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Structure-Based Drug Design (SBDD) focuses on generating valid ligands that strongly and specifically bind to a designated protein pocket. Several methods use machine learning for SBDD to generate these ligands in 3D space, conditioned on the structure of a desired protein pocket. Recently, diffusion models have shown success here by modeling the underlying distributions of atomic positions and types. While these methods are effective in considering the structural details of the protein pocket, they often fail to explicitly consider the binding affinity. Binding affinity characterizes how tightly the ligand binds to the protein pocket, and is measured by the change in free energy associated with the binding process. It is one of the most crucial metrics for benchmarking the effectiveness of the interaction between a ligand and protein pocket. To address this, we propose BADGER: Binding Affinity Diffusion Guidance with Enhanced Refinement. BADGER is a general guidance method to steer the diffusion sampling process towards improved protein-ligand binding, allowing us to adjust the distribution of the binding affinity between ligands and proteins. Our method is enabled by using a neural network (NN) to model the energy function, which is commonly approximated by AutoDock Vina (ADV). ADV's energy function is non-differentiable, and estimates the affinity based on the interactions between a ligand and target protein receptor. By using a NN as a differentiable energy function proxy, we utilize the gradient of our learned energy function as a guidance method on top of any trained diffusion model. We show that our method improves the binding affinity of generated ligands to their protein receptors by up to 60\%, significantly surpassing previous machine learning methods. We also show that our guidance method is flexible and can be easily applied to other diffusion-based SBDD frameworks.

Mitigating biases in machine learning models has become an increasing concern in Natural Language Processing (NLP), particularly in developing fair text embeddings, which are crucial yet challenging for real-world applications like search engines. In response, this paper proposes a novel method for learning fair text embeddings. First, we define a novel content-conditional equal distance (CCED) fairness for text embeddings, ensuring content-conditional independence between sensitive attributes and text embeddings. Building on CCED, we introduce a content-conditional debiasing (CCD) loss to ensure that embeddings of texts with different sensitive attributes but identical content maintain the same distance from the embedding of their corresponding neutral text. Additionally, we tackle the issue of insufficient training data by using Large Language Models (LLMs) with instructions to fairly augment texts into different sensitive groups. Our extensive evaluations show that our approach effectively enhances fairness while maintaining the utility of embeddings. Furthermore, our augmented dataset, combined with the CCED metric, serves as an new benchmark for evaluating fairness.

Mixed Boolean-Arithmetic (MBA) obfuscation is a common technique used to transform simple expressions into semantically equivalent but more complex combinations of boolean and arithmetic operators. Its widespread usage in DRM systems, malware, and software protectors is well documented. In 2021, Liu et al. proposed a groundbreaking method of simplifying linear MBAs, utilizing a hidden two-way transformation between 1-bit and n-bit variables. In 2022, Reichenwallner et al. proposed a similar but more effective method of simplifying linear MBAs, SiMBA, relying on a similar but more involved theorem. However, because current linear MBA simplifiers operate in 1-bit space, they cannot handle expressions which utilize constants inside of their bitwise operands, e.g. (x&1), (x&1111) + (y&1111). We propose an extension to SiMBA that enables simplification of this broader class of expressions. It surpasses peer tools, achieving efficient simplification of a class of MBAs that current simplifiers struggle with.

Magnetic Particle Imaging is an emerging imaging modality through which it is possible to detect tracers containing superparamagnetic nanoparticles. The exposure of the particles to dynamic magnetic fields generates a non-linear response that is used to locate the particles and produce an image of their distribution. The bounding box that can be covered by a single scan curve depends on the strength of the gradients of the magnetic fields applied, which is limited due to the risk of causing peripheral nerve stimulation (PNS) in the patients. To address this issue, multiple scans are performed. The scan data must be merged together to produce reconstructions of larger regions of interest. In this paper we propose a mathematical framework which can deal with rather general multi-patching scenarios including rigid transformations of the field of view (FoV), the specimen and of the scanner. We show the flexibility of this framework in a variety of different scanning scenarios. Moreover, we describe an iterative reconstruction algorithm that yields a reconstruction of the target distribution by minimizing a convex functional which includes positivity constraints and sparsity enforcing priors. We show its convergence to a minimizer and perform numerical experiments on simulated data.

Click-Through Rate (CTR) prediction has become an essential task in digital industries, such as digital advertising or online shopping. Many deep learning-based methods have been implemented and have become state-of-the-art models in the domain. To further improve the performance of CTR models, Knowledge Distillation based approaches have been widely used. However, most of the current CTR prediction models do not have much complex architectures, so it's hard to call one of them 'cumbersome' and the other one 'tiny'. On the other hand, the performance gap is also not very large between complex and simple models. So, distilling knowledge from one model to the other could not be worth the effort. Under these considerations, Mutual Learning could be a better approach, since all the models could be improved mutually. In this paper, we showed how useful the mutual learning algorithm could be when it is between equals. In our experiments on the Criteo and Avazu datasets, the mutual learning algorithm improved the performance of the model by up to 0.66% relative improvement.

Federated Knowledge Graph Embedding (FKGE) has recently garnered considerable interest due to its capacity to extract expressive representations from distributed knowledge graphs, while concurrently safeguarding the privacy of individual clients. Existing FKGE methods typically harness the arithmetic mean of entity embeddings from all clients as the global supplementary knowledge, and learn a replica of global consensus entities embeddings for each client. However, these methods usually neglect the inherent semantic disparities among distinct clients. This oversight not only results in the globally shared complementary knowledge being inundated with too much noise when tailored to a specific client, but also instigates a discrepancy between local and global optimization objectives. Consequently, the quality of the learned embeddings is compromised. To address this, we propose Personalized Federated knowledge graph Embedding with client-wise relation Graph (PFedEG), a novel approach that employs a client-wise relation graph to learn personalized embeddings by discerning the semantic relevance of embeddings from other clients. Specifically, PFedEG learns personalized supplementary knowledge for each client by amalgamating entity embedding from its neighboring clients based on their "affinity" on the client-wise relation graph. Each client then conducts personalized embedding learning based on its local triples and personalized supplementary knowledge. We conduct extensive experiments on four benchmark datasets to evaluate our method against state-of-the-art models and results demonstrate the superiority of our method.

Reconfigurable Intelligent Surface (RIS) is a pivotal technology in communication, offering an alternative path that significantly enhances the link quality in wireless communication environments. In this paper, we propose a RIS-assisted internet of vehicles (IoV) network, considering the vehicle-to-everything (V2X) communication method. In addition, in order to improve the timeliness of vehicle-to-infrastructure (V2I) links and the stability of vehicle-to-vehicle (V2V) links, we introduce the age of information (AoI) model and the payload transmission probability model. Therefore, with the objective of minimizing the AoI of V2I links and prioritizing transmission of V2V links payload, we construct this optimization problem as an Markov decision process (MDP) problem in which the BS serves as an agent to allocate resources and control phase-shift for the vehicles using the soft actor-critic (SAC) algorithm, which gradually converges and maintains a high stability. A AoI-aware joint vehicular resource allocation and RIS phase-shift control scheme based on SAC algorithm is proposed and simulation results show that its convergence speed, cumulative reward, AoI performance, and payload transmission probability outperforms those of proximal policy optimization (PPO), deep deterministic policy gradient (DDPG), twin delayed deep deterministic policy gradient (TD3) and stochastic algorithms.

Few-shot Knowledge Graph (KG) completion is a focus of current research, where each task aims at querying unseen facts of a relation given its few-shot reference entity pairs. Recent attempts solve this problem by learning static representations of entities and references, ignoring their dynamic properties, i.e., entities may exhibit diverse roles within task relations, and references may make different contributions to queries. This work proposes an adaptive attentional network for few-shot KG completion by learning adaptive entity and reference representations. Specifically, entities are modeled by an adaptive neighbor encoder to discern their task-oriented roles, while references are modeled by an adaptive query-aware aggregator to differentiate their contributions. Through the attention mechanism, both entities and references can capture their fine-grained semantic meanings, and thus render more expressive representations. This will be more predictive for knowledge acquisition in the few-shot scenario. Evaluation in link prediction on two public datasets shows that our approach achieves new state-of-the-art results with different few-shot sizes.

Representation learning on a knowledge graph (KG) is to embed entities and relations of a KG into low-dimensional continuous vector spaces. Early KG embedding methods only pay attention to structured information encoded in triples, which would cause limited performance due to the structure sparseness of KGs. Some recent attempts consider paths information to expand the structure of KGs but lack explainability in the process of obtaining the path representations. In this paper, we propose a novel Rule and Path-based Joint Embedding (RPJE) scheme, which takes full advantage of the explainability and accuracy of logic rules, the generalization of KG embedding as well as the supplementary semantic structure of paths. Specifically, logic rules of different lengths (the number of relations in rule body) in the form of Horn clauses are first mined from the KG and elaborately encoded for representation learning. Then, the rules of length 2 are applied to compose paths accurately while the rules of length 1 are explicitly employed to create semantic associations among relations and constrain relation embeddings. Besides, the confidence level of each rule is also considered in optimization to guarantee the availability of applying the rule to representation learning. Extensive experimental results illustrate that RPJE outperforms other state-of-the-art baselines on KG completion task, which also demonstrate the superiority of utilizing logic rules as well as paths for improving the accuracy and explainability of representation learning.

How can we estimate the importance of nodes in a knowledge graph (KG)? A KG is a multi-relational graph that has proven valuable for many tasks including question answering and semantic search. In this paper, we present GENI, a method for tackling the problem of estimating node importance in KGs, which enables several downstream applications such as item recommendation and resource allocation. While a number of approaches have been developed to address this problem for general graphs, they do not fully utilize information available in KGs, or lack flexibility needed to model complex relationship between entities and their importance. To address these limitations, we explore supervised machine learning algorithms. In particular, building upon recent advancement of graph neural networks (GNNs), we develop GENI, a GNN-based method designed to deal with distinctive challenges involved with predicting node importance in KGs. Our method performs an aggregation of importance scores instead of aggregating node embeddings via predicate-aware attention mechanism and flexible centrality adjustment. In our evaluation of GENI and existing methods on predicting node importance in real-world KGs with different characteristics, GENI achieves 5-17% higher NDCG@100 than the state of the art.