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Multi-probe attention neural network for COVID-19 semantic indexing
BackgroundThe COVID-19 pandemic has increasingly accelerated the publication pace of scientific literature. How to efficiently curate and index this...
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UDA-seq: universal droplet microfluidics-based combinatorial indexing for massive-scale multimodal single-cell sequencing
The use of single-cell combinatorial indexing sequencing via droplet microfluidics presents an attractive approach for balancing cost, scalability,...
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Semantic embeddings reveal and address taxonomic incommensurability in psychological measurement
Taxonomic incommensurability denotes the difficulty in comparing scientific theories due to different uses of concepts and operationalizations. To...
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Uncertainty aversion predicts the neural expansion of semantic representations
Correctly identifying the meaning of a stimulus requires activating the appropriate semantic representation among many alternatives. One way to...
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Toward a standard formal semantic representation of the model card report
BackgroundModel card reports aim to provide informative and transparent description of machine learning models to stakeholders. This report document...
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High-content single-cell combinatorial indexing
Single-cell combinatorial indexing (sci) with transposase-based library construction increases the throughput of single-cell genomics assays but...
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txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility
We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to...
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Benchmarking computational methods for single-cell chromatin data analysis
BackgroundSingle-cell chromatin accessibility assays, such as scATAC-seq, are increasingly employed in individual and joint multi-omic profiling of...
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Scalable single-cell profiling of chromatin modifications with sciCUT&Tag
Cleavage under targets and tagmentation (CUT&Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing immune...
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MedKG: enabling drug discovery through a unified biomedical knowledge graph
Biomedical knowledge graphs have emerged as powerful tools for drug discovery, but existing platforms often suffer from outdated information, limited...
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Valsci: an open-source, self-hostable literature review utility for automated large-batch scientific claim verification using large language models
BackgroundThe exponential growth of scientific publications poses a formidable challenge for researchers seeking to validate emerging hypotheses or...
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Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development
The brain is a complex tissue whose function relies on coordinated anatomical and molecular features. However, the molecular annotation of the...
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Dyport: dynamic importance-based biomedical hypothesis generation benchmarking technique
BackgroundAutomated hypothesis generation (HG) focuses on uncovering hidden connections within the extensive information that is publicly available....
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Combining word embeddings to extract chemical and drug entities in biomedical literature
BackgroundNatural language processing (NLP) and text mining technologies for the extraction and indexing of chemical and drug entities are key to...
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A benchmark of computational pipelines for single-cell histone modification data
BackgroundSingle-cell histone post translational modification (scHPTM) assays such as scCUT&Tag or scChIP-seq allow single-cell mapping of diverse...
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Biomedical semantic indexing by deep neural network with multi-task learning
BackgroundBiomedical semantic indexing is important for information retrieval and many other research fields in bioinformatics. It annotates...
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VAIV bio-discovery service using transformer model and retrieval augmented generation
BackgroundThere has been a considerable advancement in AI technologies like LLM and machine learning to support biomedical knowledge discovery.
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IT-scC&T-seq streamlines scalable, parallel profiling of protein–DNA interactions in single cells
Single-cell profiling protein-chromatin interactions is often constrained by complex workflows, high cost, or dependence on specialized equipment. We...
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Hippocampal neurons code individual episodic memories in humans
The hippocampus is an essential hub for episodic memory processing. However, how human hippocampal single neurons code multi-element associations...
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NeuroXiv: AI-powered open databasing and dynamic mining of brain-wide neuron morphometry
Neuron morphology has been extensively reconstructed at the whole-brain scale by various projects in recent years. Here, to facilitate interactive...
