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Large Transformers pretrained over clinical notes from Electronic Health Records (EHR) have afforded substantial gains in performance on predictive clinical tasks. The cost of training such models (and the necessity of data access to do so) coupled with their utility motivates parameter sharing, i.e., the release of pretrained models such as ClinicalBERT. While most efforts have used deidentified EHR, many researchers have access to large sets of sensitive, non-deidentified EHR with which they might train a BERT model (or similar). Would it be safe to release the weights of such a model if they did? In this work, we design a battery of approaches intended to recover Personal Health Information (PHI) from a trained BERT. Specifically, we attempt to recover patient names and conditions with which they are associated. We find that simple probing methods are not able to meaningfully extract sensitive information from BERT trained over the MIMIC-III corpus of EHR. However, more sophisticated &quot;attacks&quot; may succeed in doing so: To facilitate such research, we make our experimental setup and baseline probing models available at this link: https://github.com/elehman16/exposing_patient_data_release.

NAACL 2021

Does BERT Pretrained on Clinical Notes Reveal Sensitive Data?

2021 Annual Conference of the North American Chapter of the Association for Computational Linguistics.

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Large Transformers pretrained over clinical notes from Electronic Health Records (EHR) have afforded substantial gains in performance on predictive clinical tasks. The cost of training such models (and the necessity of data access to do so) coupled with their utility motivates parameter sharing, i.e., the release of pretrained models such as ClinicalBERT. While most efforts have used deidentified EHR, many researchers have access to large sets of sensitive, non-deidentified EHR with which they might train a BERT model (or similar). Would it be safe to release the weights of such a model if they did? In this work, we design a battery of approaches intended to recover Personal Health Information (PHI) from a trained BERT. Specifically, we attempt to recover patient names and conditions with which they are associated. We find that simple probing methods are not able to meaningfully extract sensitive information from BERT trained over the MIMIC-III corpus of EHR. However, more sophisticated "attacks" may succeed in doing so: To facilitate such research, we make our experimental setup and baseline probing models available at this link: https://github.com/elehman16/exposing_patient_data_release.

technical paper

We present the first study on using large-scale pre-trained language models for automated generation of an event-level temporal graph for a document. Despite the huge success of neural pre-training methods in NLP tasks, its potential for temporal reasoning over event graphs has not been sufficiently explored. Part of the reason is the difficulty in obtaining large training corpora with human-annotated events and temporal links. We address this challenge by using existing IE/NLP tools to automatically generate a large quantity (89,000) of system-produced document-graph pairs, and propose a novel formulation of the contextualized graph generation problem as a sequence-to-sequence mapping task. These strategies enable us to leverage and fine-tune pre-trained language models on the system-induced training data for the graph generation task. Our experiments show that our approach is highly effective in generating structurally and semantically valid graphs. Further, evaluation on a challenging hand-labeled, out-of-domain corpus shows that our method outperforms the closest existing method by a large margin on several metrics.

Neural Language Modeling for Contextualized Temporal Graph Generation

Knowledge bases often consist of facts that are harvested from a variety of sources, many of which are noisy and some of which conflict, resulting in a level of uncertainty for each triple. Knowledge bases are also often incomplete, prompting the use of embedding methods to generalize from known facts, however existing embedding methods only model triple-level uncertainty, and reasoning results lack global consistency. To address these shortcomings, we propose BEUrRE, a novel uncertain knowledge graph embedding method with calibrated probabilistic semantics. BEUrRE models each entity as a box (i.e. axis-aligned hyperrectangle) and relations between two entities as affine transformations on the head and tail entity boxes. The geometry of the boxes allows for efficient calculation of intersections and volumes, endowing the model with calibrated probabilistic semantics and facilitating the incorporation of relational constraints. Extensive experiments on two benchmark datasets show that BEUrRE consistently outperforms baselines on confidence prediction and fact ranking due to its probabilistic calibration and ability to capture high-order dependencies among facts.

Probabilistic Box Embeddings for Uncertain Knowledge Graph Reasoning

Event extraction has long been treated as a sentence-level task in the IE community. We argue that this setting does not match human information-seeking behavior and leads to incomplete and uninformative extraction results.

Document-Level Event Argument Extraction by Conditional Generation

In entity linking, mentions of named entities in raw text are disambiguated against a knowledge base (KB). This work focuses on linking to unseen KBs that do not have training data and whose schema is unknown during training. Our approach relies on methods to flexibly convert entities with several attribute-value pairs from arbitrary KBs into flat strings, which we use in conjunction with state-of-the-art models for zero-shot linking. We further improve the generalization of our model using two regularization schemes based on shuffling of entity attributes and handling of unseen attributes. Experiments on English datasets where models are trained on the CoNLL dataset, and tested on the TAC-KBP 2010 dataset show that our models are 12% (absolute) more accurate than baseline models that simply flatten entities from the target KB. Unlike prior work, our approach also allows for seamlessly combining multiple training datasets. We test this ability by adding both a completely different dataset (Wikia), as well as increasing amount of training data from the TAC-KBP 2010 training set. Our models are more accurate across the board compared to baselines.

Linking Entities to Unseen Knowledge Bases with Arbitrary Schemas

State-of-the-art deep neural networks require large-scale labeled training data that is often expensive to obtain or not available for many tasks. Weak supervision in the form of domain-specific rules has been shown to be useful in such settings to automatically generate weakly labeled training data. However, learning with weak rules is challenging due to their inherent heuristic and noisy nature. An additional challenge is rule coverage and overlap, where prior work on weak supervision only considers instances that are covered by weak rules, thus leaving valuable unlabeled data behind.

Self-Training with Weak Supervision

Understanding and executing natural language instructions in a grounded domain is one of the hallmarks of artificial intelligence. In this paper, we focus on instruction understanding in the blocks world domain and investigate the language understanding abilities of two top-performing systems for this task. We aim to understand if the test performance of these models indicates an understanding of the spatial domain and of the natural language instructions relative to it, or whether they merely overfit spurious signals in the data-set. We formulate a set of expectations one might have from an instruction following model and concretely characterize the different dimensions of robustness such a model should possess. Despite decent test performance, we find that state-of-the-art models fall short of these expectations and are extremely brittle. We then propose a learning strategy that involves data augmentation and show through extensive experiments that the proposed learning strategy yields models that are competitive on the original test set while satisfying our expectations much better.

Generalization in Instruction Following Systems

Multi-layer multi-head self-attention mechanism is widely applied in modern neural language models. Attention redundancy has been observed among attention heads but has not been deeply studied in the literature. Using BERT-base model as an example, this paper provides a comprehensive study on attention redundancy which is helpful for model interpretation and model compression. We analyze the attention redundancy with Five-Ws and How. (What) We define and focus the study on redundancy matrices generated from pre-trained and fine-tuned BERT-base model for GLUE datasets. (How) We use both token-based and sentence-based distance functions to measure the redundancy. (Where) Clear and similar redundancy patterns (cluster structure) are observed among attention heads. (When) Redundancy patterns are similar in both pre-training and fine-tuning phases. (Who) We discover that redundancy patterns are task-agnostic. Similar redundancy patterns even exist for randomly generated token sequences. (“Why”) We also evaluate influences of the pre-training dropout ratios on attention redundancy. Based on the phase-independent and task-agnostic attention redundancy patterns, we propose a simple zero-shot pruning method as a case study. Experiments on fine-tuning GLUE tasks verify its effectiveness. The comprehensive analyses on attention redundancy make model understanding and zero-shot model pruning promising.

On Attention Redundancy: A Comprehensive Study

Recent studies indicate that NLU models are prone to rely on shortcut features for prediction, without achieving true language understanding. As a result, these models fail to generalize to real-world out-of-distribution data. In this work, we show that the words in the NLU training set can be modeled as a long-tailed distribution. There are two findings: 1) NLU models have strong preference for features located at the head of the long-tailed distribution, and 2) Shortcut features are picked up during very early few iterations of the model training. These two observations are further employed to formulate a measurement which can quantify the shortcut degree of each training sample. Based on this shortcut measurement, we propose a shortcut mitigation framework LTGR, to suppress the model from making overconfident predictions for samples with large shortcut degree. Experimental results on three NLU benchmarks demonstrate that our long-tailed distribution explanation accurately reflects the shortcut learning behavior of NLU models. Experimental analysis further indicates that LTGR can improve the generalization accuracy on OOD data, while preserving the accuracy on in-distribution data.

Towards Interpreting and Mitigating Shortcut Learning Behavior of NLU models

The dominant approach in probing neural networks for linguistic properties is to train a new shallow multi-layer perceptron (MLP) on top of the model's internal representations. This approach can detect properties encoded in the model, but at the cost of adding new parameters that may learn the task directly. We instead propose a subtractive pruning-based probe, where we find an existing subnetwork that performs the linguistic task of interest. Compared to an MLP, the subnetwork probe achieves both higher accuracy on pre-trained models and lower accuracy on random models, so it is both better at finding properties of interest and worse at learning on its own. Next, by varying the complexity of each probe, we show that subnetwork probing Pareto-dominates MLP probing in that it achieves higher accuracy given any budget of probe complexity. Finally, we analyze the resulting subnetworks across various tasks to locate where each task is encoded, and we find that lower-level tasks are captured in lower layers, reproducing similar findings in past work.

Low-Complexity Probing via Finding Subnetworks

Widespread adoption of deep models has motivated a pressing need for approaches to interpret network outputs and to facilitate model debugging. Instance attribution methods constitute one means of accomplishing these goals by retrieving training instances that (may have) led to a particular prediction. Influence functions (IF; Koh and Liang 2017) provide machinery for doing this by quantifying the effect that perturbing individual train instances would have on a specific test prediction. However, even approximating the IF is computationally expensive, to the degree that may be prohibitive in many cases. Might simpler approaches (e.g., retrieving train examples most similar to a given test point) perform comparably? In this work, we evaluate the degree to which different potential instance attribution agree with respect to the importance of training samples. We find that simple retrieval methods yield training instances that differ from those identified via gradient-based methods (such as IFs), but that nonetheless exhibit desirable characteristics similar to more complex attribution methods. Code for all methods and experiments in this paper is available at: https://github.com/successar/instance_attributions_NLP.

Does BERT Pretrained on Clinical Notes Reveal Sensitive Data?

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Does BERT Pretrained on Clinical Notes Reveal Sensitive Data?

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Next from NAACL 2021

Neural Language Modeling for Contextualized Temporal Graph Generation

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ReinforceBug: A Framework to Generate Adversarial Textual Examples

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