Case-Based Reasoning Enhances the Predictive Power of LLMs in Drug-Drug Interaction

Drug-drug interaction (DDI) prediction is critical for treatment safety. While large language models (LLMs) show promise in pharmaceutical tasks, their effectiveness in DDI prediction remains challenging. Inspired by the well-established clinical practice where physicians routinely reference similar historical cases to guide their decisions through case-based reasoning (CBR), we propose CBR-DDI, a novel framework that distills pharmacological principles from historical cases to improve LLM reasoning for DDI tasks. CBR-DDI constructs a knowledge repository by leveraging LLMs to extract pharmacological insights and graph neural networks (GNNs) to model drug associations. A hybrid retrieval mechanism and dual-layer knowledge-enhanced prompting allow LLMs to effectively retrieve and reuse relevant cases. We further introduce a representative sampling strategy for dynamic case refinement. Extensive experiments demonstrate that CBR-DDI achieves state-of-the-art performance, with a significant 28.7% accuracy improvement over both popular LLMs and CBR baseline, while maintaining high interpretability and flexibility.

Dense Communication between Language Models

As higher-level intelligence emerges from the combination of modular components with lower-level intelligence, many works combines Large Language Models (LLMs) for collective intelligence. Such combination is achieved by building communications among LLMs. While current systems primarily facilitate such communication through natural language, this paper proposes a novel paradigm of direct dense vector communication between LLMs. Our approach eliminates the unnecessary embedding and de-embedding steps when LLM interact with another, enabling more efficient information transfer, fully differentiable optimization pathways, and exploration of capabilities beyond human heuristics. We use such stripped LLMs as vertexes and optimizable seq2seq modules as edges to construct LMNet, with similar structure as MLPs. By utilizing smaller pre-trained LLMs as vertexes, we train a LMNet that achieves comparable performance with LLMs in similar size with only less than 0.1% training cost. This offers a new perspective on scaling for general intelligence rather than training a monolithic LLM from scratch. Besides, the proposed method can be used for other applications, like customizing LLM with limited data, showing its versatility.

Generalizing Hyperedge Expansion for Hyper-relational Knowledge Graph Modeling

By representing knowledge in a primary triple associated with additional attribute-value qualifiers, hyper-relational knowledge graph (HKG) that generalizes triple-based knowledge graph (KG) has been attracting research attention recently. Compared with KG, HKG is enriched with the semantic qualifiers as well as the hyper-relational graph structure. However, to model HKG, existing studies mainly focus on either semantic information or structural information therein, which however fail to capture both simultaneously. To tackle this issue, in this paper, we generalize the hyperedge expansion in hypergraph learning and propose an equivalent transformation for HKG modeling, referred to as TransEQ. Specifically, the equivalent transformation transforms a HKG to a KG, which considers both semantic and structural characteristics. Then an encoder-decoder framework is developed to bridge the modeling research between KG and HKG. In the encoder part, KG-based graph neural networks are leveraged for structural modeling; while in the decoder part, various HKG-based scoring functions are exploited for semantic modeling. Especially, we design the sharing embedding mechanism in the encoder-decoder framework with semantic relatedness captured. We further theoretically prove that TransEQ preserves complete information in the equivalent transformation, and also achieves full expressivity. Finally, extensive experiments on three benchmarks demonstrate the superior performance of TransEQ in terms of both effectiveness and efficiency. On the largest benchmark WikiPeople, TransEQ significantly improves the state-of-the-art models by 15\% on MRR.

Customized Subgraph Selection and Encoding for Drug-drug Interaction Prediction

Subgraph-based methods have proven to be effective and interpretable in predicting drug-drug interactions (DDIs), which are essential for medical practice and drug development. Subgraph selection and encoding are critical stages in these methods, yet customizing these components remains underexplored due to the high cost of manual adjustments. In this study, inspired by the success of neural architecture search (NAS), we propose a method to search for data-specific components within subgraph-based frameworks. Specifically, we introduce extensive subgraph selection and encoding spaces that account for the diverse contexts of drug interactions in DDI prediction. To address the challenge of large search spaces and high sampling costs, we design a relaxation mechanism that uses an approximation strategy to efficiently explore optimal subgraph configurations. This approach allows for robust exploration of the search space. Extensive experiments demonstrate the effectiveness and superiority of the proposed method, with the discovered subgraphs and encoding functions highlighting the model's adaptability.

Benchmarking Graph Learning for Drug-Drug Interaction Prediction

Predicting drug-drug interaction (DDI) plays an important role in pharmacology and healthcare for identifying potential adverse interactions and beneficial combination therapies between drug pairs. Recently, a flurry of graph learning methods have been introduced to predict drug-drug interactions. However, evaluating existing methods has several limitations, such as the absence of a unified comparison framework for DDI prediction methods, lack of assessments in meaningful real-world scenarios, and insufficient exploration of side information usage. In order to address these unresolved limitations in the literature, we propose a DDI prediction benchmark on graph learning. We first conduct unified evaluation comparison among existing methods. To meet realistic scenarios, we further evaluate the performance of different methods in settings with new drugs involved and examine the performance across different DDI types. Component analysis is conducted on the biomedical network to better utilize side information. Through this work, we hope to provide more insights for the problem of DDI prediction. Our implementation and data is open-sourced at https://anonymous.4open.science/r/DDI-Benchmark-ACD9/.

Neural Symbolic Regression of Complex Network Dynamics

Complex networks describe important structures in nature and society, composed of nodes and the edges that connect them. The evolution of these networks is typically described by dynamics, which are labor-intensive and require expert knowledge to derive. However, because the complex network involves noisy observations from multiple trajectories of nodes, existing symbolic regression methods are either not applicable or ineffective on its dynamics. In this paper, we propose Physically Inspired Neural Dynamics Symbolic Regression (PI-NDSR), a method based on neural networks and genetic programming to automatically learn the symbolic expression of dynamics. Our method consists of two key components: a Physically Inspired Neural Dynamics (PIND) to augment and denoise trajectories through observed trajectory interpolation; and a coordinated genetic search algorithm to derive symbolic expressions. This algorithm leverages references of node dynamics and edge dynamics from neural dynamics to avoid overfitted expressions in symbolic space. We evaluate our method on synthetic datasets generated by various dynamics and real datasets on disease spreading. The results demonstrate that PI-NDSR outperforms the existing method in terms of both recovery probability and error.

ConML: A Universal Meta-Learning Framework with Task-Level Contrastive Learning

Meta-learning enables learning systems to adapt quickly to new tasks, similar to humans. To emulate this human-like rapid learning and enhance alignment and discrimination abilities, we propose ConML, a universal meta-learning framework that can be applied to various meta-learning algorithms without relying on specific model architectures nor target models. The core of ConML is task-level contrastive learning, which extends contrastive learning from the representation space in unsupervised learning to the model space in meta-learning. By leveraging task identity as an additional supervision signal during meta-training, we contrast the outputs of the meta-learner in the model space, minimizing inner-task distance (between models trained on different subsets of the same task) and maximizing inter-task distance (between models from different tasks). We demonstrate that ConML integrates seamlessly with optimization-based, metric-based, and amortization-based meta-learning algorithms, as well as in-context learning, resulting in performance improvements across diverse few-shot learning tasks.

UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation

The remarkable success of Large Language Models (LLMs) across diverse tasks has driven the research community to extend their capabilities to molecular applications. However, most molecular LLMs employ adapter-based architectures that do not treat molecule and text modalities equally and lack a supervision signal for the molecule modality. To address these issues, we introduce UniMoT, a Unified Molecule-Text LLM adopting a tokenizer-based architecture that expands the vocabulary of LLM with molecule tokens. Specifically, we introduce a Vector Quantization-driven tokenizer that incorporates a Q-Former to bridge the modality gap between molecule and text. This tokenizer transforms molecules into sequences of molecule tokens with causal dependency, encapsulating high-level molecular and textual information. Equipped with this tokenizer, UniMoT can unify molecule and text modalities under a shared token representation and an autoregressive training paradigm, enabling it to interpret molecules as a foreign language and generate them as text. Following a four-stage training scheme, UniMoT emerges as a multi-modal generalist capable of performing both molecule-to-text and text-to-molecule tasks. Extensive experiments demonstrate that UniMoT achieves state-of-the-art performance across a wide range of molecule comprehension and generation tasks.

Warming Up Cold-Start CTR Prediction by Learning Item-Specific Feature Interactions

In recommendation systems, new items are continuously introduced, initially lacking interaction records but gradually accumulating them over time. Accurately predicting the click-through rate (CTR) for these items is crucial for enhancing both revenue and user experience. While existing methods focus on enhancing item ID embeddings for new items within general CTR models, they tend to adopt a global feature interaction approach, often overshadowing new items with sparse data by those with abundant interactions. Addressing this, our work introduces EmerG, a novel approach that warms up cold-start CTR prediction by learning item-specific feature interaction patterns. EmerG utilizes hypernetworks to generate an item-specific feature graph based on item characteristics, which is then processed by a Graph Neural Network (GNN). This GNN is specially tailored to provably capture feature interactions at any order through a customized message passing mechanism. We further design a meta learning strategy that optimizes parameters of hypernetworks and GNN across various item CTR prediction tasks, while only adjusting a minimal set of item-specific parameters within each task. This strategy effectively reduces the risk of overfitting when dealing with limited data. Extensive experiments on benchmark datasets validate that EmerG consistently performs the best given no, a few and sufficient instances of new items.

Knowledge-Aware Parsimony Learning: A Perspective from Relational Graphs

The scaling law, a strategy that involves the brute-force scaling of the training dataset and learnable parameters, has become a prevalent approach for developing stronger learning models. In this paper, we examine its rationale in terms of learning from relational graphs. We demonstrate that directly adhering to such a scaling law does not necessarily yield stronger models due to architectural incompatibility and representation bottlenecks. To tackle this challenge, we propose a novel framework for learning from relational graphs via knowledge-aware parsimony learning. Our method draws inspiration from the duality between data and knowledge inherent in these graphs. Specifically, we first extract knowledge (like symbolic logic and physical laws) during the learning process, and then apply combinatorial generalization to the task at hand. This extracted knowledge serves as the ``building blocks'' for achieving parsimony learning. By applying this philosophy to architecture, parameters, and inference, we can effectively achieve versatile, sample-efficient, and interpretable learning. Experimental results show that our proposed framework surpasses methods that strictly follow the traditional scaling-up roadmap. This highlights the importance of incorporating knowledge in the development of next-generation learning technologies.