Therapeutic peptides represent a unique class of pharmaceutical agents crucial for the treatment of human diseases. Recently, deep generative models have exhibited remarkable potential for generating therapeutic peptides, but they only utilize sequence or structure information alone, which hinders the performance in generation. In this study, we propose a Multi-Modal Contrastive Diffusion model (MMCD), fusing both sequence and structure modalities in a diffusion framework to co-generate novel peptide sequences and structures. Specifically, MMCD constructs the sequence-modal and structure-modal diffusion models, respectively, and devises a multi-modal contrastive learning strategy with intercontrastive and intra-contrastive in each diffusion timestep, aiming to capture the consistency between two modalities and boost model performance. The inter-contrastive aligns sequences and structures of peptides by maximizing the agreement of their embeddings, while the intra-contrastive differentiates therapeutic and non-therapeutic peptides by maximizing the disagreement of their sequence/structure embeddings simultaneously. The extensive experiments demonstrate that MMCD performs better than other state-of-theart deep generative methods in generating therapeutic peptides across various metrics, including antimicrobial/anticancer score, diversity, and peptide-docking.
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Chemical synthesis, which is crucial for advancing material synthesis and drug discovery, impacts various sectors including environmental science and healthcare. The rise of technology in chemistry has generated extensive chemical data, challenging researchers to discern patterns and refine synthesis processes. Artificial intelligence (AI) helps by analyzing data to optimize synthesis and increase yields. However, AI faces challenges in processing literature data due to the unstructured format and diverse writing style of chemical literature. To overcome these difficulties, we introduce an end-to-end AI agent framework capable of high-fidelity extraction from extensive chemical literature. This AI agent employs large language models (LLMs) for prompt generation and iterative optimization. It functions as a chemistry assistant, automating data collection and analysis, thereby saving manpower and enhancing performance. Our framework's efficacy is evaluated using accuracy, recall, and F1 score of reaction condition data, and we compared our method with human experts in terms of content correctness and time efficiency. The proposed approach marks a significant advancement in automating chemical literature extraction and demonstrates the potential for AI to revolutionize data management and utilization in chemistry.
The recognition of multi-class cell nuclei can significantly facilitate the process of histopathological diagnosis. Numerous pathological datasets are currently available, but their annotations are inconsistent. Most existing methods require individual training on each dataset to deduce the relevant labels and lack the use of common knowledge across datasets, consequently restricting the quality of recognition. In this paper, we propose a universal cell nucleus classification framework (UniCell), which employs a novel prompt learning mechanism to uniformly predict the corresponding categories of pathological images from different dataset domains. In particular, our framework adopts an end-to-end architecture for nuclei detection and classification, and utilizes flexible prediction heads for adapting various datasets. Moreover, we develop a Dynamic Prompt Module (DPM) that exploits the properties of multiple datasets to enhance features. The DPM first integrates the embeddings of datasets and semantic categories, and then employs the integrated prompts to refine image representations, efficiently harvesting the shared knowledge among the related cell types and data sources. Experimental results demonstrate that the proposed method effectively achieves the state-of-the-art results on four nucleus detection and classification benchmarks. Code and models are available at //github.com/lhaof/UniCell
Accurate frictional contact is critical in simulating the assembly of rod-like structures in the practical world, such as knots, hairs, flagella, and more. Due to their high geometric nonlinearity and elasticity, rod-on-rod contact remains a challenging problem tackled by researchers in both computational mechanics and computer graphics. Typically, frictional contact is regarded as constraints for the equations of motions of a system. Such constraints are often computed independently at every time step in a dynamic simulation, thus slowing down the simulation and possibly introducing numerical convergence issues. This paper proposes a fully implicit penalty-based frictional contact method, Implicit Contact Model (IMC), that efficiently and robustly captures accurate frictional contact responses. We showcase our algorithm's performance in achieving visually realistic results for the challenging and novel contact scenario of flagella bundling in fluid medium, a significant phenomenon in biology that motivates novel engineering applications in soft robotics. In addition to this, we offer a side-by-side comparison with Incremental Potential Contact (IPC), a state-of-the-art contact handling algorithm. We show that IMC possesses comparable performance to IPC while converging at a faster rate.
Surface vibration tactile feedback is capable of conveying various semantic information to humans via the handheld electronic devices, like smartphone, touch panel,and game controller. However, covering the whole device contacting surface with dense actuator arrangement can affect its normal use, how to produce desired vibration patterns at any contact point with only several sparse actuators deployed on the handled device surface remains a significant challenge. In this work, we develop a tactile feedback board with only five actuators in the size of a smartphone, and achieve the precise vibration pattern production that can focus at any desired position all over the board. Specifically, we investigate the vibration characteristics of single passive coil actuator, and construct its vibration pattern model at any position on the feedback board surface. Optimal phase and amplitude modulation, found with the simulated annealing algorithm, is employed with five actuators in a sparse array. And all actuators' vibration patterns are superimposed linearly to synthetically generate different onboard vibration energy distribution for tactile sensing. Experiments demonstrated that for point-wise vibration pattern production on our tactile board achieved an average level of about 0.9 in the Structural Similarity Index Measure (SSIM) evaluation, when compared to the ideal single-point-focused target vibration pattern. The sparse actuator array can be easily embedded into usual handheld electronic devices, which shows a good significant implication for enriching their haptic interaction functionalities.
To promote precision medicine, individualized treatment regimes (ITRs) are crucial for optimizing the expected clinical outcome based on patient-specific characteristics. However, existing ITR research has primarily focused on scenarios with categorical treatment options and a single outcome. In reality, clinicians often encounter scenarios with continuous treatment options and multiple, potentially competing outcomes, such as medicine efficacy and unavoidable toxicity. To balance these outcomes, a proper weight is necessary, which should be learned in a data-driven manner that considers both patient preference and clinician expertise. In this paper, we present a novel algorithm for developing individualized treatment regimes (ITRs) that incorporate continuous treatment options and multiple outcomes, utilizing observational data. Our approach assumes that clinicians are optimizing individualized patient utilities with sub-optimal treatment decisions that are at least better than random assignment. Treatment assignment is assumed to directly depend on the true underlying utility of the treatment rather than patient characteristics. The proposed method simultaneously estimates the weighting of composite outcomes and the decision-making process, allowing for construction of individualized treatment regimes with continuous doses. The proposed estimators can be used for inference and variable selection, facilitating the identification of informative treatment assignments and preference-associated variables. We evaluate the finite sample performance of our proposed method via simulation studies and apply it to a real data application of radiation oncology analysis.
Fingerprint recognition stands as a pivotal component of biometric technology, with diverse applications from identity verification to advanced search tools. In this paper, we propose a unique method for deriving robust fingerprint representations by leveraging enhancement-based pre-training. Building on the achievements of U-Net-based fingerprint enhancement, our method employs a specialized encoder to derive representations from fingerprint images in a self-supervised manner. We further refine these representations, aiming to enhance the verification capabilities. Our experimental results, tested on publicly available fingerprint datasets, reveal a marked improvement in verification performance against established self-supervised training techniques. Our findings not only highlight the effectiveness of our method but also pave the way for potential advancements. Crucially, our research indicates that it is feasible to extract meaningful fingerprint representations from degraded images without relying on enhanced samples.
The use of hyperspectral imaging for medical applications is becoming more common in recent years. One of the main obstacles that researchers find when developing hyperspectral algorithms for medical applications is the lack of specific, publicly available, and hyperspectral medical data. The work described in this paper was developed within the framework of the European project HELICoiD (HypErspectraL Imaging Cancer Detection), which had as a main goal the application of hyperspectral imaging to the delineation of brain tumors in real-time during neurosurgical operations. In this paper, the methodology followed to generate the first hyperspectral database of in-vivo human brain tissues is presented. Data was acquired employing a customized hyperspectral acquisition system capable of capturing information in the Visual and Near InfraRed (VNIR) range from 400 to 1000 nm. Repeatability was assessed for the cases where two images of the same scene were captured consecutively. The analysis reveals that the system works more efficiently in the spectral range between 450 and 900 nm. A total of 36 hyperspectral images from 22 different patients were obtained. From these data, more than 300 000 spectral signatures were labeled employing a semi-automatic methodology based on the spectral angle mapper algorithm. Four different classes were defined: normal tissue, tumor tissue, blood vessel, and background elements. All the hyperspectral data has been made available in a public repository.
Magnetic resonance imaging (MRI) is crucial for enhancing diagnostic accuracy in clinical settings. However, the inherent long scan time of MRI restricts its widespread applicability. Deep learning-based image super-resolution (SR) methods exhibit promise in improving MRI resolution without additional cost. Due to lacking of aligned high-resolution (HR) and low-resolution (LR) MRI image pairs, unsupervised approaches are widely adopted for SR reconstruction with unpaired MRI images. However, these methods still require a substantial number of HR MRI images for training, which can be difficult to acquire. To this end, we propose an unpaired MRI SR approach that employs contrastive learning to enhance SR performance with limited HR training data. Empirical results presented in this study underscore significant enhancements in the peak signal-to-noise ratio and structural similarity index, even when a paucity of HR images is available. These findings accentuate the potential of our approach in addressing the challenge of limited HR training data, thereby contributing to the advancement of MRI in clinical applications.
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.
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