In silico methods evaluating the mutation effects of missense mutations are providing an important approach for understanding mutations in personal genomes and identifying disease-relevant biomarkers. However, existing methods, including deep learning methods, heavily rely on sequence-aware information, and do not fully leverage the potential of available 3D structural information. In addition, these methods may exhibit an inability to predict mutations in domains difficult to formulate sequence-based embeddings. In this study, we introduce a novel rationale-guided graph neural network AlphaGMut to evaluate mutation effects and to distinguish pathogenic mutations from neutral mutations. We compute the alpha shapes of protein structures to obtain atomic-resolution edge connectivities and map them to an accurate residue-level graph representation. We then compute structural-, topological-, biophysical-, and sequence properties of the mutation sites, which are assigned as node attributes in the graph. These node attributes could effectively guide the graph neural network to learn the difference between pathogenic and neutral mutations using k-hop message passing with a short training period. We demonstrate that AlphaGMut outperforms state-of-the-art methods, including DeepMind's AlphaMissense, in many performance metrics. In addition, AlphaGMut has the advantage of performing well in alignment-free settings, which provides broader prediction coverage and better generalization compared to current methods requiring deep sequence-aware information.

Dialogue state tracking (DST) aims to record user queries and goals during a conversational interaction achieved by maintaining a predefined set of slots and their corresponding values. Current approaches decide slot values opaquely, while humans usually adopt a more deliberate approach by collecting information from relevant dialogue turns and then reasoning the appropriate values. In this work, we focus on the steps needed to figure out slot values by proposing a model named Chain-of-Thought-Explanation (CoTE) for the DST task. CoTE, which is built on the generative DST framework, is designed to create detailed explanations step by step after determining the slot values. This process leads to more accurate and reliable slot values. More-over, to improve the reasoning ability of the CoTE, we further construct more fluent and high-quality explanations with automatic paraphrasing, leading the method CoTE-refined. Experimental results on three widely recognized DST benchmarks-MultiWOZ 2.2, WoZ 2.0, and M2M-demonstrate the remarkable effectiveness of the CoTE. Furthermore, through a meticulous fine-grained analysis, we observe significant benefits of our CoTE on samples characterized by longer dialogue turns, user responses, and reasoning steps.

Knowledge-grounded dialogue systems aim to generate coherent and engaging responses based on the dialogue contexts and selected external knowledge. Previous knowledge selection methods tend to rely too heavily on the dialogue contexts or over-emphasize the new information in the selected knowledge, resulting in the selection of repetitious or incongruous knowledge and further generating repetitive or incoherent responses, as the generation of the response depends on the chosen knowledge. To address these shortcomings, we introduce a Coherent and Engaging Topic Transition (CET2) framework to model topic transitions for selecting knowledge that is coherent to the context of the conversations while providing adequate knowledge diversity for topic development. Our CET2 framework considers multiple factors for knowledge selection, including valid transition logic from dialogue contexts to the following topics and systematic comparisons between available knowledge candidates. Extensive experiments on two public benchmarks demonstrate the superiority and the better generalization ability of CET2 on knowledge selection. This is due to our well-designed transition features and comparative knowledge selection strategy, which are more transferable to conversations about unseen topics. Analysis of fine-grained knowledge selection accuracy also shows that CET2 can better balance topic entailment (contextual coherence) and development (knowledge diversity) in dialogue than existing approaches.

Large Language Models (LLMs) have marked a significant advancement in the field of natural language processing, demonstrating exceptional capabilities in reasoning, tool usage, and memory. As their applications extend into multi-agent environments, a need has arisen for a comprehensive evaluation framework that captures their abilities in reasoning, planning, collaboration, and more. This work introduces a novel benchmarking framework specifically tailored to assess LLMs within multi-agent settings, providing quantitative metrics to evaluate their judgment, reasoning, deception, self-awareness, cooperation, coordination, and rationality. We utilize games such as Chameleon and Undercover, alongside game theory scenarios like Cost Sharing, Multi-player Prisoner's Dilemma, and Public Good, to create diverse testing environments. Our framework is fortified with the Probabilistic Graphical Modeling (PGM) method, enhancing the LLMs' capabilities in navigating complex social and cognitive dimensions. The benchmark evaluates seven multi-agent systems powered by different LLMs, quantitatively highlighting a significant capability gap over threefold between the strongest, GPT-4, and the weakest, Llama-2-70B. It also confirms that our PGM enhancement boosts the inherent abilities of all selected models by 50% on average. Our codes are released here https://github.com/cathyxl/MAgIC.

In this paper, we present our solution for the {\it IJCAI--PRICAI--20 3D AI Challenge: 3D Object Reconstruction from A Single Image}. We develop a variant of AtlasNet that consumes single 2D images and generates 3D point clouds through 2D to 3D mapping. To push the performance to the limit and present guidance on crucial implementation choices, we conduct extensive experiments to analyze the influence of decoder design and different settings on the normalization, projection, and sampling methods. Our method achieves 2nd place in the final track with a score of $70.88$, a chamfer distance of $36.87$, and a mean f-score of $59.18$. The source code of our method will be available at https://github.com/em-data/Enhanced_AtlasNet_3DReconstruction.

Scale variation is one of the most challenging problems in face detection. Modern face detectors employ feature pyramids to deal with scale variation. However, it might break the feature consistency across different scales of faces. In this paper, we propose a simple yet effective method named the receptive field pyramids (RFP) method to enhance the representation ability of feature pyramids. It can learn different receptive fields in each feature map adaptively based on the varying scales of detected faces. Empirical results on two face detection benchmark datasets, i.e., WIDER FACE and UFDD, demonstrate that our proposed method can accelerate the inference rate significantly while achieving state-of-the-art performance. The source code of our method is available at \url{https://github.com/emdata-ailab/EMface}.

Many efforts have been devoted to designing sampling, mining, and weighting strategies in high-level deep metric learning (DML) loss objectives. However, little attention has been paid to low-level but essential data transformation. In this paper, we develop a novel mechanism, the independent domain embedding augmentation learning ({IDEAL}) method. It can simultaneously learn multiple independent embedding spaces for multiple domains generated by predefined data transformations. Our IDEAL is orthogonal to existing DML techniques and can be seamlessly combined with prior DML approaches for enhanced performance. Empirical results on visual retrieval tasks demonstrate the superiority of the proposed method. For example, the IDEAL improves the performance of MS loss by a large margin, 84.5\% $\rightarrow$ 87.1\% on Cars-196, and 65.8\% $\rightarrow$ 69.5\% on CUB-200 at Recall$@1$. Our IDEAL with MS loss also achieves the new state-of-the-art performance on three image retrieval benchmarks, \ie, \emph{Cars-196}, \emph{CUB-200}, and \emph{SOP}. It outperforms the most recent DML approaches, such as Circle loss and XBM, significantly. The source code and pre-trained models of our method will be available at\emph{\url{https://github.com/emdata-ailab/IDEAL}}.

There is growing evidence showing the significant role of social determinant of health (SDOH) on a wide variety of health outcomes. In the era of artificial intelligence (AI), electronic health records (EHRs) have been widely used to conduct observational studies. However, how to make the best of SDOH information from EHRs is yet to be studied. In this paper, we systematically reviewed recently published papers and provided a methodology review of AI methods using the SDOH information in EHR data. A total of 1250 articles were retrieved from the literature between 2010 and 2020, and 74 papers were included in this review after abstract and full-text screening. We summarized these papers in terms of general characteristics (including publication years, venues, countries etc.), SDOH types, disease areas, study outcomes, AI methods to extract SDOH from EHRs and AI methods using SDOH for healthcare outcomes. Finally, we conclude this paper with discussion on the current trends, challenges, and future directions on using SDOH from EHRs.

Developing conversational agents to interact with patients and provide primary clinical advice has attracted increasing attention due to its huge application potential, especially in the time of COVID-19 Pandemic. However, the training of end-to-end neural-based medical dialogue system is restricted by an insufficient quantity of medical dialogue corpus. In this work, we make the first attempt to build and release a large-scale high-quality Medical Dialogue dataset related to 12 types of common Gastrointestinal diseases named MedDG, with more than 17K conversations collected from the online health consultation community. Five different categories of entities, including diseases, symptoms, attributes, tests, and medicines, are annotated in each conversation of MedDG as additional labels. To push forward the future research on building expert-sensitive medical dialogue system, we proposes two kinds of medical dialogue tasks based on MedDG dataset. One is the next entity prediction and the other is the doctor response generation. To acquire a clear comprehension on these two medical dialogue tasks, we implement several state-of-the-art benchmarks, as well as design two dialogue models with a further consideration on the predicted entities. Experimental results show that the pre-train language models and other baselines struggle on both tasks with poor performance in our dataset, and the response quality can be enhanced with the help of auxiliary entity information. From human evaluation, the simple retrieval model outperforms several state-of-the-art generative models, indicating that there still remains a large room for improvement on generating medically meaningful responses.

Parkinson's Disease (PD) is a neurodegenerative disease that currently does not have a cure. In order to facilitate disease management and reduce the speed of symptom progression, early diagnosis is essential. The current clinical, diagnostic approach is to have radiologists perform human visual analysis of the degeneration of dopaminergic neurons in the substantia nigra region of the brain. Clinically, dopamine levels are monitored through observing dopamine transporter (DaT) activity. One method of DaT activity analysis is performed with the injection of an Iodine-123 fluoropropyl (123I-FP-CIT) tracer combined with single photon emission computerized tomography (SPECT) imaging. The tracer illustrates the region of interest in the resulting DaTscan SPECT images. Human visual analysis is slow and vulnerable to subjectivity between radiologists, so the goal was to develop an introductory implementation of a deep convolutional neural network that can objectively and accurately classify DaTscan SPECT images as Parkinson's Disease or normal. This study illustrates the approach of using a deep convolutional neural network and evaluates its performance on DaTscan SPECT image classification. The data used in this study was obtained through a database provided by the Parkinson's Progression Markers Initiative (PPMI). The deep neural network in this study utilizes the InceptionV3 architecture, 1st runner up in the 2015 ImageNet Large Scale Visual Recognition Competition (ILSVRC), as a base model. A custom, binary classifier block was added on top of this base. In order to account for the small dataset size, a ten fold cross validation was implemented to evaluate the model's performance.