Christoph Angerer

Suraj Kothawade, Donna Roy, Michele Fenzi et al.

Retrieving images with objects that are semantically similar to objects of interest (OOI) in a query image has many practical use cases. A few examples include fixing failures like false negatives/positives of a learned model or mitigating class imbalance in a dataset. The targeted selection task requires finding the relevant data from a large-scale pool of unlabeled data. Manual mining at this scale is infeasible. Further, the OOI are often small and occupy less than 1% of image area, are occluded, and co-exist with many semantically different objects in cluttered scenes. Existing semantic image retrieval methods often focus on mining for larger sized geographical landmarks, and/or require extra labeled data, such as images/image-pairs with similar objects, for mining images with generic objects. We propose a fast and robust template matching algorithm in the DNN feature space, that retrieves semantically similar images at the object-level from a large unlabeled pool of data. We project the region(s) around the OOI in the query image to the DNN feature space for use as the template. This enables our method to focus on the semantics of the OOI without requiring extra labeled data. In the context of autonomous driving, we evaluate our system for targeted selection by using failure cases of object detectors as OOI. We demonstrate its efficacy on a large unlabeled dataset with 2.2M images and show high recall in mining for images with small-sized OOI. We compare our method against a well-known semantic image retrieval method, which also does not require extra labeled data. Lastly, we show that our method is flexible and retrieves images with one or more semantically different co-occurring OOI seamlessly.

Ahmed Elnaggar, Wei Ding, Llion Jones et al.

Currently, a growing number of mature natural language processing applications make people's life more convenient. Such applications are built by source code - the language in software engineering. However, the applications for understanding source code language to ease the software engineering process are under-researched. Simultaneously, the transformer model, especially its combination with transfer learning, has been proven to be a powerful technique for natural language processing tasks. These breakthroughs point out a promising direction for process source code and crack software engineering tasks. This paper describes CodeTrans - an encoder-decoder transformer model for tasks in the software engineering domain, that explores the effectiveness of encoder-decoder transformer models for six software engineering tasks, including thirteen sub-tasks. Moreover, we have investigated the effect of different training strategies, including single-task learning, transfer learning, multi-task learning, and multi-task learning with fine-tuning. CodeTrans outperforms the state-of-the-art models on all the tasks. To expedite future works in the software engineering domain, we have published our pre-trained models of CodeTrans. https://github.com/agemagician/CodeTrans

Ahmed Elnaggar, Michael Heinzinger, Christian Dallago et al.

Computational biology and bioinformatics provide vast data gold-mines from protein sequences, ideal for Language Models taken from NLP. These LMs reach for new prediction frontiers at low inference costs. Here, we trained two auto-regressive models (Transformer-XL, XLNet) and four auto-encoder models (BERT, Albert, Electra, T5) on data from UniRef and BFD containing up to 393 billion amino acids. The LMs were trained on the Summit supercomputer using 5616 GPUs and TPU Pod up-to 1024 cores. Dimensionality reduction revealed that the raw protein LM-embeddings from unlabeled data captured some biophysical features of protein sequences. We validated the advantage of using the embeddings as exclusive input for several subsequent tasks. The first was a per-residue prediction of protein secondary structure (3-state accuracy Q3=81%-87%); the second were per-protein predictions of protein sub-cellular localization (ten-state accuracy: Q10=81%) and membrane vs. water-soluble (2-state accuracy Q2=91%). For the per-residue predictions the transfer of the most informative embeddings (ProtT5) for the first time outperformed the state-of-the-art without using evolutionary information thereby bypassing expensive database searches. Taken together, the results implied that protein LMs learned some of the grammar of the language of life. To facilitate future work, we released our models at https://github.com/agemagician/ProtTrans.