Diffusion Models for Molecules: A Survey of Methods and Tasks

Generative tasks about molecules, including but not limited to molecule generation, are crucial for drug discovery and material design, and have consistently attracted significant attention. In recent years, diffusion models have emerged as an impressive class of deep generative models, sparking extensive research and leading to numerous studies on their application to molecular generative tasks. Despite the proliferation of related work, there remains a notable lack of up-to-date and systematic surveys in this area. Particularly, due to the diversity of diffusion model formulations, molecular data modalities, and generative task types, the research landscape is challenging to navigate, hindering understanding and limiting the area's growth. To address this, this paper conducts a comprehensive survey of diffusion model-based molecular generative methods. We systematically review the research from the perspectives of methodological formulations, data modalities, and task types, offering a novel taxonomy. This survey aims to facilitate understanding and further flourishing development in this area. The relevant papers are summarized at: https://github.com/AzureLeon1/awesome-molecular-diffusion-models.

mmE5: Improving Multimodal Multilingual Embeddings via High-quality Synthetic Data

Multimodal embedding models have gained significant attention for their ability to map data from different modalities, such as text and images, into a unified representation space. However, the limited labeled multimodal data often hinders embedding performance. Recent approaches have leveraged data synthesis to address this problem, yet the quality of synthetic data remains a critical bottleneck. In this work, we identify three criteria for high-quality synthetic multimodal data. First, broad scope ensures that the generated data covers diverse tasks and modalities, making it applicable to various downstream scenarios. Second, robust cross-modal alignment makes different modalities semantically consistent. Third, high fidelity ensures that the synthetic data maintains realistic details to enhance its reliability. Guided by these principles, we synthesize datasets that: (1) cover a wide range of tasks, modality combinations, and languages, (2) are generated via a deep thinking process within a single pass of a multimodal large language model, and (3) incorporate real-world images with accurate and relevant texts, ensuring fidelity through self-evaluation and refinement. Leveraging these high-quality synthetic and labeled datasets, we train a multimodal multilingual E5 model mmE5. Extensive experiments demonstrate that mmE5 achieves state-of-the-art performance on the MMEB Benchmark and superior multilingual performance on the XTD benchmark. Our codes, datasets and models are released in https://github.com/haon-chen/mmE5.

Examining False Positives under Inference Scaling for Mathematical Reasoning

Recent advancements in language models have led to significant improvements in mathematical reasoning across various benchmarks. However, most of these benchmarks rely on automatic evaluation methods that only compare final answers using heuristics, without verifying the underlying reasoning steps. This limitation results in false positive solutions, where models may produce correct final answers but with flawed deduction paths. In this paper, we systematically examine the prevalence of false positive solutions in mathematical problem solving for language models. We analyze the characteristics and extent of this issue across different open-source models, datasets of varying difficulty levels, and decoding strategies. Specifically, we explore how false positives influence the inference time scaling behavior of language models. Our experimental results reveal that: (1) false positive solutions persist across different models, datasets, and decoding methods, (2) sampling-based inference time scaling methods do not alleviate the problem, and (3) the pass@N evaluation metric is more susceptible to false positives, suggesting a significantly lower scaling ceiling than what automatic evaluations indicate. Additionally, we analyze specific instances of false positives and discuss potential limitations in self-improvement techniques and synthetic data generation under such conditions.

Conformal Uncertainty Indicator for Continual Test-Time Adaptation

Continual Test-Time Adaptation (CTTA) aims to adapt models to sequentially changing domains during testing, relying on pseudo-labels for self-adaptation. However, incorrect pseudo-labels can accumulate, leading to performance degradation. To address this, we propose a Conformal Uncertainty Indicator (CUI) for CTTA, leveraging Conformal Prediction (CP) to generate prediction sets that include the true label with a specified coverage probability. Since domain shifts can lower the coverage than expected, making CP unreliable, we dynamically compensate for the coverage by measuring both domain and data differences. Reliable pseudo-labels from CP are then selectively utilized to enhance adaptation. Experiments confirm that CUI effectively estimates uncertainty and improves adaptation performance across various existing CTTA methods.

DAGPrompT: Pushing the Limits of Graph Prompting with a Distribution-aware Graph Prompt Tuning Approach

The pre-train then fine-tune approach has advanced GNNs by enabling general knowledge capture without task-specific labels. However, an objective gap between pre-training and downstream tasks limits its effectiveness. Recent graph prompting methods aim to close this gap through task reformulations and learnable prompts. Despite this, they struggle with complex graphs like heterophily graphs. Freezing the GNN encoder can reduce the impact of prompting, while simple prompts fail to handle diverse hop-level distributions. This paper identifies two key challenges in adapting graph prompting methods for complex graphs: (1) adapting the model to new distributions in downstream tasks to mitigate pre-training and fine-tuning discrepancies from heterophily and (2) customizing prompts for hop-specific node requirements. To overcome these challenges, we propose Distribution-aware Graph Prompt Tuning (DAGPrompT), which integrates a GLoRA module for optimizing the GNN encoder's projection matrix and message-passing schema through low-rank adaptation. DAGPrompT also incorporates hop-specific prompts accounting for varying graph structures and distributions among hops. Evaluations on 10 datasets and 14 baselines demonstrate that DAGPrompT improves accuracy by up to 4.79 in node and graph classification tasks, setting a new state-of-the-art while preserving efficiency. Codes are available at GitHub.

Chain-of-Retrieval Augmented Generation

This paper introduces an approach for training o1-like RAG models that retrieve and reason over relevant information step by step before generating the final answer. Conventional RAG methods usually perform a single retrieval step before the generation process, which limits their effectiveness in addressing complex queries due to imperfect retrieval results. In contrast, our proposed method, CoRAG (Chain-of-Retrieval Augmented Generation), allows the model to dynamically reformulate the query based on the evolving state. To train CoRAG effectively, we utilize rejection sampling to automatically generate intermediate retrieval chains, thereby augmenting existing RAG datasets that only provide the correct final answer. At test time, we propose various decoding strategies to scale the model's test-time compute by controlling the length and number of sampled retrieval chains. Experimental results across multiple benchmarks validate the efficacy of CoRAG, particularly in multi-hop question answering tasks, where we observe more than 10 points improvement in EM score compared to strong baselines. On the KILT benchmark, CoRAG establishes a new state-of-the-art performance across a diverse range of knowledge-intensive tasks. Furthermore, we offer comprehensive analyses to understand the scaling behavior of CoRAG, laying the groundwork for future research aimed at developing factual and grounded foundation models.

Attention-guided Self-reflection for Zero-shot Hallucination Detection in Large Language Models

Hallucination has emerged as a significant barrier to the effective application of Large Language Models (LLMs). In this work, we introduce a novel Attention-Guided SElf-Reflection (AGSER) approach for zero-shot hallucination detection in LLMs. The AGSER method utilizes attention contributions to categorize the input query into attentive and non-attentive queries. Each query is then processed separately through the LLMs, allowing us to compute consistency scores between the generated responses and the original answer. The difference between the two consistency scores serves as a hallucination estimator. In addition to its efficacy in detecting hallucinations, AGSER notably reduces computational complexity, requiring only three passes through the LLM and utilizing two sets of tokens. We have conducted extensive experiments with four widely-used LLMs across three different hallucination benchmarks, demonstrating that our approach significantly outperforms existing methods in zero-shot hallucination detection.

TimeRAF: Retrieval-Augmented Foundation model for Zero-shot Time Series Forecasting

Time series forecasting plays a crucial role in data mining, driving rapid advancements across numerous industries. With the emergence of large models, time series foundation models (TSFMs) have exhibited remarkable generalization capabilities, such as zero-shot learning, through large-scale pre-training. Meanwhile, Retrieval-Augmented Generation (RAG) methods have been widely employed to enhance the performance of foundation models on unseen data, allowing models to access to external knowledge. In this paper, we introduce TimeRAF, a Retrieval-Augmented Forecasting model that enhance zero-shot time series forecasting through retrieval-augmented techniques. We develop customized time series knowledge bases that are tailored to the specific forecasting tasks. TimeRAF employs an end-to-end learnable retriever to extract valuable information from the knowledge base. Additionally, we propose Channel Prompting for knowledge integration, which effectively extracts relevant information from the retrieved knowledge along the channel dimension. Extensive experiments demonstrate the effectiveness of our model, showing significant improvement across various domains and datasets.

Bootstrap Your Own Context Length

We introduce a bootstrapping approach to train long-context language models by exploiting their short-context capabilities only. Our method utilizes a simple agent workflow to synthesize diverse long-context instruction tuning data, thereby eliminating the necessity for manual data collection and annotation. The proposed data synthesis workflow requires only a short-context language model, a text retriever, and a document collection, all of which are readily accessible within the open-source ecosystem. Subsequently, language models are fine-tuned using the synthesized data to extend their context lengths. In this manner, we effectively transfer the short-context capabilities of language models to long-context scenarios through a bootstrapping process. We conduct experiments with the open-source Llama-3 family of models and demonstrate that our method can successfully extend the context length to up to 1M tokens, achieving superior performance across various benchmarks.

S$^2$DN: Learning to Denoise Unconvincing Knowledge for Inductive Knowledge Graph Completion

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) the semantic inconsistencies of similar relations, and (ii) noisy interactions inherent in KGs due to the presence of unconvincing knowledge for emerging entities. To address these challenges, we propose a Semantic Structure-aware Denoising Network (S$^2$DN) for inductive KGC. Our goal is to learn adaptable general semantics and reliable structures to distill consistent semantic knowledge while preserving reliable interactions within KGs. Specifically, we introduce a semantic smoothing module over the enclosing subgraphs to retain the universal semantic knowledge of relations. We incorporate a structure refining module to filter out unreliable interactions and offer additional knowledge, retaining robust structure surrounding target links. Extensive experiments conducted on three benchmark KGs demonstrate that S$^2$DN surpasses the performance of state-of-the-art models. These results demonstrate the effectiveness of S$^2$DN in preserving semantic consistency and enhancing the robustness of filtering out unreliable interactions in contaminated KGs.