Publications (14)
Messenger RNA Design via Expected Partition Function and Continuous Optimization
Ning Dai, Wei Yu Tang, Tianshuo Zhou +2
The tasks of designing RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we form…
Geometry-Aware Losses for Structure-Preserving Text-to-Sign Language Generation
Zetian Wu, Tianshuo Zhou, Stefan Lee +1
Sign language translation from text to video plays a crucial role in enabling effective communication for Deaf and hard--of--hearing individuals. A major challenge lies in generati…
Sampling-based Continuous Optimization for Messenger RNA Design
Feipeng Yue, Ning Dai, Wei Yu Tang +3
Designing messenger RNA (mRNA) sequences for a fixed target protein requires searching an exponentially large synonymous space while optimizing properties that affect stability and…
MARVEL: Unlocking the Multi-Modal Capability of Dense Retrieval via Visual Module Plugin
Tianshuo Zhou, Sen Mei, Xinze Li +5
This paper proposes Multi-modAl Retrieval model via Visual modulE pLugin (MARVEL), which learns an embedding space for queries and multi-modal documents to conduct retrieval. MARVE…
Designing RNAs with Language Models
Milan Gautam, Ning Dai, Tianshuo Zhou +3
RNA design, the task of finding a sequence that folds into a target secondary structure, has broad biological and biomedical impact but remains computationally challenging due to t…
Undesignable RNA Structure Identification via Rival Structure Generation and Structure Decomposition
Tianshuo Zhou, Wei Yu Tang, David H. Mathews +1
RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design m…
GREASE: A Generative Model for Relevance Search over Knowledge Graphs
Tianshuo Zhou, Ziyang Li, Gong Cheng +2
Relevance search is to find top-ranked entities in a knowledge graph (KG) that are relevant to a query entity. Relevance is ambiguous, particularly over a schema-rich KG like DBped…
Scalable and Interpretable Identification of Minimal Undesignable RNA Structure Motifs with Rotational Invariance
Tianshuo Zhou, Wei Yu Tang, Apoorv Malik +2
RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fol…
Probabilistic RNA Designability via Interpretable Ensemble Approximation and Dynamic Decomposition
Tianshuo Zhou, David H. Mathews, Liang Huang
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures…
Evaluating MLLMs with Multimodal Multi-image Reasoning Benchmark
Ziming Cheng, Binrui Xu, Lisheng Gong +14
With enhanced capabilities and widespread applications, Multimodal Large Language Models (MLLMs) are increasingly required to process and reason over multiple images simultaneously…
GUI-World: A Video Benchmark and Dataset for Multimodal GUI-oriented Understanding
Dongping Chen, Yue Huang, Siyuan Wu +17
Recently, Multimodal Large Language Models (MLLMs) have been used as agents to control keyboard and mouse inputs by directly perceiving the Graphical User Interface (GUI) and gener…
Fast and Versatile RNA Design via Motif-level Divide-and-Conquer and Structure-level Rival Search
Tianshuo Zhou, David H. Mathews, Liang Huang
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on…
Benchmarking Retrieval-Augmented Generation in Multi-Modal Contexts
Zhenghao Liu, Xingsheng Zhu, Tianshuo Zhou +5
With the rapid advancement of Multi-modal Large Language Models (MLLMs), their capability in understanding both images and text has greatly improved. However, their potential for l…
Sampling-based Continuous Optimization with Coupled Variables for RNA Design
Wei Yu Tang, Ning Dai, Tianshuo Zhou +2
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been prov…