Deconvolute individual genomes from metagenome sequences through short read clustering.

Metagenome assembly from short next-generation sequencing data is a challenging process due to its large scale and computational complexity. Clustering short reads by species before assembly offers a unique opportunity for parallel downstream assembly of genomes with individualized optimization. However, current read clustering methods suffer either false negative (under-clustering) or false positive (over-clustering) problems. Here we extended our previous read clustering software, SpaRC, by exploiting statistics derived from multiple samples in a dataset to reduce the under-clustering problem. Using synthetic and real-world datasets we demonstrated that this method has the potential to cluster almost all of the short reads from genomes with sufficient sequencing coverage. The improved read clustering in turn leads to improved downstream genome assembly quality

Few-Shot Semantic Parsing for New Predicates

In this work, we investigate the problems of semantic parsing in a few-shot learning setting. In this setting, we are provided with utterance-logical form pairs per new predicate. The state-of-the-art neural semantic parsers achieve less than 25% accuracy on benchmark datasets when k= 1. To tackle this problem, we proposed to i) apply a designated meta-learning method to train the model; ii) regularize attention scores with alignment statistics; iii) apply a smoothing technique in pre-training. As a result, our method consistently outperforms all the baselines in both one and two-shot settings.Comment: Accepted to EACL 202

Molecular basis for heat desensitization of TRPV1 ion channels.

The transient receptor potential vanilloid 1 (TRPV1) ion channel is a prototypical molecular sensor for noxious heat in mammals. Its role in sustained heat response remains poorly understood, because rapid heat-induced desensitization (Dh) follows tightly heat-induced activation (Ah). To understand the physiological role and structural basis of Dh, we carried out a comparative study of TRPV1 channels in mouse (mV1) and those in platypus (pV1), which naturally lacks Dh. Here we show that a temperature-sensitive interaction between the N- and C-terminal domains of mV1 but not pV1 drives a conformational rearrangement in the pore leading to Dh. We further show that knock-in mice expressing pV1 sensed heat normally but suffered scald damages in a hot environment. Our findings suggest that Dh evolved late during evolution as a protective mechanism and a delicate balance between Ah and Dh is crucial for mammals to sense and respond to noxious heat

Inequalities for Permanents and Permanental Minors of Row Substochastic Matrices

In this paper, some inequalities for permanents and permanental minors of row substochastic matrices are proved. The convexity of the permanent function on the interval between the identity matrix and an arbitrary row substochastic matrix is also proved. In addition, a conjecture about the permanent and permanental minors of square row substochastic matrices with fixed row and column sums is formulated