Predicting gene and protein expression levels from DNA and protein sequences with Perceiver

Background and objective: The functions of an organism and its biological processes result from the expression of genes and proteins. Therefore quantifying and predicting mRNA and protein levels is a crucial aspect of scientific research. Concerning the prediction of mRNA levels, the available approaches use the sequence upstream and downstream of the Transcription Start Site (TSS) as input to neural networks. The State-of-the-art models (e.g., Xpresso and Basenjii) predict mRNA levels exploiting Convolutional (CNN) or Long Short Term Memory (LSTM) Networks. However, CNN prediction depends on convolutional kernel size, and LSTM suffers from capturing long-range dependencies in the sequence. Concerning the prediction of protein levels, as far as we know, there is no model for predicting protein levels by exploiting the gene or protein sequences. Methods: Here, we exploit a new model type (called Perceiver) for mRNA and protein level prediction, exploiting a Transformer-based architecture with an attention module to attend to long-range interactions in the sequences. In addition, the Perceiver model overcomes the quadratic complexity of the standard Transformer architectures. This work's contributions are 1. DNAPerceiver model to predict mRNA levels from the sequence upstream and downstream of the TSS; 2. ProteinPerceiver model to predict protein levels from the protein sequence; 3. Protein&DNAPerceiver model to predict protein levels from TSS and protein sequences. Results: The models are evaluated on cell lines, mice, glioblastoma, and lung cancer tissues. The results show the effectiveness of the Perceiver-type models in predicting mRNA and protein levels. Conclusions: This paper presents a Perceiver architecture for mRNA and protein level prediction. In the future, inserting regulatory and epigenetic information into the model could improve mRNA and protein level predictions. The source code is freely available at https://github.com/MatteoStefanini/DNAPerceiver

Meshed-Memory Transformer for Image Captioning

Transformer-based architectures represent the state of the art in sequence modeling tasks like machine translation and language understanding. Their applicability to multi-modal contexts like image captioning, however, is still largely under-explored. With the aim of filling this gap, we present M² - a Meshed Transformer with Memory for Image Captioning. The architecture improves both the image encoding and the language generation steps: it learns a multi-level representation of the relationships between image regions integrating learned a priori knowledge, and uses a mesh-like connectivity at decoding stage to exploit low- and high-level features. Experimentally, we investigate the performance of the M² Transformer and different fully-attentive models in comparison with recurrent ones. When tested on COCO, our proposal achieves a new state of the art in single-model and ensemble configurations on the "Karpathy" test split and on the online test server. We also assess its performances when describing objects unseen in the training set. Trained models and code for reproducing the experiments are publicly available at :https://github.com/aimagelab/meshed-memory-transformer

Relations between Effects and Structure of Small Bicyclic Molecules on the Complex Model System Saccharomyces cerevisiae

The development of compounds able to modify biological functions largely took advantage of parallel synthesis to generate a broad chemical variance of compounds to be tested for the desired effect(s). The budding yeast Saccharomyces cerevisiae is a model for pharmacological studies since a long time as it represents a relatively simple system to explore the relations among chemical variance and bioactivity. To identify relations between the chemical features of the molecules and their activity, we delved into the effects of a library of small compounds on the viability of a set of S. cerevisiae strains. Thanks to the high degree of chemical diversity of the tested compounds and to the measured effect on the yeast growth rate, we were able to scale-down the chemical library and to gain information on the most effective structures at the substituent level. Our results represent a valuable source for the selection, rational design, and optimization of bioactive compounds

A Hybrid Adaptive Controller for Soft Robot Interchangeability

Soft robots have been leveraged in considerable areas like surgery, rehabilitation, and bionics due to their softness, flexibility, and safety. However, it is challenging to produce two same soft robots even with the same mold and manufacturing process owing to the complexity of soft materials. Meanwhile, widespread usage of a system requires the ability to fabricate replaceable components, which is interchangeability. Due to the necessity of this property, a hybrid adaptive controller is introduced to achieve interchangeability from the perspective of control approaches. This method utilizes an offline trained recurrent neural network controller to cope with the nonlinear and delayed response from soft robots. Furthermore, an online optimizing kinematics controller is applied to decrease the error caused by the above neural network controller. Soft pneumatic robots with different deformation properties but the same mold have been included for validation experiments. In the experiments, the systems with different actuation configurations and the different robots follow the desired trajectory with errors of 0.040 and 0.030 compared with the working space length, respectively. Such an adaptive controller also shows good performance on different control frequencies and desired velocities. This controller endows soft robots with the potential for wide application, and future work may include different offline and online controllers. A weight parameter adjusting strategy may also be proposed in the future.Comment: 8 pages, 9 figures, 4 table

Kineococcus radiotolerans Dps forms a heteronuclear Mn-Fe ferroxidase center that may explain the Mn-dependent protection against oxidative stress

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