Anfinsen Goes Neural: a Graphical Model for Conditional Antibody Design

Antibody design plays a pivotal role in advancing therapeutics. Although deep learning has made rapid progress in this field, existing methods make limited use of general protein knowledge and assume a graphical model (GM) that violates empirical findings on proteins. To address these limitations, we present Anfinsen Goes Neural (AGN), a graphical model that uses a pre-trained protein language model (pLM) and encodes a seminal finding on proteins called Anfinsen's dogma. Our framework follows a two-step process of sequence generation with pLM and structure prediction with graph neural network (GNN). Experiments show that our approach outperforms state-of-the-art results on benchmark experiments. We also address a critical limitation of non-autoregressive models -- namely, that they tend to generate unrealistic sequences with overly repeating tokens. To resolve this, we introduce a composition-based regularization term to the cross-entropy objective that allows an efficient trade-off between high performance and low token repetition. We demonstrate that our approach establishes a Pareto frontier over the current state-of-the-art. Our code is available at https://github.com/lkny123/AGN.

STANCE-C3: Domain-adaptive Cross-target Stance Detection via Contrastive Learning and Counterfactual Generation

Stance detection is the process of inferring a person's position or standpoint on a specific issue to deduce prevailing perceptions toward topics of general or controversial interest, such as health policies during the COVID-19 pandemic. Existing models for stance detection are trained to perform well for a single domain (e.g., COVID-19) and a specific target topic (e.g., masking protocols), but are generally ineffectual in other domains or targets due to distributional shifts in the data. However, constructing high-performing, domain-specific stance detection models requires an extensive corpus of labeled data relevant to the targeted domain, yet such datasets are not readily available. This poses a challenge as the process of annotating data is costly and time-consuming. To address these challenges, we introduce a novel stance detection model coined domain-adaptive Cross-target STANCE detection via Contrastive learning and Counterfactual generation (STANCE-C3) that uses counterfactual data augmentation to enhance domain-adaptive training by enriching the target domain dataset during the training process and requiring significantly less information from the new domain. We also propose a modified self-supervised contrastive learning as a component of STANCE-C3 to prevent overfitting for the existing domain and target and enable cross-target stance detection. Through experiments on various datasets, we show that STANCE-C3 shows performance improvement over existing state-of-the-art methods.

Debiasing Word Embeddings with Nonlinear Geometry

Debiasing word embeddings has been largely limited to individual and independent social categories. However, real-world corpora typically present multiple social categories that possibly correlate or intersect with each other. For instance, "hair weaves" is stereotypically associated with African American females, but neither African American nor females alone. Therefore, this work studies biases associated with multiple social categories: joint biases induced by the union of different categories and intersectional biases that do not overlap with the biases of the constituent categories. We first empirically observe that individual biases intersect non-trivially (i.e., over a one-dimensional subspace). Drawing from the intersectional theory in social science and the linguistic theory, we then construct an intersectional subspace to debias for multiple social categories using the nonlinear geometry of individual biases. Empirical evaluations corroborate the efficacy of our approach. Data and implementation code can be downloaded at https://github.com/GitHubLuCheng/Implementation-of-JoSEC-COLING-22.