GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype

Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene regulatory networks (GRN) is essential to understand and predict the effects of genetic perturbations. However, current methods fail to fully leverage gene-related information, and solely rely on simple evaluation metrics to construct coarse-grained GRN. More importantly, they ignore functional differences between biotypes, limiting the ability to capture potential gene interactions. In this work, we leverage pre-trained large language model and DNA sequence model to extract features from gene descriptions and DNA sequence data, respectively, which serve as the initialization for gene representations. Additionally, we introduce gene biotype information for the first time in genetic perturbation, simulating the distinct roles of genes with different biotypes in regulating cellular processes, while capturing implicit gene relationships through graph structure learning (GSL). We propose GRAPE, a heterogeneous graph neural network (HGNN) that leverages gene representations initialized with features from descriptions and sequences, models the distinct roles of genes with different biotypes, and dynamically refines the GRN through GSL. The results on publicly available datasets show that our method achieves state-of-the-art performance.

ImageScope: Unifying Language-Guided Image Retrieval via Large Multimodal Model Collective Reasoning

With the proliferation of images in online content, language-guided image retrieval (LGIR) has emerged as a research hotspot over the past decade, encompassing a variety of subtasks with diverse input forms. While the development of large multimodal models (LMMs) has significantly facilitated these tasks, existing approaches often address them in isolation, requiring the construction of separate systems for each task. This not only increases system complexity and maintenance costs, but also exacerbates challenges stemming from language ambiguity and complex image content, making it difficult for retrieval systems to provide accurate and reliable results. To this end, we propose ImageScope, a training-free, three-stage framework that leverages collective reasoning to unify LGIR tasks. The key insight behind the unification lies in the compositional nature of language, which transforms diverse LGIR tasks into a generalized text-to-image retrieval process, along with the reasoning of LMMs serving as a universal verification to refine the results. To be specific, in the first stage, we improve the robustness of the framework by synthesizing search intents across varying levels of semantic granularity using chain-of-thought (CoT) reasoning. In the second and third stages, we then reflect on retrieval results by verifying predicate propositions locally, and performing pairwise evaluations globally. Experiments conducted on six LGIR datasets demonstrate that ImageScope outperforms competitive baselines. Comprehensive evaluations and ablation studies further confirm the effectiveness of our design.

TimeFound: A Foundation Model for Time Series Forecasting

We present TimeFound, an encoder-decoder transformer-based time series foundation model for out-of-the-box zero-shot forecasting. To handle time series data from various domains, TimeFound employs a multi-resolution patching strategy to capture complex temporal patterns at multiple scales. We pre-train our model with two sizes (200M and 710M parameters) on a large time-series corpus comprising both real-world and synthetic datasets. Over a collection of unseen datasets across diverse domains and forecasting horizons, our empirical evaluations suggest that TimeFound can achieve superior or competitive zero-shot forecasting performance, compared to state-of-the-art time series foundation models.

NodeReg: Mitigating the Imbalance and Distribution Shift Effects in Semi-Supervised Node Classification via Norm Consistency

Aggregating information from neighboring nodes benefits graph neural networks (GNNs) in semi-supervised node classification tasks. Nevertheless, this mechanism also renders nodes susceptible to the influence of their neighbors. For instance, this will occur when the neighboring nodes are imbalanced or the neighboring nodes contain noise, which can even affect the GNN's ability to generalize out of distribution. We find that ensuring the consistency of the norm for node representations can significantly reduce the impact of these two issues on GNNs. To this end, we propose a regularized optimization method called NodeReg that enforces the consistency of node representation norms. This method is simple but effective and satisfies Lipschitz continuity, thus facilitating stable optimization and significantly improving semi-supervised node classification performance under the above two scenarios. To illustrate, in the imbalance scenario, when training a GCN with an imbalance ratio of 0.1, NodeReg outperforms the most competitive baselines by 1.4%-25.9% in F1 score across five public datasets. Similarly, in the distribution shift scenario, NodeReg outperforms the most competitive baseline by 1.4%-3.1% in accuracy.

CHAT: Beyond Contrastive Graph Transformer for Link Prediction in Heterogeneous Networks

Link prediction in heterogeneous networks is crucial for understanding the intricacies of network structures and forecasting their future developments. Traditional methodologies often face significant obstacles, including over-smoothing-wherein the excessive aggregation of node features leads to the loss of critical structural details-and a dependency on human-defined meta-paths, which necessitate extensive domain knowledge and can be inherently restrictive. These limitations hinder the effective prediction and analysis of complex heterogeneous networks. In response to these challenges, we propose the Contrastive Heterogeneous grAph Transformer (CHAT). CHAT introduces a novel sampling-based graph transformer technique that selectively retains nodes of interest, thereby obviating the need for predefined meta-paths. The method employs an innovative connection-aware transformer to encode node sequences and their interconnections with high fidelity, guided by a dual-faceted loss function specifically designed for heterogeneous network link prediction. Additionally, CHAT incorporates an ensemble link predictor that synthesizes multiple samplings to achieve enhanced prediction accuracy. We conducted comprehensive evaluations of CHAT using three distinct drug-target interaction (DTI) datasets. The empirical results underscore CHAT's superior performance, outperforming both general-task approaches and models specialized in DTI prediction. These findings substantiate the efficacy of CHAT in addressing the complex problem of link prediction in heterogeneous networks.

Improving Retrieval Augmented Language Model with Self-Reasoning

The Retrieval-Augmented Language Model (RALM) has shown remarkable performance on knowledge-intensive tasks by incorporating external knowledge during inference, which mitigates the factual hallucinations inherited in large language models (LLMs). Despite these advancements, challenges persist in the implementation of RALMs, particularly concerning their reliability and traceability. To be specific, the irrelevant document retrieval may result in unhelpful response generation or even deteriorate the performance of LLMs, while the lack of proper citations in generated outputs complicates efforts to verify the trustworthiness of the models. To this end, we propose a novel self-reasoning framework aimed at improving the reliability and traceability of RALMs, whose core idea is to leverage reasoning trajectories generated by the LLM itself. The framework involves constructing self-reason trajectories with three processes: a relevance-aware process, an evidence-aware selective process, and a trajectory analysis process. We have evaluated our framework across four public datasets (two short-form QA datasets, one long-form QA dataset, and one fact verification dataset) to demonstrate the superiority of our method, which can outperform existing state-of-art models and can achieve comparable performance with GPT-4, while only using 2,000 training samples.

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.

Unifying Sequences, Structures, and Descriptions for Any-to-Any Protein Generation with the Large Multimodal Model HelixProtX

Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language models (LLMs) for protein research, current methodologies predominantly focus on limited specialized tasks -- often predicting one protein modality from another. These approaches restrict the understanding and generation of multimodal protein data. In contrast, large multimodal models have demonstrated potential capabilities in generating any-to-any content like text, images, and videos, thus enriching user interactions across various domains. Integrating these multimodal model technologies into protein research offers significant promise by potentially transforming how proteins are studied. To this end, we introduce HelixProtX, a system built upon the large multimodal model, aiming to offer a comprehensive solution to protein research by supporting any-to-any protein modality generation. Unlike existing methods, it allows for the transformation of any input protein modality into any desired protein modality. The experimental results affirm the advanced capabilities of HelixProtX, not only in generating functional descriptions from amino acid sequences but also in executing critical tasks such as designing protein sequences and structures from textual descriptions. Preliminary findings indicate that HelixProtX consistently achieves superior accuracy across a range of protein-related tasks, outperforming existing state-of-the-art models. By integrating multimodal large models into protein research, HelixProtX opens new avenues for understanding protein biology, thereby promising to accelerate scientific discovery.

NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for \emph{de novo} peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for \emph{de novo} peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and $\pi$-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development. The benchmark will be open-sourced to facilitate future research and application.

Enhancing Trust and Privacy in Distributed Networks: A Comprehensive Survey on Blockchain-based Federated Learning

While centralized servers pose a risk of being a single point of failure, decentralized approaches like blockchain offer a compelling solution by implementing a consensus mechanism among multiple entities. Merging distributed computing with cryptographic techniques, decentralized technologies introduce a novel computing paradigm. Blockchain ensures secure, transparent, and tamper-proof data management by validating and recording transactions via consensus across network nodes. Federated Learning (FL), as a distributed machine learning framework, enables participants to collaboratively train models while safeguarding data privacy by avoiding direct raw data exchange. Despite the growing interest in decentralized methods, their application in FL remains underexplored. This paper presents a thorough investigation into Blockchain-based FL (BCFL), spotlighting the synergy between blockchain's security features and FL's privacy-preserving model training capabilities. First, we present the taxonomy of BCFL from three aspects, including decentralized, separate networks, and reputation-based architectures. Then, we summarize the general architecture of BCFL systems, providing a comprehensive perspective on FL architectures informed by blockchain. Afterward, we analyze the application of BCFL in healthcare, IoT, and other privacy-sensitive areas. Finally, we identify future research directions of BCFL.