Analyzing and Improving Representations with the Soft Nearest Neighbor Loss

We explore and expand the $\textit{Soft Nearest Neighbor Loss}$ to measure the $\textit{entanglement}$ of class manifolds in representation space: i.e., how close pairs of points from the same class are relative to pairs of points from different classes. We demonstrate several use cases of the loss. As an analytical tool, it provides insights into the evolution of class similarity structures during learning. Surprisingly, we find that $\textit{maximizing}$ the entanglement of representations of different classes in the hidden layers is beneficial for discrimination in the final layer, possibly because it encourages representations to identify class-independent similarity structures. Maximizing the soft nearest neighbor loss in the hidden layers leads not only to improved generalization but also to better-calibrated estimates of uncertainty on outlier data. Data that is not from the training distribution can be recognized by observing that in the hidden layers, it has fewer than the normal number of neighbors from the predicted class

Karyopherin binding interactions and nuclear import mechanism of nuclear pore complex protein Tpr

<p>Abstract</p> <p>Background</p> <p>Tpr is a large protein with an extended coiled-coil domain that is localized within the nuclear basket of the nuclear pore complex. Previous studies <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> involving antibody microinjection into mammalian cells suggested a role for Tpr in nuclear export of proteins via the CRM1 export receptor. In addition, Tpr was found to co-immunoprecipitate with importins α and β from <it>Xenopus laevis </it>egg extracts <abbrgrp><abbr bid="B2">2</abbr></abbrgrp>, although the function of this is unresolved. Yeast Mlp1p and Mlp2p, which are homologous to vertebrate Tpr, have been implicated in mRNA surveillance to retain unspliced mRNAs in the nucleus<abbrgrp><abbr bid="B3">3</abbr><abbr bid="B4">4</abbr></abbrgrp>. To augment an understanding of the role of Tpr in nucleocytoplasmic trafficking, we explored the interactions of recombinant Tpr with the karyopherins CRM1, importin β and importin α by solid phase binding assays. We also investigated the conditions required for nuclear import of Tpr using an <it>in vitro </it>assay.</p> <p>Results</p> <p>We found that Tpr binds strongly and specifically to importin α, importin β, and a CRM1 containing trimeric export complex, and that the binding sites for importins α and β are distinct. We also determined that the nuclear import of Tpr is dependent on cytosolic factors and energy and is efficiently mediated by the importin α/β import pathway.</p> <p>Conclusion</p> <p>Based on the binding and nuclear import assays, we propose that Tpr is imported into the nucleus by the importin α/β heterodimer. In addition, we suggest that Tpr can serve as a nucleoporin binding site for importin β during import of importin β cargo complexes and/or importin β recycling. Our finding that Tpr bound preferentially to CRM1 in an export complex strengthens the notion that Tpr is involved in protein export.</p