Dominican Republic

We propose a new task, Text2Mol, to retrieve molecules using natural language descriptions as queries. Natural language and molecules encode information in very different ways, which leads to the exciting but challenging problem of integrating these two very different modalities. Although some work has been done on text-based retrieval and structure-based retrieval, this new task requires integrating molecules and natural language more directly. Moreover, this can be viewed as an especially challenging cross-lingual retrieval problem by considering the molecules as a language with a very unique grammar. We construct a paired dataset of molecules and their corresponding text descriptions, which we use to learn an aligned common semantic embedding space for retrieval. We extend this to create a cross-modal attention-based model for explainability and reranking by interpreting the attentions as association rules. We also employ an ensemble approach to integrate our different architectures, which significantly improves results from 0.372 to 0.499 MRR. This new multimodal approach opens a new perspective on solving problems in chemistry literature understanding and molecular machine learning.

EMNLP 2021

Text2Mol: Cross-Modal Molecule Retrieval with Natural Language Queries

EMNLP 2021 is planned to be a hybrid event in Punta Cana, Dominican Republic, with both on-site and fully virtual participation possible. The experience for on-site participants would closely approximate a normal pre-COVID *ACL conference, with 5-6 thematically organized parallel sessions and live Q/A and interactive discussion immediately after the talks. Presentations by virtual participants will be equitably interleaved with those of on-site participants, projected on the auditorium screens as if on-site, and also followed immediately by live Q/A and interactive discussion at a time during reasonable waking hours for the virtual presenter. For all participants, on-site and virtual, who are unable to attend a session due to either time-zone issues or because they are participating in another session live, talk recordings and slides will be available online at a minimum after the live presentation (and in many cases before as well), and questions may be submitted in advance on session-specific discussion boards and answered live in session with the usual visual aids if desired.

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EMNLP 2021 is planned to be a hybrid event in Punta Cana, Dominican Republic, with both on-site and fully virtual participation possible.

poster

Existing text classification methods mainly focus on a fixed label set, whereas many real-world applications require extending to new fine-grained classes as the number of samples per label increases. To accommodate such requirements, we introduce a new problem called coarse-to-fine grained classification, which aims to perform fine-grained classification on coarsely annotated data. Instead of asking for new fine-grained human annotations, we opt to leverage label surface names as the only human guidance and weave in rich pre-trained generative language models into the iterative weak supervision strategy. Specifically, we first propose a label-conditioned finetuning formulation to attune these generators for our task. Furthermore, we devise a regularization objective based on the coarse-fine label constraints derived from our problem setting, giving us even further improvements over the prior formulation. Our framework uses the fine-tuned generative models to sample pseudo-training data for training the classifier, and bootstraps on real unlabeled data for model refinement. Extensive experiments and case studies on two real-world datasets demonstrate superior performance over SOTA zero-shot classification baselines.

Coarse2Fine: Fine-grained Text Classification on Coarsely-grained Annotated Data

While there exist scores of natural languages, each with its unique features and idiosyncrasies, they all share a unifying theme: enabling human communication. We may thus reasonably predict that human cognition shapes how these languages evolve and are used. Assuming that the capacity to process information is roughly constant across human populations, we expect a surprisal--duration trade-off to arise both across and within languages. We analyse this trade-off using a corpus of 600 languages and, after controlling for several potential confounds, we find strong supporting evidence in both settings. Specifically, we find that, on average, phones are produced faster in languages where they are less surprising, and vice versa. Further, we confirm that more surprising phones are longer, on average, in 319 languages out of the 600. We thus conclude that there is strong evidence of a surprisal--duration trade-off in operation, both across and within the world's languages.

A surprisal--duration trade-off across and within the world's languages

The uniform information density (UID) hypothesis posits a preference among language users for utterances structured such that information is distributed uniformly across a signal. While its implications on language production have been well explored, the hypothesis potentially makes predictions about language comprehension and linguistic acceptability as well. Further, it is unclear how uniformity in a linguistic signal—or lack thereof—should be measured, and over which linguistic unit, e.g., the sentence or language level, this uniformity should hold. Here we investigate these facets of the UID hypothesis using reading time and acceptability data. While our reading time results are generally consistent with previous work, they are also consistent with a weakly super-linear effect of surprisal, which would be compatible with UID’s predictions. For acceptability judgments, we find clearer evidence that non-uniformity in information density is predictive of lower acceptability. We then explore multiple operationalizations of UID, motivated by different interpretations of the original hypothesis, and analyze the scope over which the pressure towards uniformity is exerted. The explanatory power of a subset of the proposed operationalizations suggests that the strongest trend may be a regression towards a mean surprisal across the language, rather than the phrase, sentence, or document—a finding that supports a typical interpretation of UID, namely that it is the byproduct of language users maximizing the use of a (hypothetical) communication channel.

Revisiting the Uniform Information Density Hypothesis

Large-scale document retrieval systems often utilize two styles of neural network models which live at two different ends of the joint computation vs. accuracy spectrum. The first style is dual encoder (or two-tower) models, where the query and document representations are computed completely independently and combined with a simple dot product operation. The second style is cross-attention models, where the query and document features are concatenated in the input layer and all computation is based on the joint query-document representation. Dual encoder models are typically used for retrieval and deep re-ranking, while cross-attention models are typically used for shallow re-ranking. In this paper, we present a lightweight architecture that explores this joint cost vs. accuracy trade-off based on multi-vector attention (MVA). We thoroughly evaluate our method on the MS-MARCO passage retrieval dataset and show how to efficiently trade off retrieval accuracy with joint computation and offline document storage cost. We show that a highly compressed document representation and inexpensive joint computation can be achieved through a combination of learned pooling tokens and aggressive downprojection. Our code and model checkpoints are available on GitHub.

Multi-Vector Attention Models for Deep Re-ranking

Taxonomies of writing systems since Gelb (1952) have classified systems based on what the written symbols represent: if they represent words or morphemes, they are logographic; if syllables, syllabic; if segments, alphabetic; etc. Sproat (2000) and Rogers (2005) broke with tradition by splitting the logographic and phonographic aspects into two dimensions, with logography being graded rather than a categorical distinction. A system could be syllabic, and highly logographic; or alphabetic, and mostly non-logographic. This accords better with how writing systems actually work, but neither author proposed a method for measuring logography.
In this paper we propose a novel measure of the degree of logography that uses an attention- based sequence-to-sequence model trained to predict the spelling of a token from its pronun- ciation in context. In an ideal phonographic system, the model should need to attend to only the current token in order to compute how to spell it, and this would show in the attention matrix activations. In contrast, with a logographic system, where a given pronunciation might correspond to several different spellings, the model would need to attend to a broader context. The ratio of the activation outside the token and the total activation forms the basis of our measure. We compare this with a simple lexical measure, and an entropic measure, as well as several other neural models, and argue that on balance our attention-based measure accords best with intuition about how logographic various systems are.
Our work provides the first quantifiable measure of the notion of logography that accords with linguistic intuition and, we argue, provides better insight into what this notion means.

The Taxonomy of Writing Systems: How to Measure how Logographic a System is

We use large-scale corpora in six different gendered languages, along with tools from NLP and information theory, to test whether there is a relationship between the grammatical genders of inanimate nouns and the adjectives used to describe those nouns. For all six languages, we find that there is a statistically significant relationship. We also find that there are statistically significant relationships between the grammatical genders of inanimate nouns and the verbs that take those nouns as direct objects, as indirect objects, and as subjects. We defer deeper investigation of these relationships for future work.

On the Relationships Between the Grammatical Genders of Inanimate Nouns and Their Co-Occurring Adjectives and Verbs

Pre-trained Transformer language models~(LM) have become go-to text representation encoders. Prior research fine-tunes deep LMs to encode text sequences such as sentences and passages into single dense vector representations for efficient text comparison and retrieval. However, dense encoders require a lot of data and sophisticated techniques to effectively train and suffer in low data situations. This paper finds a key reason is that standard LMs' internal attention structure is not ready-to-use for dense encoders, which needs to aggregate text information into the dense representation. We propose to pre-train towards dense encoder with a novel Transformer architecture, Condenser, where LM prediction CONditions on DENSE Representation. Our experiments show Condenser improves over standard LM by large margins on various text retrieval and similarity tasks.

Condenser: a Pre-training Architecture for Dense Retrieval

With tightened restrictions in hospital settings, COVID-19 has greatly impacted expecting parents, newborns, and their families. However, no existing work has used natural language processing techniques to analyze impacts of COVID-19 from long-form text written by new parents explicitly describing their birthing experiences. This work investigates whether, and if so how, birthing narratives written by new parents on Reddit changed during COVID-19. To this aim, 4,484 Reddit posts about birthing experiences were analyzed using computational methods including persona analysis and LDA topic modeling. The results of this research indicate that, compared to their frequencies before COVID-19, the presence of partners significantly increased and that of other family members significantly decreased in the narratives during COVID-19. In addition, themes related to induced labor significantly increased in the narratives during COVID-19. This work presents a case study in how patient experience can be analyzed from their own written narratives and perspectives.

Discovering changes in birthing narratives during COVID-19

We explore transfer learning to improve optical character recognition (OCR) post-correction, specifically for endangered language texts. We extend an existing OCR post-correction model (Rijhwani et al., 2020) by introducing an additional pretraining step on related data, such as text in a related language or available target endangered language datasets that may differ in orthography. Although cross-lingual transfer is often successful in high-resource settings, our preliminary results show that transferring from related language data decreases performance for this task. On the other hand, we observe small improvements in performance when transferring from additional target language data.

Explorations in Transfer Learning for OCR Post-Correction

We present, to our knowledge, the first ever published morphological analyser and generator for Sakha, a marginalised language of Siberia. The transducer has coverage of almost 90%, and high precision. In the development of the analyser, we have expanded linguistic knowledge about Sakha, and developed strategies for complex grammatical patterns. The transducer is already being used in downstream tasks, including computer assisted language learning applications for linguistic maintenance and computational linguistic shared tasks.

Text2Mol: Cross-Modal Molecule Retrieval with Natural Language Queries

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Coarse2Fine: Fine-grained Text Classification on Coarsely-grained Annotated Data

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