Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension

Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generative models have shown great promise in peptide generation. However, several challenges remain in designing effective peptide binders. First, not all residues contribute equally to peptide-target interactions. Second, the generated peptides must adopt valid geometries due to the constraints of peptide bonds. Third, realistic tasks for peptide drug development are still lacking. To address these challenges, we introduce PepHAR, a hot-spot-driven autoregressive generative model for designing peptides targeting specific proteins. Building on the observation that certain hot spot residues have higher interaction potentials, we first use an energy-based density model to fit and sample these key residues. Next, to ensure proper peptide geometry, we autoregressively extend peptide fragments by estimating dihedral angles between residue frames. Finally, we apply an optimization process to iteratively refine fragment assembly, ensuring correct peptide structures. By combining hot spot sampling with fragment-based extension, our approach enables de novo peptide design tailored to a target protein and allows the incorporation of key hot spot residues into peptide scaffolds. Extensive experiments, including peptide design and peptide scaffold generation, demonstrate the strong potential of PepHAR in computational peptide binder design.

Contrastive Graph Condensation: Advancing Data Versatility through Self-Supervised Learning

With the increasing computation of training graph neural networks (GNNs) on large-scale graphs, graph condensation (GC) has emerged as a promising solution to synthesize a compact, substitute graph of the large-scale original graph for efficient GNN training. However, existing GC methods predominantly employ classification as the surrogate task for optimization, thus excessively relying on node labels and constraining their utility in label-sparsity scenarios. More critically, this surrogate task tends to overfit class-specific information within the condensed graph, consequently restricting the generalization capabilities of GC for other downstream tasks. To address these challenges, we introduce Contrastive Graph Condensation (CTGC), which adopts a self-supervised surrogate task to extract critical, causal information from the original graph and enhance the cross-task generalizability of the condensed graph. Specifically, CTGC employs a dual-branch framework to disentangle the generation of the node attributes and graph structures, where a dedicated structural branch is designed to explicitly encode geometric information through nodes' positional embeddings. By implementing an alternating optimization scheme with contrastive loss terms, CTGC promotes the mutual enhancement of both branches and facilitates high-quality graph generation through the model inversion technique. Extensive experiments demonstrate that CTGC excels in handling various downstream tasks with a limited number of labels, consistently outperforming state-of-the-art GC methods.

Epidemiology-informed Graph Neural Network for Heterogeneity-aware Epidemic Forecasting

Among various spatio-temporal prediction tasks, epidemic forecasting plays a critical role in public health management. Recent studies have demonstrated the strong potential of spatio-temporal graph neural networks (STGNNs) in extracting heterogeneous spatio-temporal patterns for epidemic forecasting. However, most of these methods bear an over-simplified assumption that two locations (e.g., cities) with similar observed features in previous time steps will develop similar infection numbers in the future. In fact, for any epidemic disease, there exists strong heterogeneity of its intrinsic evolution mechanisms across geolocation and time, which can eventually lead to diverged infection numbers in two ``similar'' locations. However, such mechanistic heterogeneity is non-trivial to be captured due to the existence of numerous influencing factors like medical resource accessibility, virus mutations, mobility patterns, etc., most of which are spatio-temporal yet unreachable or even unobservable. To address this challenge, we propose a Heterogeneous Epidemic-Aware Transmission Graph Neural Network (HeatGNN), a novel epidemic forecasting framework. By binding the epidemiology mechanistic model into a GNN, HeatGNN learns epidemiology-informed location embeddings of different locations that reflect their own transmission mechanisms over time. With the time-varying mechanistic affinity graphs computed with the epidemiology-informed location embeddings, a heterogeneous transmission graph network is designed to encode the mechanistic heterogeneity among locations, providing additional predictive signals to facilitate accurate forecasting. Experiments on three benchmark datasets have revealed that HeatGNN outperforms various strong baselines. Moreover, our efficiency analysis verifies the real-world practicality of HeatGNN on datasets of different sizes.

Epidemiology-informed Network for Robust Rumor Detection

The rapid spread of rumors on social media has posed significant challenges to maintaining public trust and information integrity. Since an information cascade process is essentially a propagation tree, recent rumor detection models leverage graph neural networks to additionally capture information propagation patterns, thus outperforming text-only solutions. Given the variations in topics and social impact of the root node, different source information naturally has distinct outreach capabilities, resulting in different heights of propagation trees. This variation, however, impedes the data-driven design of existing graph-based rumor detectors. Given a shallow propagation tree with limited interactions, it is unlikely for graph-based approaches to capture sufficient cascading patterns, questioning their ability to handle less popular news or early detection needs. In contrast, a deep propagation tree is prone to noisy user responses, and this can in turn obfuscate the predictions. In this paper, we propose a novel Epidemiology-informed Network (EIN) that integrates epidemiological knowledge to enhance performance by overcoming data-driven methods sensitivity to data quality. Meanwhile, to adapt epidemiology theory to rumor detection, it is expected that each users stance toward the source information will be annotated. To bypass the costly and time-consuming human labeling process, we take advantage of large language models to generate stance labels, facilitating optimization objectives for learning epidemiology-informed representations. Our experimental results demonstrate that the proposed EIN not only outperforms state-of-the-art methods on real-world datasets but also exhibits enhanced robustness across varying tree depths.

On-device Content-based Recommendation with Single-shot Embedding Pruning: A Cooperative Game Perspective

Content-based Recommender Systems (CRSs) play a crucial role in shaping user experiences in e-commerce, online advertising, and personalized recommendations. However, due to the vast amount of categorical features, the embedding tables used in CRS models pose a significant storage bottleneck for real-world deployment, especially on resource-constrained devices. To address this problem, various embedding pruning methods have been proposed, but most existing ones require expensive retraining steps for each target parameter budget, leading to enormous computation costs. In reality, this computation cost is a major hurdle in real-world applications with diverse storage requirements, such as federated learning and streaming settings. In this paper, we propose Shapley Value-guided Embedding Reduction (Shaver) as our response. With Shaver, we view the problem from a cooperative game perspective, and quantify each embedding parameter's contribution with Shapley values to facilitate contribution-based parameter pruning. To address the inherently high computation costs of Shapley values, we propose an efficient and unbiased method to estimate Shapley values of a CRS's embedding parameters. Moreover, in the pruning stage, we put forward a field-aware codebook to mitigate the information loss in the traditional zero-out treatment. Through extensive experiments on three real-world datasets, Shaver has demonstrated competitive performance with lightweight recommendation models across various parameter budgets. The source code is available at https://anonymous.4open.science/r/shaver-E808

Sparser Training for On-Device Recommendation Systems

Recommender systems often rely on large embedding tables that map users and items to dense vectors of uniform size, leading to substantial memory consumption and inefficiencies. This is particularly problematic in memory-constrained environments like mobile and Web of Things (WoT) applications, where scalability and real-time performance are critical. Various research efforts have sought to address these issues. Although embedding pruning methods utilizing Dynamic Sparse Training (DST) stand out due to their low training and inference costs, consistent sparsity, and end-to-end differentiability, they face key challenges. Firstly, they typically initializes the mask matrix, which is used to prune redundant parameters, with random uniform sparse initialization. This strategy often results in suboptimal performance as it creates unstructured and inefficient connections. Secondly, they tend to favor the users/items sampled in the single batch immediately before weight exploration when they reactivate pruned parameters with large gradient magnitudes, which does not necessarily improve the overall performance. Thirdly, while they use sparse weights during forward passes, they still need to compute dense gradients during backward passes. In this paper, we propose SparseRec, an lightweight embedding method based on DST, to address these issues. Specifically, SparseRec initializes the mask matrix using Nonnegative Matrix Factorization. It accumulates gradients to identify the inactive parameters that can better improve the model performance after activation. Furthermore, it avoids dense gradients during backpropagation by sampling a subset of important vectors. Gradients are calculated only for parameters in this subset, thus maintaining sparsity during training in both forward and backward passes.

Progressive Generalization Risk Reduction for Data-Efficient Causal Effect Estimation

Causal effect estimation (CEE) provides a crucial tool for predicting the unobserved counterfactual outcome for an entity. As CEE relaxes the requirement for ``perfect'' counterfactual samples (e.g., patients with identical attributes and only differ in treatments received) that are impractical to obtain and can instead operate on observational data, it is usually used in high-stake domains like medical treatment effect prediction. Nevertheless, in those high-stake domains, gathering a decently sized, fully labelled observational dataset remains challenging due to hurdles associated with costs, ethics, expertise and time needed, etc., of which medical treatment surveys are a typical example. Consequently, if the training dataset is small in scale, low generalization risks can hardly be achieved on any CEE algorithms. Unlike existing CEE methods that assume the constant availability of a dataset with abundant samples, in this paper, we study a more realistic CEE setting where the labelled data samples are scarce at the beginning, while more can be gradually acquired over the course of training -- assuredly under a limited budget considering their expensive nature. Then, the problem naturally comes down to actively selecting the best possible samples to be labelled, e.g., identifying the next subset of patients to conduct the treatment survey. However, acquiring quality data for reducing the CEE risk under limited labelling budgets remains under-explored until now. To fill the gap, we theoretically analyse the generalization risk from an intriguing perspective of progressively shrinking its upper bound, and develop a principled label acquisition pipeline exclusively for CEE tasks. With our analysis, we propose the Model Agnostic Causal Active Learning (MACAL) algorithm for batch-wise label acquisition, which aims to reduce both the CEE model's uncertainty and the post-acquisition ...

Generative Adapter: Contextualizing Language Models in Parameters with A Single Forward Pass

Large language models (LMs) are typically adapted to improve performance on new contexts (\eg text prompts that define new tasks or domains) through fine-tuning or prompting. However, there is an accuracy compute tradeoff -- fine-tuning incurs significant training cost and prompting increases inference overhead. We introduce $GenerativeAdapter$, an effective and efficient adaptation method that directly maps new contexts to low-rank LM adapters, thereby significantly reducing inference overhead with no need for finetuning. The adapter generator is trained via self-supervised learning, and can be used to adapt a single frozen LM for any new task simply by mapping the associated task or domain context to a new adapter. We apply $GenerativeAdapter$ to two pretrained LMs (Mistral-7B-Instruct and Llama2-7B-Chat) and evaluate the adapted models in three adaption scenarios: knowledge acquisition from documents, learning from demonstrations, and personalization for users. In StreamingQA, our approach is effective in injecting knowledge into the LM's parameters, achieving a 63.5% improvement in F1 score over the model with supervised fine-tuning (from $19.5$ to $31.5$) for contexts as long as 32K tokens. In the MetaICL in-context learning evaluation, our method achieves an average accuracy of $44.9$ across 26 tasks, outperforming the base model. On MSC, our method proves to be highly competitive in memorizing user information from conversations with a 4x reduction in computation and memory costs compared to prompting with full conversation history. Together, these results suggest that $GenerativeAdapter$ should allow for general adaption to a wide range of different contexts.

Using Structural Similarity and Kolmogorov-Arnold Networks for Anatomical Embedding of 3-hinge Gyrus

The 3-hinge gyrus (3HG) is a newly defined folding pattern, which is the conjunction of gyri coming from three directions in cortical folding. Many studies demonstrated that 3HGs can be reliable nodes when constructing brain networks or connectome since they simultaneously possess commonality and individuality across different individual brains and populations. However, 3HGs are identified and validated within individual spaces, making it difficult to directly serve as the brain network nodes due to the absence of cross-subject correspondence. The 3HG correspondences represent the intrinsic regulation of brain organizational architecture, traditional image-based registration methods tend to fail because individual anatomical properties need to be fully respected. To address this challenge, we propose a novel self-supervised framework for anatomical feature embedding of the 3HGs to build the correspondences among different brains. The core component of this framework is to construct a structural similarity-enhanced multi-hop feature encoding strategy based on the recently developed Kolmogorov-Arnold network (KAN) for anatomical feature embedding. Extensive experiments suggest that our approach can effectively establish robust cross-subject correspondences when no one-to-one mapping exists.

DecKG: Decentralized Collaborative Learning with Knowledge Graph Enhancement for POI Recommendation

Decentralized collaborative learning for Point-of-Interest (POI) recommendation has gained research interest due to its advantages in privacy preservation and efficiency, as it keeps data locally and leverages collaborative learning among clients to train models in a decentralized manner. However, since local data is often limited and insufficient for training accurate models, a common solution is integrating external knowledge as auxiliary information to enhance model performance. Nevertheless, this solution poses challenges for decentralized collaborative learning. Due to private nature of local data, identifying relevant auxiliary information specific to each user is non-trivial. Furthermore, resource-constrained local devices struggle to accommodate all auxiliary information, which places heavy burden on local storage. To fill the gap, we propose a novel decentralized collaborative learning with knowledge graph enhancement framework for POI recommendation (DecKG). Instead of directly uploading interacted items, users generate desensitized check-in data by uploading general categories of interacted items and sampling similar items from same category. The server then pretrains KG without sensitive user-item interactions and deploys relevant partitioned sub-KGs to individual users. Entities are further refined on the device, allowing client to client communication to exchange knowledge learned from local data and sub-KGs. Evaluations across two real-world datasets demonstrate DecKG's effectiveness recommendation performance.