Browsing all papers, sorted by Most cited. Showing 25 of 39,449.
A model of saliency-based visual attention for rapid scene analysis
A visual attention system, inspired by the behavior and the neuronal architecture of the early primate visual system, is presented. Multiscale image features are combined into a single topographical saliency map. A dynamical neural network then selects attended locations in order of decreasing saliency. The system breaks down the complex problem of scene und…
A robust and high-throughput Cre reporting and characterization system for the…
The Cre/lox system is widely used in mice to achieve cell-type-specific gene expression. However, a strong and universally responding system to express genes under Cre control is still lacking. We have generated a set of Cre reporter mice with strong, ubiquitous expression of fluorescent proteins of different spectra. The robust native fluorescence of these…
Ultrasensitive fluorescent proteins for imaging neuronal activity
Fluorescent calcium sensors are widely used to image neural activity. Using structure-based mutagenesis and neuron-based screening, we developed a family of ultrasensitive protein calcium sensors (GCaMP6) that outperformed other sensors in cultured neurons and in zebrafish, flies and mice in vivo. In layer 2/3 pyramidal neurons of the mouse visual cortex, GC…
A general framework for estimating the relative pathogenicity of human genetic…
Current methods for annotating and interpreting human genetic variation tend to exploit a single information type (for example, conservation) and/or are restricted in scope (for example, to missense changes). Here we describe Combined Annotation-Dependent Depletion (CADD), a method for objectively integrating many diverse annotations into a single measure (C…
Genome-wide atlas of gene expression in the adult mouse brain
Molecular approaches to understanding the functional circuitry of the nervous system promise new insights into the relationship between genes, brain and behaviour. The cellular diversity of the brain necessitates a cellular resolution approach towards understanding the functional genomics of the nervous system. We describe here an anatomically comprehensive…
Computational modelling of visual attention
Five important trends have emerged from recent work on computational models of focal visual attention that emphasize the bottom-up, image-based control of attentional deployment. First, the perceptual saliency of stimuli critically depends on the surrounding context. Second, a unique 'saliency map' that topographically encodes for stimulus conspicuity over t…
The single-cell transcriptional landscape of mammalian organogenesis
Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of the three germ layers transform into an embryo that includes most of the major internal and external organs. Here we investigate the transcriptional dynamics of mouse organogenesis at single-cell resolution. Using single-cell combinatorial indexing, we profiled the transc…
Next-generation DNA sequencing
DNA sequence represents a single format onto which a broad range of biological phenomena can be projected for high-throughput data collection. Over the past three years, massively parallel DNA sequencing platforms have become widely available, reducing the cost of DNA sequencing by over two orders of magnitude, and democratizing the field by putting the sequ…
Think you have Solved Question Answering? Try ARC, the AI2 Reasoning Challenge
We present a new question set, text corpus, and baselines assembled to encourage AI research in advanced question answering. Together, these constitute the AI2 Reasoning Challenge (ARC), which requires far more powerful knowledge and reasoning than previous challenges such as SQuAD or SNLI. The ARC question set is partitioned into a Challenge Set and an Easy…
The origin of extracellular fields and currents — EEG, ECoG, LFP and spikes
The origin of extracellular fields and currents--EEG, ECoG, LFP and spikes. Buzsáki G(1), Anastassiou CA, Koch C.
CADD: predicting the deleteriousness of variants throughout the human genome
Combined Annotation-Dependent Depletion (CADD) is a widely used measure of variant deleteriousness that can effectively prioritize causal variants in genetic analyses, particularly highly penetrant contributors to severe Mendelian disorders. CADD is an integrative annotation built from more than 60 genomic features, and can score human single nucleotide vari…
Shifts in Selective Visual Attention: Towards the Underlying Neural Circuitry
Shifts in selective visual attention: towards the underlying neural circuitry. Koch C, Ullman S. Psychophysical and physiological evidence indicates that the visual system of primates and humans has evolved a specialized processing focus moving across the visual scene. This study addresses the question of how simple networks of neuron-like elements can accou…
Graph-Based Visual Saliency
A new bottom-up visual saliency model, Graph-Based Visual Saliency (GBVS), is proposed. It consists of two steps: first forming activation maps on certain feature \nchannels, and then normalizing them in a way which highlights conspicuity and admits combination with other maps. The model is simple, and biologically plausible \ninsofar as it is natura…
Self-Refine: Iterative Refinement with Self-Feedback
Like humans, large language models (LLMs) do not always generate the best output on their first try. Motivated by how humans refine their written text, we introduce Self-Refine, an approach for improving initial outputs from LLMs through iterative feedback and refinement. The main idea is to generate an initial output using an LLMs; then, the same LLMs provi…
An anatomically comprehensive atlas of the adult human brain transcriptome
Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising extensive histological analysis and comprehensive microarray…
A saliency-based search mechanism for overt and covert shifts of visual attenti…
A saliency-based search mechanism for overt and covert shifts of visual attention. Itti L(1), Koch C.
A mesoscale connectome of the mouse brain
Comprehensive knowledge of the brain's wiring diagram is fundamental for understanding how the nervous system processes information at both local and global scales. However, with the singular exception of the C. elegans microscale connectome, there are no complete connectivity data sets in other species. Here we report a brain-wide, cellular-level, mesoscale…
The contribution of de novo coding mutations to autism spectrum disorder
Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disruptin…
Widespread transcription at neuronal activity-regulated enhancers.
We used genome-wide sequencing methods to study stimulus-dependent enhancer function in mouse cortical neurons. We identified approximately 12,000 neuronal activity-regulated enhancers that are bound by the general transcriptional co-activator CBP in an activity-dependent manner. A function of CBP at enhancers may be to recruit RNA polymerase II (RNAPII), as…
["Animals""Basic Helix-Loop-Helix Proteins""CREB-Binding Protein""Consensus Sequence"The complete genome sequence of a Neanderthal from the Altai Mountains
We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history…
10.1038/nature24636
Sensory, motor and cognitive operations involve the coordinated action of large neuronal populations across multiple brain regions in both superficial and deep structures. Existing extracellular probes record neural activity with excellent spatial and temporal (sub-millisecond) resolution, but from only a few dozen neurons per shank. Optical Ca2+ imaging off…
Can a Suit of Armor Conduct Electricity? A New Dataset for Open Book Question A…
We present a new kind of question answering dataset, OpenBookQA, modeled after open book exams for assessing human understanding of a subject. The open book that comes with our questions is a set of 1326 elementary level science facts. Roughly 6000 questions probe an understanding of these facts and their application to novel situations. This requires combin…
Sporadic autism exomes reveal a highly interconnected protein network of de nov…
It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no previous history of ASD or related phenotypes--so-called sporad…
Learn to Explain: Multimodal Reasoning via Thought Chains for Science Question…
When answering a question, humans utilize the information available across different modalities to synthesize a consistent and complete chain of thought (CoT). This process is normally a black box in the case of deep learning models like large-scale language models. Recently, science question benchmarks have been used to diagnose the multi-hop reasoning abil…
Molecular Signature of CD8+ T Cell Exhaustion during Chronic Viral Infection
Oct 18. Molecular signature of CD8+ T cell exhaustion during chronic viral infection. Wherry EJ(1), Ha SJ, Kaech SM, Haining WN, Sarkar S, Kalia V, Subramaniam S, Blattman JN, Barber DL, Ahmed R.