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.

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.

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.

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.

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.

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.

We consider a problem of placing generators of rewards to be collected by randomly moving agents in a network. In many settings, the precise mobility pattern may be one of several possible, based on parameters outside our control, such as weather conditions. The placement should be robust to this uncertainty, to gain a competent total reward across possible networks. To study such scenarios, we introduce the Robust Reward Placement problem (RRP). Agents move randomly by a Markovian Mobility Model with a predetermined set of locations whose connectivity is chosen adversarially from a known set $\Pi$ of candidates. We aim to select a set of reward states within a budget that maximizes the minimum ratio, among all candidates in $\Pi$, of the collected total reward over the optimal collectable reward under the same candidate. We prove that RRP is NP-hard and inapproximable, and develop $\Psi$-Saturate, a pseudo-polynomial time algorithm that achieves an $\epsilon$-additive approximation by exceeding the budget constraint by a factor that scales as $O(\ln |\Pi|/\epsilon)$. In addition, we present several heuristics, most prominently one inspired by a dynamic programming algorithm for the max-min 0-1 KNAPSACK problem. We corroborate our theoretical analysis with an experimental evaluation on synthetic and real data.

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.

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences (peptides) responsible for observed spectra, challenges persist in \emph{de novo} peptide sequencing. Firstly, prior methods struggle to identify amino acids with post-translational modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in decreased peptide-level identification precision. Secondly, diverse types of noise and missing peaks in mass spectra reduce the reliability of training data (peptide-spectrum matches, PSMs). To address these challenges, we propose AdaNovo, a novel framework that calculates conditional mutual information (CMI) between the spectrum and each amino acid/peptide, using CMI for adaptive model training. Extensive experiments demonstrate AdaNovo's state-of-the-art performance on a 9-species benchmark, where the peptides in the training set are almost completely disjoint from the peptides of the test sets. Moreover, AdaNovo excels in identifying amino acids with PTMs and exhibits robustness against data noise. The supplementary materials contain the official code.

As Large Language Models (LLMs) gain great success in real-world applications, an increasing number of users are seeking to develop and deploy their customized LLMs through cloud services. Nonetheless, in some specific domains, there are still concerns regarding cost and trade-offs between privacy issues and accuracy. In this study, we introduce a cost-effective and self-adaptive LLM shaking tuning and recovery mechanism, named CypherTalk. With carefully designed horizontal and vertical shaking operators, we can achieve comparable accuracy results with SOTA privacy-preserving LLM schemes using Cryptography-based or Differential Privacy-based methods. Experiments also show that with the CypherTalk framework, users can achieve reliable accuracy when using optimized shaking operator settings. To our best knowledge, this is the first work that considers cost, and trade-off between model utility and privacy in LLM scenarios.