized datasets has become an increasingly important challenge of machine learning when applied in practice. Existing distributed learning paradigms, such as Federated Learning, enable this via model aggregation which enforces a strong form of…
Generating commonsense explanations requires reasoning about commonsense knowledge beyond what is explicitly mentioned in the context. Existing models use commonsense knowledge graphs such as ConceptNet to extract a subgraph of relevant knowledge pertaining to concepts in the input. However, due to…
Nowadays integrated circuits (ICs) are underpinning all major information technology innovations including the current trends of artificial intelligence (AI). Modern IC designs often involve analyses of complex phenomena (such as timing, noise, and power etc.) for tens of billions of electronic comp…
Datasets involving multivariate event streams are prevalent in numerous applications. We present a novel framework for modeling temporal point processes called clock logic neural networks (CLNN) which learn weighted clock logic (wCL) formulas as interpretable temporal rules by which some events prom…
Trojan attacks raise serious security concerns. In this paper, we investigate the underlying mechanism of Trojaned BERT models. We observe the attention focus drifting behavior of Trojaned models, i.e., when encountering an poisoned input, the trigger token hijacks the attention focus regardless of…
In recent years, algebraic topology and its modern development, the theory of persistent homology, has shown great potential in graph representation learning. In this paper, based on the mathematics of algebraic topology, we propose a novel solution for inductive relation prediction, an important le…
For many years, link prediction on knowledge. graphs has been a purely transductive task, not allowing for reasoning on unseen entities. Recently, increasing efforts are put into exploring semi- and fully inductive scenarios, enabling inference over unseen and emerging entities. Still, all these…
Topological features based on persistent homology capture high-order structural information so as to augment graph neural network methods. However, computing extended persistent homology summaries remains slow for large and dense graphs and can be a serious bottleneck for the learning pipeline. Insp…
Contrastive Learning has emerged as a powerful representation learning method and facilitates various downstream tasks especially when supervised data is limited. How to construct efficient contrastive samples through data augmentation is key to its success. Unlike vision tasks, the data augmentatio…
Link prediction is an important learning task for graph-structured data. In this paper, we propose a novel topological approach to characterize interactions between two nodes. Our topological feature, based on the extended persistent homology, encodes rich structural information regarding the multi-…
Timeline Summarization identifies major events from a news collection and describes them following temporal order, with key dates tagged. Previous methods generally generate summaries separately for each date after they determine the key dates of events. These methods overlook the events’ intra-stru…
Hierarchical abstractions are a methodology for solving large-scale graph problems in various disciplines. Coarsening is one such approach: it generates a pyramid of graphs whereby the one in the next level is a structural summary of the prior one. With a long history in scientific computing, many c…
Graph-structured data is prevalent in many domains. Despite the widely celebrated success of deep neural networks, their power in graph-structured data is yet to be fully explored. We propose a novel network architecture that incorporates advanced graph structural features. In particular, we leverag…
Drug-drug interaction (DDI) prediction is a challenging problem in pharmacology and clinical application, and effectively identifying potential DDIs during clinical trials is critical for patients and society. Most of existing computational models with AI techniques often concentrate on integrating…
Deep generative models have achieved remarkable success in various data domains, including images, time series, and natural languages. There remain, however, substantial challenges for combinatorial structures, including graphs. One of the key challenges lies in the difficulty of ensuring semantic v…
The graph convolutional networks (GCN) recently proposed by Kipf and Welling are an effective graph model for semi-supervised learning. Such a model, however, is transductive in nature because parameters are learned through convolutions with both training and test data. Moreover, the recursive neigh…