Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D geometry and conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics. Under the hood, gRNAde is a multi-state Graph Neural Network that generates candidate RNA sequences conditioned on one or more 3D backbone structures where the identities of the bases are unknown. On a single-state fixed backbone re-design benchmark of 14 RNA structures from the PDB identified by Das et al. [2010], gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45% on average), taking under a second to produce designs compared to the reported hours for Rosetta. We further demonstrate the utility of gRNAde on a new benchmark of multi-state design for structurally flexible RNAs, as well as zero-shot ranking of mutational fitness landscapes in a retrospective analysis of a recent RNA polymerase ribozyme structure. Open source code: //github.com/chaitjo/geometric-rna-design
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Video prediction, predicting future frames from the previous ones, has broad applications such as autonomous driving and weather forecasting. Existing state-of-the-art methods typically focus on extracting either spatial, temporal, or spatiotemporal features from videos. Different feature focuses, resulting from different network architectures, may make the resultant models excel at some video prediction tasks but perform poorly on others. Towards a more generic video prediction solution, we explicitly model these features in a unified encoder-decoder framework and propose a novel simple alternating Mixer (SIAM). The novelty of SIAM lies in the design of dimension alternating mixing (DaMi) blocks, which can model spatial, temporal, and spatiotemporal features through alternating the dimensions of the feature maps. Extensive experimental results demonstrate the superior performance of the proposed SIAM on four benchmark video datasets covering both synthetic and real-world scenarios.
Writing Plonkish constraint systems by hand is tedious and error-prone; as a result, several libraries and DSL's have emerged over the years to facilitate this task as well as techniques to directly analyze constraint systems. However, standalone languages require developers to use a foreign toolchain and leave gaps between the application and its circuits. On the other hand, Rust-embedded DSL like Halo2 or Boojum lack in modularity; furthermore, it is usually impossible to tease apart the circuit from the proof system, making it hard to reuse circuits and even to compare performance of different proof systems on the same circuits. In this paper we introduce Clap, the first Rust eDSL to propose a prover-agnostic circuit format that enables extensibility, automatic optimizations, and formal guarantees for the resulting constraint system. Clap generates Plonkish constraint systems and witness generators that are sound and complete with respect to each other, leaving no room for subtle bugs due to under- or over-constraining. A model of this equivalence is proved in the Agda proof assistant for a subset of Clap's Rust implementation that is expressive enough to capture the compositional properties of our format. In order to increase the reuse of circuits, a number of optimizations are carried out automatically, sparing the developer from over-specifying low-level constraint system details in their circuit descriptions. We test the expressivity and efficiency of Clap on an implementation of the Poseidon2 hash function that produces a constraint system that is competitive in terms of size with hand-optimized Boojum circuits.
Efforts to decode deep neural networks (DNNs) often involve mapping their predictions back to the input features. Among these methods, Integrated Gradients (IG) has emerged as a significant technique. The selection of appropriate baselines in IG is crucial for crafting meaningful and unbiased explanations of model predictions in diverse settings. The standard approach of utilizing a single baseline, however, is frequently inadequate, prompting the need for multiple baselines. Leveraging the natural link between IG and the Aumann-Shapley Value, we provide a novel outlook on baseline design. Theoretically, we demonstrate that under certain assumptions, a collection of baselines aligns with the coalitions described by the Shapley Value. Building on this insight, we develop a new baseline method called Shapley Integrated Gradients (SIG), which uses proportional sampling to mirror the Shapley Value computation process. Simulations conducted in GridWorld validate that SIG effectively emulates the distribution of Shapley Values. Moreover, empirical tests on various image processing tasks show that SIG surpasses traditional IG baseline methods by offering more precise estimates of feature contributions, providing consistent explanations across different applications, and ensuring adaptability to diverse data types with negligible additional computational demand.
Contemporary recommendation systems are designed to meet users' needs by delivering tailored lists of items that align with their specific demands or interests. In a multi-stage recommendation system, reranking plays a crucial role by modeling the intra-list correlations among items. The key challenge of reranking lies in the exploration of optimal sequences within the combinatorial space of permutations. Recent research proposes a generator-evaluator learning paradigm, where the generator generates multiple feasible sequences and the evaluator picks out the best sequence based on the estimated listwise score. The generator is of vital importance, and generative models are well-suited for the generator function. Current generative models employ an autoregressive strategy for sequence generation. However, deploying autoregressive models in real-time industrial systems is challenging. To address these issues, we propose a Non-AutoRegressive generative model for reranking Recommendation (NAR4Rec) designed to enhance efficiency and effectiveness. To tackle challenges such as sparse training samples and dynamic candidates, we introduce a matching model. Considering the diverse nature of user feedback, we employ a sequence-level unlikelihood training objective to differentiate feasible sequences from unfeasible ones. Additionally, to overcome the lack of dependency modeling in non-autoregressive models regarding target items, we introduce contrastive decoding to capture correlations among these items. Extensive offline experiments validate the superior performance of NAR4Rec over state-of-the-art reranking methods. Online A/B tests reveal that NAR4Rec significantly enhances the user experience. Furthermore, NAR4Rec has been fully deployed in a popular video app Kuaishou with over 300 million daily active users.
Before deploying outputs from foundation models in high-stakes tasks, it is imperative to ensure that they align with human values. For instance, in radiology report generation, reports generated by a vision-language model must align with human evaluations before their use in medical decision-making. This paper presents Conformal Alignment, a general framework for identifying units whose outputs meet a user-specified alignment criterion. It is guaranteed that on average, a prescribed fraction of selected units indeed meet the alignment criterion, regardless of the foundation model or the data distribution. Given any pre-trained model and new units with model-generated outputs, Conformal Alignment leverages a set of reference data with ground-truth alignment status to train an alignment predictor. It then selects new units whose predicted alignment scores surpass a data-dependent threshold, certifying their corresponding outputs as trustworthy. Through applications to question answering and radiology report generation, we demonstrate that our method is able to accurately identify units with trustworthy outputs via lightweight training over a moderate amount of reference data. En route, we investigate the informativeness of various features in alignment prediction and combine them with standard models to construct the alignment predictor.
Driven by powerful image diffusion models, recent research has achieved the automatic creation of 3D objects from textual or visual guidance. By performing score distillation sampling (SDS) iteratively across different views, these methods succeed in lifting 2D generative prior to the 3D space. However, such a 2D generative image prior bakes the effect of illumination and shadow into the texture. As a result, material maps optimized by SDS inevitably involve spurious correlated components. The absence of precise material definition makes it infeasible to relight the generated assets reasonably in novel scenes, which limits their application in downstream scenarios. In contrast, humans can effortlessly circumvent this ambiguity by deducing the material of the object from its appearance and semantics. Motivated by this insight, we propose MaterialSeg3D, a 3D asset material generation framework to infer underlying material from the 2D semantic prior. Based on such a prior model, we devise a mechanism to parse material in 3D space. We maintain a UV stack, each map of which is unprojected from a specific viewpoint. After traversing all viewpoints, we fuse the stack through a weighted voting scheme and then employ region unification to ensure the coherence of the object parts. To fuel the learning of semantics prior, we collect a material dataset, named Materialized Individual Objects (MIO), which features abundant images, diverse categories, and accurate annotations. Extensive quantitative and qualitative experiments demonstrate the effectiveness of our method.
As the potential of foundation models in visual tasks has garnered significant attention, pretraining these models before downstream tasks has become a crucial step. The three key factors in pretraining foundation models are the pretraining method, the size of the pretraining dataset, and the number of model parameters. Recently, research in the remote sensing field has focused primarily on the pretraining method and the size of the dataset, with limited emphasis on the number of model parameters. This paper addresses this gap by examining the effect of increasing the number of model parameters on the performance of foundation models in downstream tasks such as rotated object detection and semantic segmentation. We pretrained foundation models with varying numbers of parameters, including 86M, 605.26M, 1.3B, and 2.4B, to determine whether performance in downstream tasks improved with an increase in parameters. To the best of our knowledge, this is the first billion-scale foundation model in the remote sensing field. Furthermore, we propose an effective method for scaling up and fine-tuning a vision transformer in the remote sensing field. To evaluate general performance in downstream tasks, we employed the DOTA v2.0 and DIOR-R benchmark datasets for rotated object detection, and the Potsdam and LoveDA datasets for semantic segmentation. Experimental results demonstrated that, across all benchmark datasets and downstream tasks, the performance of the foundation models and data efficiency improved as the number of parameters increased. Moreover, our models achieve the state-of-the-art performance on several datasets including DIOR-R, Postdam, and LoveDA.
The advent of Large Language Models (LLMs) has ushered in a new era for design science in Information Systems, demanding a paradigm shift in tailoring LLMs design for business contexts. We propose and test a novel framework to customize LLMs for general business contexts that aims to achieve three fundamental objectives simultaneously: (1) aligning conversational patterns, (2) integrating in-depth domain knowledge, and (3) embodying theory-driven soft skills and core principles. We design methodologies that combine domain-specific theory with Supervised Fine Tuning (SFT) to achieve these objectives simultaneously. We instantiate our proposed framework in the context of medical consultation. Specifically, we carefully construct a large volume of real doctors' consultation records and medical knowledge from multiple professional databases. Additionally, drawing on medical theory, we identify three soft skills and core principles of human doctors: professionalism, explainability, and emotional support, and design approaches to integrate these traits into LLMs. We demonstrate the feasibility of our framework using online experiments with thousands of real patients as well as evaluation by domain experts and consumers. Experimental results show that the customized LLM model substantially outperforms untuned base model in medical expertise as well as consumer satisfaction and trustworthiness, and it substantially reduces the gap between untuned LLMs and human doctors, elevating LLMs to the level of human experts. Additionally, we delve into the characteristics of textual consultation records and adopt interpretable machine learning techniques to identify what drives the performance gain. Finally, we showcase the practical value of our model through a decision support system designed to assist human doctors in a lab experiment.
Recent work pre-training Transformers with self-supervised objectives on large text corpora has shown great success when fine-tuned on downstream NLP tasks including text summarization. However, pre-training objectives tailored for abstractive text summarization have not been explored. Furthermore there is a lack of systematic evaluation across diverse domains. In this work, we propose pre-training large Transformer-based encoder-decoder models on massive text corpora with a new self-supervised objective. In PEGASUS, important sentences are removed/masked from an input document and are generated together as one output sequence from the remaining sentences, similar to an extractive summary. We evaluated our best PEGASUS model on 12 downstream summarization tasks spanning news, science, stories, instructions, emails, patents, and legislative bills. Experiments demonstrate it achieves state-of-the-art performance on all 12 downstream datasets measured by ROUGE scores. Our model also shows surprising performance on low-resource summarization, surpassing previous state-of-the-art results on 6 datasets with only 1000 examples. Finally we validated our results using human evaluation and show that our model summaries achieve human performance on multiple datasets.
BERT, a pre-trained Transformer model, has achieved ground-breaking performance on multiple NLP tasks. In this paper, we describe BERTSUM, a simple variant of BERT, for extractive summarization. Our system is the state of the art on the CNN/Dailymail dataset, outperforming the previous best-performed system by 1.65 on ROUGE-L. The codes to reproduce our results are available at //github.com/nlpyang/BertSum
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