AbstractWeak supervision has shown promising results in many natural language processing tasks, such as Named Entity Recognition (NER). Existing work mainly focuses on learning deep NER models only with weak supervision, i.e., without any human annotation, and shows that by merely using weakly labeled data, one can achieve good performance, though still underperforms fully supervised NER with manually/strongly labeled data. In this paper, we consider a more practical scenario, where we have both a small amount of strongly labeled data and a large amount of weakly labeled data. Unfortunately, we observe that weakly labeled data does not necessarily improve, or even deteriorate the model performance (due to the extensive noise in the weak labels) when we train deep NER models over a simple or weighted combination of the strongly labeled and weakly labeled data. To address this issue, we propose a new multi-stage computational framework – NEEDLE with three essential ingredients: (1) weak label completion, (2) noise-aware loss function, and (3) final fine-tuning over the strongly labeled data. Through experiments on E-commerce query NER and Biomedical NER, we demonstrate that NEEDLE can effectively suppress the noise of the weak labels and outperforms existing methods. In particular, we achieve new SOTA F1-scores on 3 Biomedical NER datasets: BC5CDR-chem 93.74, BC5CDR-disease 90.69, NCBI-disease 92.28.