Scientific Large Language Models: A Survey on Biological & Chemical Domains

Large Language Models (LLMs) have emerged as a transformative power in enhancing natural language comprehension, representing a significant stride toward artificial general intelligence. The application of LLMs extends beyond conventional linguistic boundaries, encompassing specialized linguistic systems developed within various scientific disciplines. This growing interest has led to the advent of scientific LLMs, a novel subclass specifically engineered for facilitating scientific discovery. As a burgeoning area in the community of AI for Science, scientific LLMs warrant comprehensive exploration. However, a systematic and up-to-date survey introducing them is currently lacking. In this paper, we endeavor to methodically delineate the concept of "scientific language", whilst providing a thorough review of the latest advancements in scientific LLMs. Given the expansive realm of scientific disciplines, our analysis adopts a focused lens, concentrating on the biological and chemical domains. This includes an in-depth examination of LLMs for textual knowledge, small molecules, macromolecular proteins, genomic sequences, and their combinations, analyzing them in terms of model architectures, capabilities, datasets, and evaluation. Finally, we critically examine the prevailing challenges and point out promising research directions along with the advances of LLMs. By offering a comprehensive overview of technical developments in this field, this survey aspires to be an invaluable resource for researchers navigating the intricate landscape of scientific LLMs.

$E(2)$-Equivariant Vision Transformer

Vision Transformer (ViT) has achieved remarkable performance in computer vision. However, positional encoding in ViT makes it substantially difficult to learn the intrinsic equivariance in data. Initial attempts have been made on designing equivariant ViT but are proved defective in some cases in this paper. To address this issue, we design a Group Equivariant Vision Transformer (GE-ViT) via a novel, effective positional encoding operator. We prove that GE-ViT meets all the theoretical requirements of an equivariant neural network. Comprehensive experiments are conducted on standard benchmark datasets, demonstrating that GE-ViT significantly outperforms non-equivariant self-attention networks. The code is available at https://github.com/ZJUCDSYangKaifan/GEVit.

S2SNet: A Pretrained Neural Network for Superconductivity Discovery

Superconductivity allows electrical current to flow without any energy loss, and thus making solids superconducting is a grand goal of physics, material science, and electrical engineering. More than 16 Nobel Laureates have been awarded for their contribution to superconductivity research. Superconductors are valuable for sustainable development goals (SDGs), such as climate change mitigation, affordable and clean energy, industry, innovation and infrastructure, and so on. However, a unified physics theory explaining all superconductivity mechanism is still unknown. It is believed that superconductivity is microscopically due to not only molecular compositions but also the geometric crystal structure. Hence a new dataset, S2S, containing both crystal structures and superconducting critical temperature, is built upon SuperCon and Material Project. Based on this new dataset, we propose a novel model, S2SNet, which utilizes the attention mechanism for superconductivity prediction. To overcome the shortage of data, S2SNet is pre-trained on the whole Material Project dataset with Masked-Language Modeling (MLM). S2SNet makes a new state-of-the-art, with out-of-sample accuracy of 92% and Area Under Curve (AUC) of 0.92. To the best of our knowledge, S2SNet is the first work to predict superconductivity with only information of crystal structures. This work is beneficial to superconductivity discovery and further SDGs. Code and datasets are available in https://github.com/zjuKeLiu/S2SNet

Learning Universal User Representations via Self-Supervised Lifelong Behaviors Modeling

Universal user representation is an important research topic in industry, and is widely used in diverse downstream user analysis tasks, such as user profiling and user preference prediction. With the rapid development of Internet service platforms, extremely long user behavior sequences have been accumulated. However, existing researches have little ability to model universal user representation based on lifelong sequences of user behavior since registration. In this study, we propose a novel framework called Lifelong User Representation Model (LURM) to tackle this challenge. Specifically, LURM consists of two cascaded sub-models: (i) Bag of Interests (BoI) encodes user behaviors in any time period into a sparse vector with super-high dimension (e.g.,105); (ii) Self-supervised Multi-anchor EncoderNetwork (SMEN) maps sequences of BoI features to multiple low-dimensional user representations by contrastive learning. SMEN achieves almost lossless dimensionality reduction, benefiting from a novel multi-anchor module which can learn different aspects of user preferences. Experiments on several benchmark datasets show that our approach outperforms state-of-the-art unsupervised representation methods in downstream tasks

Interest-oriented Universal User Representation via Contrastive Learning

User representation is essential for providing high-quality commercial services in industry. Universal user representation has received many interests recently, with which we can be free from the cumbersome work of training a specific model for each downstream application. In this paper, we attempt to improve universal user representation from two points of views. First, a contrastive self-supervised learning paradigm is presented to guide the representation model training. It provides a unified framework that allows for long-term or short-term interest representation learning in a data-driven manner. Moreover, a novel multi-interest extraction module is presented. The module introduces an interest dictionary to capture principal interests of the given user, and then generate his/her interest-oriented representations via behavior aggregation. Experimental results demonstrate the effectiveness and applicability of the learned user representations.

AdaRNN: Adaptive Learning and Forecasting of Time Series

Time series has wide applications in the real world and is known to be difficult to forecast. Since its statistical properties change over time, its distribution also changes temporally, which will cause severe distribution shift problem to existing methods. However, it remains unexplored to model the time series in the distribution perspective. In this paper, we term this as Temporal Covariate Shift (TCS). This paper proposes Adaptive RNNs (AdaRNN) to tackle the TCS problem by building an adaptive model that generalizes well on the unseen test data. AdaRNN is sequentially composed of two novel algorithms. First, we propose Temporal Distribution Characterization to better characterize the distribution information in the TS. Second, we propose Temporal Distribution Matching to reduce the distribution mismatch in TS to learn the adaptive TS model. AdaRNN is a general framework with flexible distribution distances integrated. Experiments on human activity recognition, air quality prediction, and financial analysis show that AdaRNN outperforms the latest methods by a classification accuracy of 2.6% and significantly reduces the RMSE by 9.0%. We also show that the temporal distribution matching algorithm can be extended in Transformer structure to boost its performance.

Exploiting Adapters for Cross-lingual Low-resource Speech Recognition

Cross-lingual speech adaptation aims to solve the problem of leveraging multiple rich-resource languages to build models for a low-resource target language. Since the low-resource language has limited training data, speech recognition models can easily overfit. In this paper, we propose to use adapters to investigate the performance of multiple adapters for parameter-efficient cross-lingual speech adaptation. Based on our previous MetaAdapter that implicitly leverages adapters, we propose a novel algorithms called SimAdapter for explicitly learning knowledge from adapters. Our algorithm leverages adapters which can be easily integrated into the Transformer structure.MetaAdapter leverages meta-learning to transfer the general knowledge from training data to the test language. SimAdapter aims to learn the similarities between the source and target languages during fine-tuning using the adapters. We conduct extensive experiments on five-low-resource languages in Common Voice dataset. Results demonstrate that our MetaAdapter and SimAdapter methods can reduce WER by 2.98% and 2.55% with only 2.5% and 15.5% of trainable parameters compared to the strong full-model fine-tuning baseline. Moreover, we also show that these two novel algorithms can be integrated for better performance with up to 3.55% relative WER reduction.

Learning Invariant Representations across Domains and Tasks

Being expensive and time-consuming to collect massive COVID-19 image samples to train deep classification models, transfer learning is a promising approach by transferring knowledge from the abundant typical pneumonia datasets for COVID-19 image classification. However, negative transfer may deteriorate the performance due to the feature distribution divergence between two datasets and task semantic difference in diagnosing pneumonia and COVID-19 that rely on different characteristics. It is even more challenging when the target dataset has no labels available, i.e., unsupervised task transfer learning. In this paper, we propose a novel Task Adaptation Network (TAN) to solve this unsupervised task transfer problem. In addition to learning transferable features via domain-adversarial training, we propose a novel task semantic adaptor that uses the learning-to-learn strategy to adapt the task semantics. Experiments on three public COVID-19 datasets demonstrate that our proposed method achieves superior performance. Especially on COVID-DA dataset, TAN significantly increases the recall and F1 score by 5.0% and 7.8% compared to recently strong baselines. Moreover, we show that TAN also achieves superior performance on several public domain adaptation benchmarks.

Learning to Match Distributions for Domain Adaptation

When the training and test data are from different distributions, domain adaptation is needed to reduce dataset bias to improve the model's generalization ability. Since it is difficult to directly match the cross-domain joint distributions, existing methods tend to reduce the marginal or conditional distribution divergence using predefined distances such as MMD and adversarial-based discrepancies. However, it remains challenging to determine which method is suitable for a given application since they are built with certain priors or bias. Thus they may fail to uncover the underlying relationship between transferable features and joint distributions. This paper proposes Learning to Match (L2M) to automatically learn the cross-domain distribution matching without relying on hand-crafted priors on the matching loss. Instead, L2M reduces the inductive bias by using a meta-network to learn the distribution matching loss in a data-driven way. L2M is a general framework that unifies task-independent and human-designed matching features. We design a novel optimization algorithm for this challenging objective with self-supervised label propagation. Experiments on public datasets substantiate the superiority of L2M over SOTA methods. Moreover, we apply L2M to transfer from pneumonia to COVID-19 chest X-ray images with remarkable performance. L2M can also be extended in other distribution matching applications where we show in a trial experiment that L2M generates more realistic and sharper MNIST samples.