An emerging application of Raman spectroscopy is monitoring the state of chemical reactors during biologic drug production. Raman shift intensities scale linearly with the concentrations of chemical species and thus can be used to analytically determine real-time concentrations using non-destructive light irradiation in a label-free manner. Chemometric algorithms are used to interpret Raman spectra produced from complex mixtures of bioreactor contents as a reaction evolves. Finding the optimal algorithm for a specific bioreactor environment is challenging due to the lack of freely available Raman mixture datasets. The RaMix Python package addresses this challenge by enabling the generation of synthetic Raman mixture datasets with controllable noise levels to assess the utility of different chemometric algorithm types for real-time monitoring applications. To demonstrate the capabilities of this package and compare the performance of different chemometric algorithms, 48 datasets of simulated spectra were generated using the RaMix Python package. The four tested algorithms include partial least squares regression (PLS), a simple neural network, a simple convolutional neural network (simple CNN), and a 1D convolutional neural network with a ResNet architecture (ResNet). The performance of the PLS and simple CNN model was found to be comparable, with the PLS algorithm slightly outperforming the other models on 83\% of the data sets. The simple CNN model outperforms the other models on large, high noise datasets, demonstrating the superior capability of convolutional neural networks compared to PLS in analyzing noisy spectra. These results demonstrate the promise of CNNs to automatically extract concentration information from unprocessed, noisy spectra, allowing for better process control of industrial drug production. Code for this project is available at github.com/DexterAntonio/RaMix.
相關內容
Since thermal imagery offers a unique modality to investigate pain, the U.S. National Institutes of Health (NIH) has collected a large and diverse set of cancer patient facial thermograms for AI-based pain research. However, differing angles from camera capture between thermal and visible sensors has led to misalignment between Visible-Thermal (VT) images. We modernize the classic computer vision task of image registration by applying and modifying a generative alignment algorithm to register VT cancer faces, without the need for a reference or alignment parameters. By registering VT faces, we demonstrate that the quality of thermal images produced in the generative AI downstream task of Visible-to-Thermal (V2T) image translation significantly improves up to 52.5\%, than without registration. Images in this paper have been approved by the NIH NCI for public dissemination.
The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the molecule structures. However, automatically parsing the exact chemical structure is a formidable challenge, due to the amount of detailed information, the diversity of drawing styles, and the need for training data. In this work, we introduce MolGrapher to recognize chemical structures visually. First, a deep keypoint detector detects the atoms. Second, we treat all candidate atoms and bonds as nodes and put them in a graph. This construct allows a natural graph representation of the molecule. Last, we classify atom and bond nodes in the graph with a Graph Neural Network. To address the lack of real training data, we propose a synthetic data generation pipeline producing diverse and realistic results. In addition, we introduce a large-scale benchmark of annotated real molecule images, USPTO-30K, to spur research on this critical topic. Extensive experiments on five datasets show that our approach significantly outperforms classical and learning-based methods in most settings. Code, models, and datasets are available.
Segmenting cells and tracking their motion over time is a common task in biomedical applications. However, predicting accurate instance-wise segmentation and cell motions from microscopy imagery remains a challenging task. Using microstructured environments for analyzing single cells in a constant flow of media adds additional complexity. While large-scale labeled microscopy datasets are available, we are not aware of any large-scale dataset, including both cells and microstructures. In this paper, we introduce the trapped yeast cell (TYC) dataset, a novel dataset for understanding instance-level semantics and motions of cells in microstructures. We release $105$ dense annotated high-resolution brightfield microscopy images, including about $19$k instance masks. We also release $261$ curated video clips composed of $1293$ high-resolution microscopy images to facilitate unsupervised understanding of cell motions and morphology. TYC offers ten times more instance annotations than the previously largest dataset, including cells and microstructures. Our effort also exceeds previous attempts in terms of microstructure variability, resolution, complexity, and capturing device (microscopy) variability. We facilitate a unified comparison on our novel dataset by introducing a standardized evaluation strategy. TYC and evaluation code are publicly available under CC BY 4.0 license.
One-class classification (OCC) is a longstanding method for anomaly detection. With the powerful representation capability of the pre-trained backbone, OCC methods have witnessed significant performance improvements. Typically, most of these OCC methods employ transfer learning to enhance the discriminative nature of the pre-trained backbone's features, thus achieving remarkable efficacy. While most current approaches emphasize feature transfer strategies, we argue that the optimization objective space within OCC methods could also be an underlying critical factor influencing performance. In this work, we conducted a thorough investigation into the optimization objective of OCC. Through rigorous theoretical analysis and derivation, we unveil a key insights: any space with the suitable norm can serve as an equivalent substitute for the hypersphere center, without relying on the distribution assumption of training samples. Further, we provide guidelines for determining the feasible domain of norms for the OCC optimization objective. This novel insight sparks a simple and data-agnostic deep one-class classification method. Our method is straightforward, with a single 1x1 convolutional layer as a trainable projector and any space with suitable norm as the optimization objective. Extensive experiments validate the reliability and efficacy of our findings and the corresponding methodology, resulting in state-of-the-art performance in both one-class classification and industrial vision anomaly detection and segmentation tasks.
Automated organ at risk (OAR) segmentation is crucial for radiation therapy planning in CT scans, but the generated contours by automated models can be inaccurate, potentially leading to treatment planning issues. The reasons for these inaccuracies could be varied, such as unclear organ boundaries or inaccurate ground truth due to annotation errors. To improve the model's performance, it is necessary to identify these failure cases during the training process and to correct them with some potential post-processing techniques. However, this process can be time-consuming, as traditionally it requires manual inspection of the predicted output. This paper proposes a method to automatically identify failure cases by setting a threshold for the combination of Dice and Hausdorff distances. This approach reduces the time-consuming task of visually inspecting predicted outputs, allowing for faster identification of failure case candidates. The method was evaluated on 20 cases of six different organs in CT images from clinical expert curated datasets. By setting the thresholds for the Dice and Hausdorff distances, the study was able to differentiate between various states of failure cases and evaluate over 12 cases visually. This thresholding approach could be extended to other organs, leading to faster identification of failure cases and thereby improving the quality of radiation therapy planning.
In human-robot collaboration, unintentional physical contacts occur in the form of collisions and clamping, which must be detected and classified separately for a reaction. If certain collision or clamping situations are misclassified, reactions might occur that make the true contact case more dangerous. This work analyzes data-driven modeling based on physically modeled features like estimated external forces for clamping and collision classification with a real parallel robot. The prediction reliability of a feedforward neural network is investigated. Quantification of the classification uncertainty enables the distinction between safe versus unreliable classifications and optimal reactions like a retraction movement for collisions, structure opening for the clamping joint, and a fallback reaction in the form of a zero-g mode. This hypothesis is tested with experimental data of clamping and collision cases by analyzing dangerous misclassifications and then reducing them by the proposed uncertainty quantification. Finally, it is investigated how the approach of this work influences correctly classified clamping and collision scenarios.
Voronoi cells of varieties encode many features of their metric geometry. We prove that each Voronoi or Delaunay cell of a plane curve appears as the limit of a sequence of cells obtained from point samples of the curve. We use this result to study metric features of plane curves, including the medial axis, curvature, evolute, bottlenecks, and reach. In each case, we provide algebraic equations defining the object and, where possible, give formulas for the degrees of these algebraic varieties. We show how to identify the desired metric feature from Voronoi or Delaunay cells, and therefore how to approximate it by a finite point sample from the variety.
Single-particle traces of the diffusive motion of molecules, cells, or animals are by-now routinely measured, similar to stochastic records of stock prices or weather data. Deciphering the stochastic mechanism behind the recorded dynamics is vital in understanding the observed systems. Typically, the task is to decipher the exact type of diffusion and/or to determine system parameters. The tools used in this endeavor are currently revolutionized by modern machine-learning techniques. In this Perspective we provide an overview over recently introduced methods in machine-learning for diffusive time series, most notably, those successfully competing in the Anomalous-Diffusion-Challenge. As such methods are often criticized for their lack of interpretability, we focus on means to include uncertainty estimates and feature-based approaches, both improving interpretability and providing concrete insight into the learning process of the machine. We expand the discussion by examining predictions on different out-of-distribution data. We also comment on expected future developments.
Whenever humans use tools human performance is enhanced. Cognitive systems are a new kind of tool continually increasing in cognitive capability and are now performing high level cognitive tasks previously thought to be explicitly human. Usage of such tools, known as cogs, are expected to result in ever increasing levels of human cognitive augmentation. In a human cog ensemble, a cooperative, peer to peer, and collaborative dialog between a human and a cognitive system, human cognitive capability is augmented as a result of the interaction. The human cog ensemble is therefore able to achieve more than just the human or the cog working alone. This article presents results from two studies designed to measure the effect information supplied by a cog has on cognitive accuracy, the ability to produce the correct result, and cognitive precision, the propensity to produce only the correct result. Both cognitive accuracy and cognitive precision are shown to be increased by information of different types (policies and rules, examples, and suggestions) and with different kinds of problems (inventive problem solving and puzzles). Similar effects shown in other studies are compared.
Within the rapidly developing Internet of Things (IoT), numerous and diverse physical devices, Edge devices, Cloud infrastructure, and their quality of service requirements (QoS), need to be represented within a unified specification in order to enable rapid IoT application development, monitoring, and dynamic reconfiguration. But heterogeneities among different configuration knowledge representation models pose limitations for acquisition, discovery and curation of configuration knowledge for coordinated IoT applications. This paper proposes a unified data model to represent IoT resource configuration knowledge artifacts. It also proposes IoT-CANE (Context-Aware recommendatioN systEm) to facilitate incremental knowledge acquisition and declarative context driven knowledge recommendation.
小貼士
登錄享
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191