Accurately predicting molecular properties is a challenging but essential task in drug discovery. Recently, many mono-modal deep learning methods have been successfully applied to molecular property prediction. However, the inherent limitation of mono-modal learning arises from relying solely on one modality of molecular representation, which restricts a comprehensive understanding of drug molecules and hampers their resilience against data noise. To overcome the limitations, we construct multimodal deep learning models to cover different molecular representations. We convert drug molecules into three molecular representations, SMILES-encoded vectors, ECFP fingerprints, and molecular graphs. To process the modal information, Transformer-Encoder, bi-directional gated recurrent units (BiGRU), and graph convolutional network (GCN) are utilized for feature learning respectively, which can enhance the model capability to acquire complementary and naturally occurring bioinformatics information. We evaluated our triple-modal model on six molecule datasets. Different from bi-modal learning models, we adopt five fusion methods to capture the specific features and leverage the contribution of each modal information better. Compared with mono-modal models, our multimodal fused deep learning (MMFDL) models outperform single models in accuracy, reliability, and resistance capability against noise. Moreover, we demonstrate its generalization ability in the prediction of binding constants for protein-ligand complex molecules in the refined set of PDBbind. The advantage of the multimodal model lies in its ability to process diverse sources of data using proper models and suitable fusion methods, which would enhance the noise resistance of the model while obtaining data diversity.
相關內容
Humans learn language via multi-modal knowledge. However, due to the text-only pre-training scheme, most existing pre-trained language models (PLMs) are hindered from the multi-modal information. To inject visual knowledge into PLMs, existing methods incorporate either the text or image encoder of vision-language models (VLMs) to encode the visual information and update all the original parameters of PLMs for knowledge fusion. In this paper, we propose a new plug-and-play module, X-adapter, to flexibly leverage the aligned visual and textual knowledge learned in pre-trained VLMs and efficiently inject them into PLMs. Specifically, we insert X-adapters into PLMs, and only the added parameters are updated during adaptation. To fully exploit the potential in VLMs, X-adapters consist of two sub-modules, V-expert and T-expert, to fuse VLMs' image and text representations, respectively. We can opt for activating different sub-modules depending on the downstream tasks. Experimental results show that our method can significantly improve the performance on object-color reasoning and natural language understanding (NLU) tasks compared with PLM baselines.
Whataboutism, a potent tool for disrupting narratives and sowing distrust, remains under-explored in quantitative NLP research. Moreover, past work has not distinguished its use as a strategy for misinformation and propaganda from its use as a tool for pragmatic and semantic framing. We introduce new datasets from Twitter and YouTube, revealing overlaps as well as distinctions between whataboutism, propaganda, and the tu quoque fallacy. Furthermore, drawing on recent work in linguistic semantics, we differentiate the `what about' lexical construct from whataboutism. Our experiments bring to light unique challenges in its accurate detection, prompting the introduction of a novel method using attention weights for negative sample mining. We report significant improvements of 4% and 10% over previous state-of-the-art methods in our Twitter and YouTube collections, respectively.
A drug molecule is a substance that changes the organism's mental or physical state. Every approved drug has an indication, which refers to the therapeutic use of that drug for treating a particular medical condition. While the Large Language Model (LLM), a generative Artificial Intelligence (AI) technique, has recently demonstrated effectiveness in translating between molecules and their textual descriptions, there remains a gap in research regarding their application in facilitating the translation between drug molecules and indications, or vice versa, which could greatly benefit the drug discovery process. The capability of generating a drug from a given indication would allow for the discovery of drugs targeting specific diseases or targets and ultimately provide patients with better treatments. In this paper, we first propose a new task, which is the translation between drug molecules and corresponding indications, and then test existing LLMs on this new task. Specifically, we consider nine variations of the T5 LLM and evaluate them on two public datasets obtained from ChEMBL and DrugBank. Our experiments show the early results of using LLMs for this task and provide a perspective on the state-of-the-art. We also emphasize the current limitations and discuss future work that has the potential to improve the performance on this task. The creation of molecules from indications, or vice versa, will allow for more efficient targeting of diseases and significantly reduce the cost of drug discovery, with the potential to revolutionize the field of drug discovery in the era of generative AI.
Eulerian Formulation of the Tensor-Based Morphology Equations for Strain-Based Blood Damage Modeling
The development of blood-handling medical devices, such as ventricular assist devices, requires the analysis of their biocompatibility. Among other aspects, this includes hemolysis, i.e., red blood cell damage. For this purpose, computational fluid dynamics (CFD) methods are employed to predict blood flow in prototypes. The most basic hemolysis models directly estimate red blood cell damage from fluid stress in the resulting flow field. More advanced models explicitly resolve cell deformation. On the downside, these models are typically written in a Lagrangian formulation, i.e., they require pathline tracking. We present a new Eulerian description of cell deformation, enabling the evaluation of the solution across the whole domain. The resulting hemolysis model can be applied to any converged CFD simulation due to one-way coupling with the fluid velocity field. We discuss the efficient numerical treatment of the model equations in a stabilized finite element context. We validate the model by comparison to the original Lagrangian formulation in selected benchmark flows. Two more complex test cases demonstrate the method's capabilities in real-world applications. The results highlight the advantages over previous hemolysis models. In conclusion, the model holds great potential for the design process of future generations of medical devices.
Addressing the critical shortage of mental health resources for effective screening, diagnosis, and treatment remains a significant challenge. This scarcity underscores the need for innovative solutions, particularly in enhancing the accessibility and efficacy of therapeutic support. Embodied agents with advanced interactive capabilities emerge as a promising and cost-effective supplement to traditional caregiving methods. Crucial to these agents' effectiveness is their ability to simulate non-verbal behaviors, like backchannels, that are pivotal in establishing rapport and understanding in therapeutic contexts but remain under-explored. To improve the rapport-building capabilities of embodied agents we annotated backchannel smiles in videos of intimate face-to-face conversations over topics such as mental health, illness, and relationships. We hypothesized that both speaker and listener behaviors affect the duration and intensity of backchannel smiles. Using cues from speech prosody and language along with the demographics of the speaker and listener, we found them to contain significant predictors of the intensity of backchannel smiles. Based on our findings, we introduce backchannel smile production in embodied agents as a generation problem. Our attention-based generative model suggests that listener information offers performance improvements over the baseline speaker-centric generation approach. Conditioned generation using the significant predictors of smile intensity provides statistically significant improvements in empirical measures of generation quality. Our user study by transferring generated smiles to an embodied agent suggests that agent with backchannel smiles is perceived to be more human-like and is an attractive alternative for non-personal conversations over agent without backchannel smiles.
Modern policy optimization methods in reinforcement learning, such as TRPO and PPO, owe their success to the use of parameterized policies. However, while theoretical guarantees have been established for this class of algorithms, especially in the tabular setting, the use of general parameterization schemes remains mostly unjustified. In this work, we introduce a novel framework for policy optimization based on mirror descent that naturally accommodates general parameterizations. The policy class induced by our scheme recovers known classes, e.g., softmax, and generates new ones depending on the choice of mirror map. Using our framework, we obtain the first result that guarantees linear convergence for a policy-gradient-based method involving general parameterization. To demonstrate the ability of our framework to accommodate general parameterization schemes, we provide its sample complexity when using shallow neural networks, show that it represents an improvement upon the previous best results, and empirically validate the effectiveness of our theoretical claims on classic control tasks.
Matching problems have been widely studied in the research community, especially Ad-Auctions with many applications ranging from network design to advertising. Following the various advancements in machine learning, one natural question is whether classical algorithms can benefit from machine learning and obtain better-quality solutions. Even a small percentage of performance improvement in matching problems could result in significant gains for the studied use cases. For example, the network throughput or the revenue of Ad-Auctions can increase remarkably. This paper presents algorithms with machine learning predictions for the Online Bounded Allocation and the Online Ad-Auctions problems. We constructed primal-dual algorithms that achieve competitive performance depending on the quality of the predictions. When the predictions are accurate, the algorithms' performance surpasses previous performance bounds, while when the predictions are misleading, the algorithms maintain standard worst-case performance guarantees. We provide supporting experiments on generated data for our theoretical findings.
Nearest neighbor-based similarity searching is a common task in chemistry, with notable use cases in drug discovery. Yet, some of the most commonly used approaches for this task still leverage a brute-force approach. In practice this can be computationally costly and overly time-consuming, due in part to the sheer size of modern chemical databases. Previous computational advancements for this task have generally relied on improvements to hardware or dataset-specific tricks that lack generalizability. Approaches that leverage lower-complexity searching algorithms remain relatively underexplored. However, many of these algorithms are approximate solutions and/or struggle with typical high-dimensional chemical embeddings. Here we evaluate whether a combination of low-dimensional chemical embeddings and a k-d tree data structure can achieve fast nearest neighbor queries while maintaining performance on standard chemical similarity search benchmarks. We examine different dimensionality reductions of standard chemical embeddings as well as a learned, structurally-aware embedding -- SmallSA -- for this task. With this framework, searches on over one billion chemicals execute in less than a second on a single CPU core, five orders of magnitude faster than the brute-force approach. We also demonstrate that SmallSA achieves competitive performance on chemical similarity benchmarks.
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.
Image segmentation is considered to be one of the critical tasks in hyperspectral remote sensing image processing. Recently, convolutional neural network (CNN) has established itself as a powerful model in segmentation and classification by demonstrating excellent performances. The use of a graphical model such as a conditional random field (CRF) contributes further in capturing contextual information and thus improving the segmentation performance. In this paper, we propose a method to segment hyperspectral images by considering both spectral and spatial information via a combined framework consisting of CNN and CRF. We use multiple spectral cubes to learn deep features using CNN, and then formulate deep CRF with CNN-based unary and pairwise potential functions to effectively extract the semantic correlations between patches consisting of three-dimensional data cubes. Effective piecewise training is applied in order to avoid the computationally expensive iterative CRF inference. Furthermore, we introduce a deep deconvolution network that improves the segmentation masks. We also introduce a new dataset and experimented our proposed method on it along with several widely adopted benchmark datasets to evaluate the effectiveness of our method. By comparing our results with those from several state-of-the-art models, we show the promising potential of our method.
小貼士
登錄享
相關主題
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191