Antibodies are crucial proteins produced by the immune system to eliminate harmful foreign substances and have become pivotal therapeutic agents for treating human diseases.To accelerate the discovery of antibody therapeutics, there is growing interest in constructing language models using antibody sequences.However, the applicability of pre-trained language models for antibody discovery has not been thoroughly evaluated due to the scarcity of labeled datasets.To overcome these limitations, we introduce AVIDa-SARS-CoV-2, a dataset featuring the antigen-variable domain of heavy chain of heavy chain antibody (VHH) interactions obtained from two alpacas immunized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike proteins.AVIDa-SARS-CoV-2 includes binary labels indicating the binding or non-binding of diverse VHH sequences to 12 SARS-CoV-2 mutants, such as the Delta and Omicron variants.Furthermore, we release VHHCorpus-2M, a pre-training dataset for antibody language models, containing over two million VHH sequences.We report benchmark results for predicting SARS-CoV-2-VHH binding using VHHBERT pre-trained on VHHCorpus-2M and existing general protein and antibody-specific pre-trained language models.These results confirm that AVIDa-SARS-CoV-2 provides valuable benchmarks for evaluating the representation capabilities of antibody language models for binding prediction, thereby facilitating the development of AI-driven antibody discovery.The datasets are available at https://datasets.cognanous.com.

Machine learning (ML) is becoming increasingly popular for predicting material properties to accelerate materials discovery. Because material properties are strongly affected by its crystal structure, a key issue is converting the crystal structure into the features for input to the ML model. Currently, the most common method is to convert the crystal structure into a graph and predicting its properties using a graph neural network (GNN). Some GNN models, such as crystal graph convolutional neural network (CGCNN) and atomistic line graph neural network (ALIGNN), have achieved highly accurate predictions of material properties. Despite these successes, using a graph to represent a crystal structure has the notable limitation of losing the crystal structure's three-dimensional (3D) information. In this work, we propose DeepCrysTet, a novel deep learning approach for predicting material properties, which uses crystal structures represented as a 3D tetrahedral mesh generated by Delaunay tetrahedralization. DeepCrysTet provides a useful framework that includes a 3D mesh generation method, mesh-based feature design, and neural network design. The experimental results using the Materials Project dataset show that DeepCrysTet significantly outperforms existing GNN models in classifying crystal structures and achieves state-of-the-art performance in predicting elastic properties.

Antibodies have become an important class of therapeutic agents to treat human diseases.To accelerate therapeutic antibody discovery, computational methods, especially machine learning, have attracted considerable interest for predicting specific interactions between antibody candidates and target antigens such as viruses and bacteria.However, the publicly available datasets in existing works have notable limitations, such as small sizes and the lack of non-binding samples and exact amino acid sequences.To overcome these limitations, we have developed AVIDa-hIL6, a large-scale dataset for predicting antigen-antibody interactions in the variable domain of heavy chain of heavy chain antibodies (VHHs), produced from an alpaca immunized with the human interleukin-6 (IL-6) protein, as antigens.By leveraging the simple structure of VHHs, which facilitates identification of full-length amino acid sequences by DNA sequencing technology, AVIDa-hIL6 contains 573,891 antigen-VHH pairs with amino acid sequences.All the antigen-VHH pairs have reliable labels for binding or non-binding, as generated by a novel labeling method.Furthermore, via introduction of artificial mutations, AVIDa-hIL6 contains 30 different mutants in addition to wild-type IL-6 protein.This characteristic provides opportunities to develop machine learning models for predicting changes in antibody binding by antigen mutations.We report experimental benchmark results on AVIDa-hIL6 by using machine learning models.The results indicate that the existing models have potential, but further research is needed to generalize them to predict effective antibodies against unknown mutants.The dataset is available at https://avida-hil6.cognanous.com.

To respond to various requests from users, web service infrastructure must change system configurations quickly and flexibly without making users aware of the system configuration. However, because SSH used as a secure remote connection service to a server must send a connection request by specifying the IP address or hostname of the server, the SSH client must know the changed information when the IP address or hostname is changed. To overcome this difficulty, a method exists by which a client tool such as gcloud command obtains the IP address or hostname of the destination server based on unique label information of each server. However, this method requires restrictions and changes to the tools used by the client side. Another method is to use a proxy server, such as SSH Piper, to obtain the IP address or hostname of the destination server based on the SSH username. In existing SSH proxy servers, the source code must be changed directly to change the proxy server behavior. As described herein, we propose an SSH proxy server which can follow system changes using hook functions that can be incorporated by system administrators without requiring restrictions or changes to the clients. The proposed method has high extensibility for system changes because the proxy server behavior can be changed easily merely by modifying the hook function to be incorporated. Furthermore, using the proposed method confirmed that the overhead of establishing an SSH session is about 20 ms, which is a short time during which the SSH client does not feel a delay when logging into the server with SSH.