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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.

We consider a ubiquitous scenario in the study of Influence Maximization (IM), in which there is limited knowledge about the topology of the diffusion network. We set the IM problem in a multi-round diffusion campaign, aiming to maximize the number of distinct users that are influenced. Leveraging the capability of bandit algorithms to effectively balance the objectives of exploration and exploitation, as well as the expressivity of neural networks, our study explores the application of neural bandit algorithms to the IM problem. We propose the framework IM-GNB (Influence Maximization with Graph Neural Bandits), where we provide an estimate of the users' probabilities of being influenced by influencers (also known as diffusion seeds). This initial estimate forms the basis for constructing both an exploitation graph and an exploration one. Subsequently, IM-GNB handles the exploration-exploitation tradeoff, by selecting seed nodes in real-time using Graph Convolutional Networks (GCN), in which the pre-estimated graphs are employed to refine the influencers' estimated rewards in each contextual setting. Through extensive experiments on two large real-world datasets, we demonstrate the effectiveness of IM-GNB compared with other baseline methods, significantly improving the spread outcome of such diffusion campaigns, when the underlying network is unknown.

We develop assistive agents based on Large Language Models (LLMs) that aid interlocutors in business negotiations. Specifically, we simulate business negotiations by letting two LLM-based agents engage in role play. A third LLM acts as a remediator agent to rewrite utterances violating norms for improving negotiation outcomes. We introduce a simple tuning-free and label-free In-Context Learning (ICL) method to identify high-quality ICL exemplars for the remediator, where we propose a novel select criteria, called value impact, to measure the quality of the negotiation outcomes. We provide rich empirical evidence to demonstrate its effectiveness in negotiations across three different negotiation topics. The source code and the generated dataset will be publicly available upon acceptance.

We consider a truthful facility location problem in which there is a set of agents with private locations on the line of real numbers, and the goal is to place a number of facilities at different locations chosen from the set of those reported by the agents. Given a feasible solution, each agent suffers an individual cost that is either its total distance to all facilities (sum-variant) or its distance to the farthest facility (max-variant). For both variants, we show tight bounds on the approximation ratio of strategyproof mechanisms in terms of the social cost, the total individual cost of the agents.

Large Language Models (LLMs) have become widely adopted recently. Research explores their use both as autonomous agents and as tools for software engineering. LLM-integrated applications, on the other hand, are software systems that leverage an LLM to perform tasks that would otherwise be impossible or require significant coding effort. While LLM-integrated application engineering is emerging as new discipline, its terminology, concepts and methods need to be established. This study provides a taxonomy for LLM-integrated applications, offering a framework for analyzing and describing these systems. It also demonstrates various ways to utilize LLMs in applications, as well as options for implementing such integrations. Following established methods, we analyze a sample of recent LLM-integrated applications to identify relevant dimensions. We evaluate the taxonomy by applying it to additional cases. This review shows that applications integrate LLMs in numerous ways for various purposes. Frequently, they comprise multiple LLM integrations, which we term ``LLM components''. To gain a clear understanding of an application's architecture, we examine each LLM component separately. We identify thirteen dimensions along which to characterize an LLM component, including the LLM skills leveraged, the format of the output, and more. LLM-integrated applications are described as combinations of their LLM components. We suggest a concise representation using feature vectors for visualization. The taxonomy is effective for describing LLM-integrated applications. It can contribute to theory building in the nascent field of LLM-integrated application engineering and aid in developing such systems. Researchers and practitioners explore numerous creative ways to leverage LLMs in applications. Though challenges persist, integrating LLMs may revolutionize the way software systems are built.

Recent artificial intelligence (AI) systems have reached milestones in "grand challenges" ranging from Go to protein-folding. The capability to retrieve medical knowledge, reason over it, and answer medical questions comparably to physicians has long been viewed as one such grand challenge. Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a score of 67.2% on the MedQA dataset. However, this and other prior work suggested significant room for improvement, especially when models' answers were compared to clinicians' answers. Here we present Med-PaLM 2, which bridges these gaps by leveraging a combination of base LLM improvements (PaLM 2), medical domain finetuning, and prompting strategies including a novel ensemble refinement approach. Med-PaLM 2 scored up to 86.5% on the MedQA dataset, improving upon Med-PaLM by over 19% and setting a new state-of-the-art. We also observed performance approaching or exceeding state-of-the-art across MedMCQA, PubMedQA, and MMLU clinical topics datasets. We performed detailed human evaluations on long-form questions along multiple axes relevant to clinical applications. In pairwise comparative ranking of 1066 consumer medical questions, physicians preferred Med-PaLM 2 answers to those produced by physicians on eight of nine axes pertaining to clinical utility (p < 0.001). We also observed significant improvements compared to Med-PaLM on every evaluation axis (p < 0.001) on newly introduced datasets of 240 long-form "adversarial" questions to probe LLM limitations. While further studies are necessary to validate the efficacy of these models in real-world settings, these results highlight rapid progress towards physician-level performance in medical question answering.

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.

Aspect level sentiment classification aims to identify the sentiment expressed towards an aspect given a context sentence. Previous neural network based methods largely ignore the syntax structure in one sentence. In this paper, we propose a novel target-dependent graph attention network (TD-GAT) for aspect level sentiment classification, which explicitly utilizes the dependency relationship among words. Using the dependency graph, it propagates sentiment features directly from the syntactic context of an aspect target. In our experiments, we show our method outperforms multiple baselines with GloVe embeddings. We also demonstrate that using BERT representations further substantially boosts the performance.

Multi-relation Question Answering is a challenging task, due to the requirement of elaborated analysis on questions and reasoning over multiple fact triples in knowledge base. In this paper, we present a novel model called Interpretable Reasoning Network that employs an interpretable, hop-by-hop reasoning process for question answering. The model dynamically decides which part of an input question should be analyzed at each hop; predicts a relation that corresponds to the current parsed results; utilizes the predicted relation to update the question representation and the state of the reasoning process; and then drives the next-hop reasoning. Experiments show that our model yields state-of-the-art results on two datasets. More interestingly, the model can offer traceable and observable intermediate predictions for reasoning analysis and failure diagnosis, thereby allowing manual manipulation in predicting the final answer.

We investigate the problem of automatically determining what type of shoe left an impression found at a crime scene. This recognition problem is made difficult by the variability in types of crime scene evidence (ranging from traces of dust or oil on hard surfaces to impressions made in soil) and the lack of comprehensive databases of shoe outsole tread patterns. We find that mid-level features extracted by pre-trained convolutional neural nets are surprisingly effective descriptors for this specialized domains. However, the choice of similarity measure for matching exemplars to a query image is essential to good performance. For matching multi-channel deep features, we propose the use of multi-channel normalized cross-correlation and analyze its effectiveness. Our proposed metric significantly improves performance in matching crime scene shoeprints to laboratory test impressions. We also show its effectiveness in other cross-domain image retrieval problems: matching facade images to segmentation labels and aerial photos to map images. Finally, we introduce a discriminatively trained variant and fine-tune our system through our proposed metric, obtaining state-of-the-art performance.