Capturing molecular knowledge with representation learning approaches holds significant potential in vast scientific fields such as chemistry and life science. An effective and generalizable molecular representation is expected to capture the consensus and complementary molecular expertise from diverse views and perspectives. However, existing works fall short in learning multi-view molecular representations, due to challenges in explicitly incorporating view information and handling molecular knowledge from heterogeneous sources. To address these issues, we present MV-Mol, a molecular representation learning model that harvests multi-view molecular expertise from chemical structures, unstructured knowledge from biomedical texts, and structured knowledge from knowledge graphs. We utilize text prompts to model view information and design a fusion architecture to extract view-based molecular representations. We develop a two-stage pre-training procedure, exploiting heterogeneous data of varying quality and quantity. Through extensive experiments, we show that MV-Mol provides improved representations that substantially benefit molecular property prediction. Additionally, MV-Mol exhibits state-of-the-art performance in multi-modal comprehension of molecular structures and texts. Code and data are available at https://github.com/PharMolix/OpenBioMed.

Antimicrobial peptides (AMPs) are promising therapeutic approaches against drug-resistant pathogens. Recently, deep generative models are used to discover new AMPs. However, previous studies mainly focus on peptide sequence attributes and do not consider crucial structure information. In this paper, we propose a latent sequence-structure model for designing AMPs (LSSAMP). LSSAMP exploits multi-scale vector quantization in the latent space to represent secondary structures (e.g. alpha helix and beta sheet). By sampling in the latent space, LSSAMP can simultaneously generate peptides with ideal sequence attributes and secondary structures. Experimental results show that the peptides generated by LSSAMP have a high probability of antimicrobial activity. Our wet laboratory experiments verified that two of the 21 candidates exhibit strong antimicrobial activity. The code is released at https://github.com/dqwang122/LSSAMP.

Sponsored search auction is a crucial component of modern search engines. It requires a set of candidate bidwords that advertisers can place bids on. Existing methods generate bidwords from search queries or advertisement content. However, they suffer from the data noise in (query, bidword) and (advertisement, bidword) pairs. In this paper, we propose a triangular bidword generation model (TRIDENT), which takes the high-quality data of paired (query, advertisement) as a supervision signal to indirectly guide the bidword generation process. Our proposed model is simple yet effective: by using bidword as the bridge between search query and advertisement, the generation of search query, advertisement and bidword can be jointly learned in the triangular training framework. This alleviates the problem that the training data of bidword may be noisy. Experimental results, including automatic and human evaluations, show that our proposed TRIDENT can generate relevant and diverse bidwords for both search queries and advertisements. Our evaluation on online real data validates the effectiveness of the TRIDENT's generated bidwords for product search.

In this paper, we present the design of QuAChIE, a Question Answering based Chinese Information Extraction system. QuAChIE mainly depends on a well-trained question answering model to extract high-quality triples. The group of head entity and relation are regarded as a question given the input text as the context. For the training and evaluation of each model in the system, we build a large-scale information extraction dataset using Wikidata and Wikipedia pages by distant supervision. The advanced models implemented on top of the pre-trained language model and the enormous distant supervision data enable QuAChIE to extract relation triples from documents with cross-sentence correlations. The experimental results on the test set and the case study based on the interactive demonstration show its satisfactory Information Extraction quality on Chinese document-level texts.

Advertising (ad for short) keyword suggestion is important for sponsored search to improve online advertising and increase search revenue. There are two common challenges in this task. First, the keyword bidding problem: hot ad keywords are very expensive for most of the advertisers because more advertisers are bidding on more popular keywords, while unpopular keywords are difficult to discover. As a result, most ads have few chances to be presented to the users. Second, the inefficient ad impression issue: a large proportion of search queries, which are unpopular yet relevant to many ad keywords, have no ads presented on their search result pages. Existing retrieval-based or matching-based methods either deteriorate the bidding competition or are unable to suggest novel keywords to cover more queries, which leads to inefficient ad impressions.