This work extends the conventional back-propagation neural network (BPNN) to the classification of Chinese liquors of different flavors according to their Raman spectra. Conformal prediction is applied to assign reliable confidence measures for each classification and support an effective framework to make the machine learning on classification trustable. The BPNN can be used to predict the flavors of Chinese liquors according to their Raman spectra, and a classification rate of 88.96% can be achieved. In order to evaluate each classification, a non-conformity score is defined to generate a -value for each classification. Moreover, the validity of conformal prediction in online mode is discussed. The number of cumulative errors in the conformal prediction is much less than that without conformal prediction. The relationship between the cumulative error and confidence levels shows that a high confidence level leads to low cumulative errors, but many cumulative errors will occur under a very high confidence level. The result implies that conformal prediction is a useful framework, which can employ classification satisfying a certain level of confidence. Meanwhile, the conformal prediction can improve our classification using a BPNN, when the number of data points is limited.
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Proc Natl Acad Sci U S A
January 2025
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139.
Protein language models (PLMs) have demonstrated impressive success in modeling proteins. However, general-purpose "foundational" PLMs have limited performance in modeling antibodies due to the latter's hypervariable regions, which do not conform to the evolutionary conservation principles that such models rely on. In this study, we propose a transfer learning framework called Antibody Mutagenesis-Augmented Processing (AbMAP), which fine-tunes foundational models for antibody-sequence inputs by supervising on antibody structure and binding specificity examples.
View Article and Find Full Text PDFNat Rev Neurosci
January 2025
Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD, USA.
Transient changes in the firing of midbrain dopamine neurons have been closely tied to the unidimensional value-based prediction error contained in temporal difference reinforcement learning models. However, whereas an abundance of work has now shown how well dopamine responses conform to the predictions of this hypothesis, far fewer studies have challenged its implicit assumption that dopamine is not involved in learning value-neutral features of reward. Here, we review studies in rats and humans that put this assumption to the test, and which suggest that dopamine transients provide a much richer signal that incorporates information that goes beyond integrated value.
View Article and Find Full Text PDFACS Appl Mater Interfaces
January 2025
School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
One of the key advantages of using a hydrogel is its superb control over elasticity obtained through variations of constituent polymer and water. The underlying molecular nature of a hydrogel is a fundamental origin of hydrogel mechanics. In this article, we report a Polyacrylamide (PAAm)-based hydrogel model using the MARTINI coarse-grained (CG) force field.
View Article and Find Full Text PDFToxicology
January 2025
School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan; Advanced Research Promotion Center, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan. Electronic address:
Hexafluoropropylene oxide dimer acid (HFPO-DA), which belongs to the class of perfluoroalkyl ether carboxylic acid (PFECA), is a new alternative to perfluorooctanoic acid (PFOA). However, whether HFPO-DA is a safer alternative to PFOA in neonates remains unclear. In this study, we evaluated neonatal hepatic toxicity on postnatal days 9-10 by orally exposing pregnant CD-1 mice to 0.
View Article and Find Full Text PDFAdv Sci (Weinh)
January 2025
State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100005, China.
The dynamics of chromatin conformation involve continuous and reversible changes within the nucleus of a cell, which participate in regulating processes such as gene expression, DNA replication, and damage repair. Here, SEE is introduced, an artificial intelligence (AI) method that utilizes autoencoder and transformer techniques to analyze chromatin dynamics using single-cell RNA sequencing data and a limited number of single-cell Hi-C maps. SEE is employed to investigate chromatin dynamics across different scales, enabling the detection of (i) rearrangements in topologically associating domains (TADs), and (ii) oscillations in chromatin interactions at gene loci.
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