Nathan Ng

Nathan Ng, Ji Won Park, Jae Hyeon Lee et al.

Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate multiple subreads, or noisy observations of the same sequence. Denoising these subreads with alignment-based approaches often fails when too few subreads are available or error rates are too high. In this paper, we propose a novel method for blindly denoising sets of sequences without directly observing clean source sequence labels. Our method, Self-Supervised Set Learning (SSSL), gathers subreads together in an embedding space and estimates a single set embedding as the midpoint of the subreads in both the latent and sequence spaces. This set embedding represents the "average" of the subreads and can be decoded into a prediction of the clean sequence. In experiments on simulated long-read DNA data, SSSL methods denoise small reads of $\leq 6$ subreads with 17% fewer errors and large reads of $>6$ subreads with 8% fewer errors compared to the best baseline. On a real dataset of antibody sequences, SSSL improves over baselines on two self-supervised metrics, with a significant improvement on difficult small reads that comprise over 60% of the test set. By accurately denoising these reads, SSSL promises to better realize the potential of high-throughput DNA sequencing data for downstream scientific applications.

Myle Ott, Sergey Edunov, Alexei Baevski et al.

fairseq is an open-source sequence modeling toolkit that allows researchers and developers to train custom models for translation, summarization, language modeling, and other text generation tasks. The toolkit is based on PyTorch and supports distributed training across multiple GPUs and machines. We also support fast mixed-precision training and inference on modern GPUs. A demo video can be found at https://www.youtube.com/watch?v=OtgDdWtHvto

Kyle O'Brien, Nathan Ng, Isha Puri et al. · harvard

Machine learning models for text classification often excel on in-distribution (ID) data but struggle with unseen out-of-distribution (OOD) inputs. Most techniques for improving OOD robustness are not applicable to settings where the model is effectively a black box, such as when the weights are frozen, retraining is costly, or the model is leveraged via an API. Test-time augmentation (TTA) is a simple post-hoc technique for improving robustness that sidesteps black-box constraints by aggregating predictions across multiple augmentations of the test input. TTA has seen limited use in NLP due to the challenge of generating effective natural language augmentations. In this work, we propose LLM-TTA, which uses LLM-generated augmentations as TTA's augmentation function. LLM-TTA outperforms conventional augmentation functions across sentiment, toxicity, and news classification tasks for BERT and T5 models, with BERT's OOD robustness improving by an average of 4.48 percentage points without regressing average ID performance. We explore selectively augmenting inputs based on prediction entropy to reduce the rate of expensive LLM augmentations, allowing us to maintain performance gains while reducing the average number of generated augmentations by 57.74\%. LLM-TTA is agnostic to the task model architecture, does not require OOD labels, and is effective across low and high-resource settings. We share our data, models, and code for reproducibility.

Nathan Ng, Marzyeh Ghassemi, Narendran Thangarajan et al.

Building user trust in dialogue agents requires smooth and consistent dialogue exchanges. However, agents can easily lose conversational context and generate irrelevant utterances. These situations are called dialogue breakdown, where agent utterances prevent users from continuing the conversation. Building systems to detect dialogue breakdown allows agents to recover appropriately or avoid breakdown entirely. In this paper we investigate the use of semi-supervised learning methods to improve dialogue breakdown detection, including continued pre-training on the Reddit dataset and a manifold-based data augmentation method. We demonstrate the effectiveness of these methods on the Dialogue Breakdown Detection Challenge (DBDC) English shared task. Our submissions to the 2020 DBDC5 shared task place first, beating baselines and other submissions by over 12\% accuracy. In ablations on DBDC4 data from 2019, our semi-supervised learning methods improve the performance of a baseline BERT model by 2\% accuracy. These methods are applicable generally to any dialogue task and provide a simple way to improve model performance.

Nathan Ng, Kyunghyun Cho, Marzyeh Ghassemi

Models that perform well on a training domain often fail to generalize to out-of-domain (OOD) examples. Data augmentation is a common method used to prevent overfitting and improve OOD generalization. However, in natural language, it is difficult to generate new examples that stay on the underlying data manifold. We introduce SSMBA, a data augmentation method for generating synthetic training examples by using a pair of corruption and reconstruction functions to move randomly on a data manifold. We investigate the use of SSMBA in the natural language domain, leveraging the manifold assumption to reconstruct corrupted text with masked language models. In experiments on robustness benchmarks across 3 tasks and 9 datasets, SSMBA consistently outperforms existing data augmentation methods and baseline models on both in-domain and OOD data, achieving gains of 0.8% accuracy on OOD Amazon reviews, 1.8% accuracy on OOD MNLI, and 1.4 BLEU on in-domain IWSLT14 German-English.

Tingfung Lau, Nathan Ng, Julian Gingold et al.

To optimize clinical outcomes, fertility clinics must strategically select which embryos to transfer. Common selection heuristics are formulas expressed in terms of the durations required to reach various developmental milestones, quantities historically annotated manually by experienced embryologists based on time-lapse EmbryoScope videos. We propose a new method for automatic embryo staging that exploits several sources of structure in this time-lapse data. First, noting that in each image the embryo occupies a small subregion, we jointly train a region proposal network with the downstream classifier to isolate the embryo. Notably, because we lack ground-truth bounding boxes, our we weakly supervise the region proposal network optimizing its parameters via reinforcement learning to improve the downstream classifier's loss. Moreover, noting that embryos reaching the blastocyst stage progress monotonically through earlier stages, we develop a dynamic-programming-based decoder that post-processes our predictions to select the most likely monotonic sequence of developmental stages. Our methods outperform vanilla residual networks and rival the best numbers in contemporary papers, as measured by both per-frame accuracy and transition prediction error, despite operating on smaller data than many.

Nathan Ng, Rodney A Gabriel, Julian McAuley et al.

Scheduling surgeries is a challenging task due to the fundamental uncertainty of the clinical environment, as well as the risks and costs associated with under- and over-booking. We investigate neural regression algorithms to estimate the parameters of surgery case durations, focusing on the issue of heteroscedasticity. We seek to simultaneously estimate the duration of each surgery, as well as a surgery-specific notion of our uncertainty about its duration. Estimating this uncertainty can lead to more nuanced and effective scheduling strategies, as we are able to schedule surgeries more efficiently while allowing an informed and case-specific margin of error. Using surgery records %from the UC San Diego Health System, from a large United States health system we demonstrate potential improvements on the order of 20% (in terms of minutes overbooked) compared to current scheduling techniques. Moreover, we demonstrate that surgery durations are indeed heteroscedastic. We show that models that estimate case-specific uncertainty better fit the data (log likelihood). Additionally, we show that the heteroscedastic predictions can more optimally trade off between over and under-booking minutes, especially when idle minutes and scheduling collisions confer disparate costs.