AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences (peptides) responsible for observed spectra, challenges persist in \emph{de novo} peptide sequencing. Firstly, prior methods struggle to identify amino acids with post-translational modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in decreased peptide-level identification precision. Secondly, diverse types of noise and missing peaks in mass spectra reduce the reliability of training data (peptide-spectrum matches, PSMs). To address these challenges, we propose AdaNovo, a novel framework that calculates conditional mutual information (CMI) between the spectrum and each amino acid/peptide, using CMI for adaptive model training. Extensive experiments demonstrate AdaNovo's state-of-the-art performance on a 9-species benchmark, where the peptides in the training set are almost completely disjoint from the peptides of the test sets. Moreover, AdaNovo excels in identifying amino acids with PTMs and exhibits robustness against data noise. The supplementary materials contain the official code.

kNN-BOX: A Unified Framework for Nearest Neighbor Generation

Augmenting the base neural model with a token-level symbolic datastore is a novel generation paradigm and has achieved promising results in machine translation (MT). In this paper, we introduce a unified framework kNN-BOX, which enables quick development and interactive analysis for this novel paradigm. kNN-BOX decomposes the datastore-augmentation approach into three modules: datastore, retriever and combiner, thus putting diverse kNN generation methods into a unified way. Currently, kNN-BOX has provided implementation of seven popular kNN-MT variants, covering research from performance enhancement to efficiency optimization. It is easy for users to reproduce these existing works or customize their own models. Besides, users can interact with their kNN generation systems with kNN-BOX to better understand the underlying inference process in a visualized way. In the experiment section, we apply kNN-BOX for machine translation and three other seq2seq generation tasks, namely, text simplification, paraphrase generation and question generation. Experiment results show that augmenting the base neural model with kNN-BOX leads to a large performance improvement in all these tasks. The code and document of kNN-BOX is available at https://github.com/NJUNLP/knn-box.

Insights from an Industrial Collaborative Assembly Project: Lessons in Research and Collaboration

Significant progress in robotics reveals new opportunities to advance manufacturing. Next-generation industrial automation will require both integration of distinct robotic technologies and their application to challenging industrial environments. This paper presents lessons from a collaborative assembly project between three academic research groups and an industry partner. The goal of the project is to develop a flexible, safe, and productive manufacturing cell for sub-centimeter precision assembly. Solving this problem in a high-mix, low-volume production line motivates multiple research thrusts in robotics. This work identifies new directions in collaborative robotics for industrial applications and offers insight toward strengthening collaborations between institutions in academia and industry on the development of new technologies.