Simultaneously Improve Transferability and Discriminability for Adversarial Domain Adaptation

Although adversarial domain adaptation enhances feature transferability, the feature discriminability will be degraded in the process of adversarial learning. Moreover, most domain adaptation methods only focus on distribution matching in the feature space; however, shifts in the joint distributions of input features and output labels linger in the network, and thus, the transferability is not fully exploited. In this paper, we propose a matrix rank embedding (MRE) method to enhance feature discriminability and transferability simultaneously. MRE restores a low-rank structure for data in the same class and enforces a maximum separation structure for data in different classes. In this manner, the variations within the subspace are reduced, and the separation between the subspaces is increased, resulting in improved discriminability. In addition to statistically aligning the class-conditional distribution in the feature space, MRE forces the data of the same class in different domains to exhibit an approximate low-rank structure, thereby aligning the class-conditional distribution in the label space, resulting in improved transferability. MRE is computationally efficient and can be used as a plug-and-play term for other adversarial domain adaptation networks. Comprehensive experiments demonstrate that MRE can advance state-of-the-art domain adaptation methods.

Identifying cell-to-cell variability in internalisation using flow cytometry

Biological heterogeneity is a primary contributor to the variation observed in experiments that probe dynamical processes, such as internalisation. Given that internalisation is the primary means by which cells absorb drugs, viruses and other material, quantifying cell-to-cell variability in internalisation is of high biological interest. Yet, it is common for studies of internalisation to neglect cell-to-cell variability. We develop a simple mathematical model of internalisation that captures the dynamical behaviour, cell-to-cell variation, and extrinsic noise introduced by flow cytometry. We calibrate our model through a novel distribution-matching approximate Bayesian computation algorithm to flow cytometry data collected from an experiment that probes the internalisation of antibody by transferrin receptors in C1R cells. Our model reproduces experimental observations, identifies cell-to-cell variability in the internalisation and recycling rates, and, importantly, provides information relating to inferential uncertainty. Given that our approach is agnostic to sample size and signal-to-noise ratio, our modelling framework is broadly applicable to identify biological variability in single-cell data from experiments that probe a range of dynamical processes.

Distribution-Based Similarity Measures Applied to Laboratory Results Matching

The use of international laboratory terminologies inside hospital information systems is required to conduct data reuse analyses through inter-hospital databases. While most terminology matching techniques performing semantic interoperability are language-based, another strategy is to use distribution matching that performs terms matching based on the statistical similarity. In this work, our objective is to design and assess a structured framework to perform distribution matching on concepts described by continuous variables. We propose a framework that combines distribution matching and machine learning techniques. Using a training sample consisting of correct and incorrect correspondences between different terminologies, a match probability score is built. For each term, best candidates are returned and sorted in decreasing order using the probability given by the model. Searching 101 terms from Lille University Hospital among the same list of concepts in MIMIC-III, the model returned the correct match in the top 5 candidates for 96 of them (95%). Using this open-source framework with a top-k suggestions system could make the expert validation of terminologies alignment easier.

Molecular generation by Fast Assembly of (Deep)SMILES fragments

Background In recent years, in silico molecular design is regaining interest. To generate on a computer molecules with optimized properties, scoring functions can be coupled with a molecular generator to design novel molecules with a desired property profile. Results In this article, a simple method is described to generate only valid molecules at high frequency ($$>300,000$$ > 300 , 000 molecule/s using a single CPU core), given a molecular training set. The proposed method generates diverse SMILES (or DeepSMILES) encoded molecules while also showing some propensity at training set distribution matching. When working with DeepSMILES, the method reaches peak performance ($$>340,000$$ > 340 , 000 molecule/s) because it relies almost exclusively on string operations. The “Fast Assembly of SMILES Fragments” software is released as open-source at https://github.com/UnixJunkie/FASMIFRA. Experiments regarding speed, training set distribution matching, molecular diversity and benchmark against several other methods are also shown.

Extension of M Dwarf Spectra Based on Adversarial AutoEncoder

M dwarfs are main sequence stars and they exist in all stages of galaxy evolution. As the living fossils of cosmic evolution, the study of M dwarfs is of great significance to the understanding of stars and the stellar populations of the Milky Way. Previously, M dwarf research was limited due to insufficient spectroscopic spectra. Recently, the data volume of M dwarfs was greatly increased with the launch of large sky survey telescopes such as Sloan Digital Sky Survey and Large Sky Area Multi-Object Fiber Spectroscopy Telescope. However, the spectra of M dwarfs mainly concentrate in the subtypes of M0–M4, and the number of M5–M9 is still relatively limited. With the continuous development of machine learning, the generative model was improved and provides methods to solve the shortage of specified training samples. In this paper, the Adversarial AutoEncoder is proposed and implemented to solve this problem. Adversarial AutoEncoder is a probabilistic AutoEncoder that uses the Generative Adversarial Nets to generate data by matching the posterior of the hidden code vector of the original data extracted by the AutoEncoder with a prior distribution. Matching the posterior to the prior ensures each part of prior space generated results in meaningful data. To verify the quality of the generated spectra data, we performed qualitative and quantitative verification. The experimental results indicate the generation spectra data enhance the measured spectra data and have scientific applicability.