Graph Sparsification for Enhanced Conformal Prediction in Graph Neural Networks

Conformal Prediction is a robust framework that ensures reliable coverage across machine learning tasks. Although recent studies have applied conformal prediction to graph neural networks, they have largely emphasized post-hoc prediction set generation. Improving conformal prediction during the training stage remains unaddressed. In this work, we tackle this challenge from a denoising perspective by introducing SparGCP, which incorporates graph sparsification and a conformal prediction-specific objective into GNN training. SparGCP employs a parameterized graph sparsification module to filter out task-irrelevant edges, thereby improving conformal prediction efficiency. Extensive experiments on real-world graph datasets demonstrate that SparGCP outperforms existing methods, reducing prediction set sizes by an average of 32\% and scaling seamlessly to large networks on commodity GPUs.

Benchmarking Graph Conformal Prediction: Empirical Analysis, Scalability, and Theoretical Insights

Conformal prediction has become increasingly popular for quantifying the uncertainty associated with machine learning models. Recent work in graph uncertainty quantification has built upon this approach for conformal graph prediction. The nascent nature of these explorations has led to conflicting choices for implementations, baselines, and method evaluation. In this work, we analyze the design choices made in the literature and discuss the tradeoffs associated with existing methods. Building on the existing implementations for existing methods, we introduce techniques to scale existing methods to large-scale graph datasets without sacrificing performance. Our theoretical and empirical results justify our recommendations for future scholarship in graph conformal prediction.

REASONS: A benchmark for REtrieval and Automated citationS Of scieNtific Sentences using Public and Proprietary LLMs

Automatic citation generation for sentences in a document or report is paramount for intelligence analysts, cybersecurity, news agencies, and education personnel. In this research, we investigate whether large language models (LLMs) are capable of generating references based on two forms of sentence queries: (a) Direct Queries, LLMs are asked to provide author names of the given research article, and (b) Indirect Queries, LLMs are asked to provide the title of a mentioned article when given a sentence from a different article. To demonstrate where LLM stands in this task, we introduce a large dataset called REASONS comprising abstracts of the 12 most popular domains of scientific research on arXiv. From around 20K research articles, we make the following deductions on public and proprietary LLMs: (a) State-of-the-art, often called anthropomorphic GPT-4 and GPT-3.5, suffers from high pass percentage (PP) to minimize the hallucination rate (HR). When tested with Perplexity.ai (7B), they unexpectedly made more errors; (b) Augmenting relevant metadata lowered the PP and gave the lowest HR; (c) Advance retrieval-augmented generation (RAG) using Mistral demonstrates consistent and robust citation support on indirect queries and matched performance to GPT-3.5 and GPT-4. The HR across all domains and models decreased by an average of 41.93% and the PP was reduced to 0% in most cases. In terms of generation quality, the average F1 Score and BLEU were 68.09% and 57.51%, respectively; (d) Testing with adversarial samples showed that LLMs, including the Advance RAG Mistral, struggle to understand context, but the extent of this issue was small in Mistral and GPT-4-Preview. Our study con tributes valuable insights into the reliability of RAG for automated citation generation tasks.

HeteroMILE: a Multi-Level Graph Representation Learning Framework for Heterogeneous Graphs

Heterogeneous graphs are ubiquitous in real-world applications because they can represent various relationships between different types of entities. Therefore, learning embeddings in such graphs is a critical problem in graph machine learning. However, existing solutions for this problem fail to scale to large heterogeneous graphs due to their high computational complexity. To address this issue, we propose a Multi-Level Embedding framework of nodes on a heterogeneous graph (HeteroMILE) - a generic methodology that allows contemporary graph embedding methods to scale to large graphs. HeteroMILE repeatedly coarsens the large sized graph into a smaller size while preserving the backbone structure of the graph before embedding it, effectively reducing the computational cost by avoiding time-consuming processing operations. It then refines the coarsened embedding to the original graph using a heterogeneous graph convolution neural network. We evaluate our approach using several popular heterogeneous graph datasets. The experimental results show that HeteroMILE can substantially reduce computational time (approximately 20x speedup) and generate an embedding of better quality for link prediction and node classification.

Grounding from an AI and Cognitive Science Lens

Grounding is a challenging problem, requiring a formal definition and different levels of abstraction. This article explores grounding from both cognitive science and machine learning perspectives. It identifies the subtleties of grounding, its significance for collaborative agents, and similarities and differences in grounding approaches in both communities. The article examines the potential of neuro-symbolic approaches tailored for grounding tasks, showcasing how they can more comprehensively address grounding. Finally, we discuss areas for further exploration and development in grounding.

Masked LoGoNet: Fast and Accurate 3D Image Analysis for Medical Domain

Standard modern machine-learning-based imaging methods have faced challenges in medical applications due to the high cost of dataset construction and, thereby, the limited labeled training data available. Additionally, upon deployment, these methods are usually used to process a large volume of data on a daily basis, imposing a high maintenance cost on medical facilities. In this paper, we introduce a new neural network architecture, termed LoGoNet, with a tailored self-supervised learning (SSL) method to mitigate such challenges. LoGoNet integrates a novel feature extractor within a U-shaped architecture, leveraging Large Kernel Attention (LKA) and a dual encoding strategy to capture both long-range and short-range feature dependencies adeptly. This is in contrast to existing methods that rely on increasing network capacity to enhance feature extraction. This combination of novel techniques in our model is especially beneficial in medical image segmentation, given the difficulty of learning intricate and often irregular body organ shapes, such as the spleen. Complementary, we propose a novel SSL method tailored for 3D images to compensate for the lack of large labeled datasets. The method combines masking and contrastive learning techniques within a multi-task learning framework and is compatible with both Vision Transformer (ViT) and CNN-based models. We demonstrate the efficacy of our methods in numerous tasks across two standard datasets (i.e., BTCV and MSD). Benchmark comparisons with eight state-of-the-art models highlight LoGoNet's superior performance in both inference time and accuracy.

Modeling Sequences as Star Graphs to Address Over-smoothing in Self-attentive Sequential Recommendation

Self-attention (SA) mechanisms have been widely used in developing sequential recommendation (SR) methods, and demonstrated state-of-the-art performance. However, in this paper, we show that self-attentive SR methods substantially suffer from the over-smoothing issue that item embeddings within a sequence become increasingly similar across attention blocks. As widely demonstrated in the literature, this issue could lead to a loss of information in individual items, and significantly degrade models' scalability and performance. To address the over-smoothing issue, in this paper, we view items within a sequence constituting a star graph and develop a method, denoted as MSSG, for SR. Different from existing self-attentive methods, MSSG introduces an additional internal node to specifically capture the global information within the sequence, and does not require information propagation among items. This design fundamentally addresses the over-smoothing issue and enables MSSG a linear time complexity with respect to the sequence length. We compare MSSG with ten state-of-the-art baseline methods on six public benchmark datasets. Our experimental results demonstrate that MSSG significantly outperforms the baseline methods, with an improvement of as much as 10.10%. Our analysis shows the superior scalability of MSSG over the state-of-the-art self-attentive methods. Our complexity analysis and run-time performance comparison together show that MSSG is both theoretically and practically more efficient than self-attentive methods. Our analysis of the attention weights learned in SA-based methods indicates that on sparse recommendation data, modeling dependencies in all item pairs using the SA mechanism yields limited information gain, and thus, might not benefit the recommendation performance

Towards Efficient and Effective Adaptation of Large Language Models for Sequential Recommendation

In recent years, with large language models (LLMs) achieving state-of-the-art performance in context understanding, increasing efforts have been dedicated to developing LLM-enhanced sequential recommendation (SR) methods. Considering that most existing LLMs are not specifically optimized for recommendation tasks, adapting them for SR becomes a critical step in LLM-enhanced SR methods. Though numerous adaptation methods have been developed, it still remains a significant challenge to adapt LLMs for SR both efficiently and effectively. To address this challenge, in this paper, we introduce a novel side sequential network adaptation method, denoted as SSNA, for LLM enhanced SR. SSNA features three key designs to allow both efficient and effective LLM adaptation. First, SSNA learns adapters separate from LLMs, while fixing all the pre-trained parameters within LLMs to allow efficient adaptation. In addition, SSNA adapts the top-a layers of LLMs jointly, and integrates adapters sequentially for enhanced effectiveness (i.e., recommendation performance). We compare SSNA against five state-of-the-art baseline methods on five benchmark datasets using three LLMs. The experimental results demonstrate that SSNA significantly outperforms all the baseline methods in terms of recommendation performance, and achieves substantial improvement over the best-performing baseline methods at both run-time and memory efficiency during training. Our analysis shows the effectiveness of integrating adapters in a sequential manner. Our parameter study demonstrates the effectiveness of jointly adapting the top-a layers of LLMs.

Multi-modality Meets Re-learning: Mitigating Negative Transfer in Sequential Recommendation

Learning effective recommendation models from sparse user interactions represents a fundamental challenge in developing sequential recommendation methods. Recently, pre-training-based methods have been developed to tackle this challenge. Though promising, in this paper, we show that existing methods suffer from the notorious negative transfer issue, where the model adapted from the pre-trained model results in worse performance compared to the model learned from scratch in the task of interest (i.e., target task). To address this issue, we develop a method, denoted as ANT, for transferable sequential recommendation. ANT mitigates negative transfer by 1) incorporating multi-modality item information, including item texts, images and prices, to effectively learn more transferable knowledge from related tasks (i.e., auxiliary tasks); and 2) better capturing task-specific knowledge in the target task using a re-learning-based adaptation strategy. We evaluate ANT against eight state-of-the-art baseline methods on five target tasks. Our experimental results demonstrate that ANT does not suffer from the negative transfer issue on any of the target tasks. The results also demonstrate that ANT substantially outperforms baseline methods in the target tasks with an improvement of as much as 15.2%. Our analysis highlights the superior effectiveness of our re-learning-based strategy compared to fine-tuning on the target tasks.

Shape-conditioned 3D Molecule Generation via Equivariant Diffusion Models

Ligand-based drug design aims to identify novel drug candidates of similar shapes with known active molecules. In this paper, we formulated an in silico shape-conditioned molecule generation problem to generate 3D molecule structures conditioned on the shape of a given molecule. To address this problem, we developed a translation- and rotation-equivariant shape-guided generative model ShapeMol. ShapeMol consists of an equivariant shape encoder that maps molecular surface shapes into latent embeddings, and an equivariant diffusion model that generates 3D molecules based on these embeddings. Experimental results show that ShapeMol can generate novel, diverse, drug-like molecules that retain 3D molecular shapes similar to the given shape condition. These results demonstrate the potential of ShapeMol in designing drug candidates of desired 3D shapes binding to protein target pockets.