In the expansive realm of drug discovery, with approximately 15,000 known drugs and only around 4,200 approved, the combinatorial nature of the chemical space presents a formidable challenge. While Artificial Intelligence (AI) has emerged as a powerful ally, traditional AI frameworks face significant hurdles. This manuscript introduces CardiGraphormer, a groundbreaking approach that synergizes self-supervised learning (SSL), Graph Neural Networks (GNNs), and Cardinality Preserving Attention to revolutionize drug discovery. CardiGraphormer, a novel combination of Graphormer and Cardinality Preserving Attention, leverages SSL to learn potent molecular representations and employs GNNs to extract molecular fingerprints, enhancing predictive performance and interpretability while reducing computation time. It excels in handling complex data like molecular structures and performs tasks associated with nodes, pairs of nodes, subgraphs, or entire graph structures. CardiGraphormer's potential applications in drug discovery and drug interactions are vast, from identifying new drug targets to predicting drug-to-drug interactions and enabling novel drug discovery. This innovative approach provides an AI-enhanced methodology in drug development, utilizing SSL combined with GNNs to overcome existing limitations and pave the way for a richer exploration of the vast combinatorial chemical space in drug discovery.
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As Large Language Models (LLMs) are integrated into critical real-world applications, their strategic and logical reasoning abilities are increasingly crucial. This paper evaluates LLMs' reasoning abilities in competitive environments through game-theoretic tasks, e.g., board and card games that require pure logic and strategic reasoning to compete with opponents. We first propose GTBench, a language-driven environment composing 10 widely-recognized tasks, across a comprehensive game taxonomy: complete versus incomplete information, dynamic versus static, and probabilistic versus deterministic scenarios. Then, we investigate two key problems: (1) Characterizing game-theoretic reasoning of LLMs; (2) LLM-vs-LLM competitions as reasoning evaluation. We observe that (1) LLMs have distinct behaviors regarding various gaming scenarios; for example, LLMs fail in complete and deterministic games yet they are competitive in probabilistic gaming scenarios; (2) Open-source LLMs, e.g., CodeLlama-34b-Instruct, are less competitive than commercial LLMs, e.g., GPT-4, in complex games. In addition, code-pretraining greatly benefits strategic reasoning, while advanced reasoning methods such as Chain-of-Thought (CoT) and Tree-of-Thought (ToT) do not always help. Detailed error profiles are also provided for a better understanding of LLMs' behavior.
Compared with static knowledge graphs, temporal knowledge graphs (tKG), which can capture the evolution and change of information over time, are more realistic and general. However, due to the complexity that the notion of time introduces to the learning of the rules, an accurate graph reasoning, e.g., predicting new links between entities, is still a difficult problem. In this paper, we propose TILP, a differentiable framework for temporal logical rules learning. By designing a constrained random walk mechanism and the introduction of temporal operators, we ensure the efficiency of our model. We present temporal features modeling in tKG, e.g., recurrence, temporal order, interval between pair of relations, and duration, and incorporate it into our learning process. We compare TILP with state-of-the-art methods on two benchmark datasets. We show that our proposed framework can improve upon the performance of baseline methods while providing interpretable results. In particular, we consider various scenarios in which training samples are limited, data is biased, and the time range between training and inference are different. In all these cases, TILP works much better than the state-of-the-art methods.
Existing retrieval-based methods have made significant strides in maintaining long-term conversations. However, these approaches face challenges in memory database management and accurate memory retrieval, hindering their efficacy in dynamic, real-world interactions. This study introduces a novel framework, COmpressive Memory-Enhanced Dialogue sYstems (COMEDY), which eschews traditional retrieval modules and memory databases. Instead, COMEDY adopts a ''One-for-All'' approach, utilizing a single language model to manage memory generation, compression, and response generation. Central to this framework is the concept of compressive memory, which intergrates session-specific summaries, user-bot dynamics, and past events into a concise memory format. To support COMEDY, we curated a large-scale Chinese instruction-tuning dataset, Dolphin, derived from real user-chatbot interactions. Comparative evaluations demonstrate COMEDY's superiority over traditional retrieval-based methods in producing more nuanced and human-like conversational experiences. Our codes are available at //github.com/nuochenpku/COMEDY.
The precise prediction of molecular properties is essential for advancements in drug development, particularly in virtual screening and compound optimization. The recent introduction of numerous deep learning-based methods has shown remarkable potential in enhancing molecular property prediction (MPP), especially improving accuracy and insights into molecular structures. Yet, two critical questions arise: does the integration of domain knowledge augment the accuracy of molecular property prediction and does employing multi-modal data fusion yield more precise results than unique data source methods? To explore these matters, we comprehensively review and quantitatively analyze recent deep learning methods based on various benchmarks. We discover that integrating molecular information will improve both MPP regression and classification tasks by upto 3.98% and 1.72%, respectively. We also discover that the utilizing 3-dimensional information with 1-dimensional and 2-dimensional information simultaneously can substantially enhance MPP upto 4.2%. The two consolidated insights offer crucial guidance for future advancements in drug discovery.
This study explores the impact of peer acknowledgement on learner engagement and implicit psychological attributes in written annotations on an online social reading platform. Participants included 91 undergraduates from a large North American University. Using log file data, we analyzed the relationship between learners' received peer acknowledgement and their subsequent annotation behaviours using cross-lag regression. Higher peer acknowledgements correlate with increased initiation of annotations and responses to peer annotations. By applying text mining techniques and calculating Shapley values to analyze 1,969 social annotation entries, we identified prominent psychological themes within three dimensions (i.e., affect, cognition, and motivation) that foster peer acknowledgment in digital social annotation. These themes include positive affect, openness to learning and discussion, and expression of motivation. The findings assist educators in improving online learning communities and provide guidance to technology developers in designing effective prompts, drawing from both implicit psychological cues and explicit learning behaviours.
Recently, a range of neural network-based methods for image rendering have been introduced. One such widely-researched neural radiance field (NeRF) relies on a neural network to represent 3D scenes, allowing for realistic view synthesis from a small number of 2D images. However, most NeRF models are constrained by long training and inference times. In comparison, Gaussian Splatting (GS) is a novel, state-of-the-art technique for rendering points in a 3D scene by approximating their contribution to image pixels through Gaussian distributions, warranting fast training and swift, real-time rendering. A drawback of GS is the absence of a well-defined approach for its conditioning due to the necessity to condition several hundred thousand Gaussian components. To solve this, we introduce the Gaussian Mesh Splatting (GaMeS) model, which allows modification of Gaussian components in a similar way as meshes. We parameterize each Gaussian component by the vertices of the mesh face. Furthermore, our model needs mesh initialization on input or estimated mesh during training. We also define Gaussian splats solely based on their location on the mesh, allowing for automatic adjustments in position, scale, and rotation during animation. As a result, we obtain a real-time rendering of editable GS.
Due to various sources of uncertainty, emergent behavior, and ongoing changes, the reliability of many socio-technical systems depends on an iterative and collaborative process in which organizations (1) analyze and learn from system failures, and then (2) co-evolve both the technical and human parts of their systems based on what they learn. Many organizations have defined processes for learning from failure, often involving postmortem analyses conducted after any system failures that are judged to be sufficiently severe. Despite established processes and tool support, our preliminary research, and professional experience, suggest that it is not straightforward to take what was learned from a failure and successfully improve the reliability of the socio-technical system. To better understand this collaborative process and the associated challenges, we are conducting a study of how teams learn from failure. We are gathering incident reports from multiple organizations and conducting interviews with engineers and managers with relevant experience. Our analytic interest is in what is learned by teams as they reflect on failures, the learning processes involved, and how they use what is learned. Our data collection and analysis are not yet complete, but we have so far analyzed 13 incident reports and seven interviews. In this short paper we (1) present our preliminary findings, and (2) outline our broader research plans.
In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.
Small data challenges have emerged in many learning problems, since the success of deep neural networks often relies on the availability of a huge amount of labeled data that is expensive to collect. To address it, many efforts have been made on training complex models with small data in an unsupervised and semi-supervised fashion. In this paper, we will review the recent progresses on these two major categories of methods. A wide spectrum of small data models will be categorized in a big picture, where we will show how they interplay with each other to motivate explorations of new ideas. We will review the criteria of learning the transformation equivariant, disentangled, self-supervised and semi-supervised representations, which underpin the foundations of recent developments. Many instantiations of unsupervised and semi-supervised generative models have been developed on the basis of these criteria, greatly expanding the territory of existing autoencoders, generative adversarial nets (GANs) and other deep networks by exploring the distribution of unlabeled data for more powerful representations. While we focus on the unsupervised and semi-supervised methods, we will also provide a broader review of other emerging topics, from unsupervised and semi-supervised domain adaptation to the fundamental roles of transformation equivariance and invariance in training a wide spectrum of deep networks. It is impossible for us to write an exclusive encyclopedia to include all related works. Instead, we aim at exploring the main ideas, principles and methods in this area to reveal where we are heading on the journey towards addressing the small data challenges in this big data era.
In order to answer natural language questions over knowledge graphs, most processing pipelines involve entity and relation linking. Traditionally, entity linking and relation linking has been performed either as dependent sequential tasks or independent parallel tasks. In this paper, we propose a framework called "EARL", which performs entity linking and relation linking as a joint single task. EARL uses a graph connection based solution to the problem. We model the linking task as an instance of the Generalised Travelling Salesman Problem (GTSP) and use GTSP approximate algorithm solutions. We later develop EARL which uses a pair-wise graph-distance based solution to the problem.The system determines the best semantic connection between all keywords of the question by referring to a knowledge graph. This is achieved by exploiting the "connection density" between entity candidates and relation candidates. The "connection density" based solution performs at par with the approximate GTSP solution.We have empirically evaluated the framework on a dataset with 5000 questions. Our system surpasses state-of-the-art scores for entity linking task by reporting an accuracy of 0.65 to 0.40 from the next best entity linker.
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