Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling

Structure-based drug design aims at generating high affinity ligands with prior knowledge of 3D target structures. Existing methods either use conditional generative model to learn the distribution of 3D ligands given target binding sites, or iteratively modify molecules to optimize a structure-based activity estimator. The former is highly constrained by data quantity and quality, which leaves optimization-based approaches more promising in practical scenario. However, existing optimization-based approaches choose to edit molecules in 2D space, and use molecular docking to estimate the activity using docking predicted 3D target-ligand complexes. The misalignment between the action space and the objective hinders the performance of these models, especially for those employ deep learning for acceleration. In this work, we propose MolEdit3D to combine 3D molecular generation with optimization frameworks. We develop a novel 3D graph editing model to generate molecules using fragments, and pre-train this model on abundant 3D ligands for learning target-independent properties. Then we employ a target-guided self-learning strategy to improve target-related properties using self-sampled molecules. MolEdit3D achieves state-of-the-art performance on majority of the evaluation metrics, and demonstrate strong capability of capturing both target-dependent and -independent properties.

Where It Really Matters: Few-Shot Environmental Conservation Media Monitoring for Low-Resource Languages

Environmental conservation organizations routinely monitor news content on conservation in protected areas to maintain situational awareness of developments that can have an environmental impact. Existing automated media monitoring systems require large amounts of data labeled by domain experts, which is only feasible at scale for high-resource languages like English. However, such tools are most needed in the global south where news of interest is mainly in local low-resource languages, and far fewer experts are available to annotate datasets sustainably. In this paper, we propose NewsSerow, a method to automatically recognize environmental conservation content in low-resource languages. NewsSerow is a pipeline of summarization, in-context few-shot classification, and self-reflection using large language models (LLMs). Using at most 10 demonstration example news articles in Nepali, NewsSerow significantly outperforms other few-shot methods and achieves comparable performance with models fully fine-tuned using thousands of examples. The World Wide Fund for Nature (WWF) has deployed NewsSerow for media monitoring in Nepal, significantly reducing their operational burden, and ensuring that AI tools for conservation actually reach the communities that need them the most. NewsSerow has also been deployed for countries with other languages like Colombia.

Perils of Self-Feedback: Self-Bias Amplifies in Large Language Models

Recent studies show that self-feedback improves large language models (LLMs) on certain tasks while worsens other tasks. We discovered that such a contrary is due to LLM's bias towards their own output. In this paper, we formally define LLM's self-bias -- the tendency to favor its own generation -- using two statistics. We analyze six LLMs on translation, constrained text generation, and mathematical reasoning tasks. We find that self-bias is prevalent in all examined LLMs across multiple languages and tasks. Our analysis reveals that while the self-refine pipeline improves the fluency and understandability of model outputs, it further amplifies self-bias. To mitigate such biases, we discover that larger model size and external feedback with accurate assessment can significantly reduce bias in the self-refine pipeline, leading to actual performance improvement in downstream tasks.

DE-COP: Detecting Copyrighted Content in Language Models Training Data

How can we detect if copyrighted content was used in the training process of a language model, considering that the training data is typically undisclosed? We are motivated by the premise that a language model is likely to identify verbatim excerpts from its training text. We propose DE-COP, a method to determine whether a piece of copyrighted content was included in training. DE-COP's core approach is to probe an LLM with multiple-choice questions, whose options include both verbatim text and their paraphrases. We construct BookTection, a benchmark with excerpts from 165 books published prior and subsequent to a model's training cutoff, along with their paraphrases. Our experiments show that DE-COP surpasses the prior best method by 9.6% in detection performance (AUC) on models with logits available. Moreover, DE-COP also achieves an average accuracy of 72% for detecting suspect books on fully black-box models where prior methods give $\approx$ 4% accuracy. Our code and datasets are available at https://github.com/avduarte333/DE-COP_Method

Improving Factual Error Correction for Abstractive Summarization via Data Distillation and Conditional-generation Cloze

Improving factual consistency in abstractive summarization has been a focus of current research. One promising approach is the post-editing method. However, previous works have yet to make sufficient use of factual factors in summaries and suffers from the negative effect of the training datasets. In this paper, we first propose a novel factual error correction model FactCloze based on a conditional-generation cloze task. FactCloze can construct the causality among factual factors while being able to determine whether the blank can be answered or not. Then, we propose a data distillation method to generate a more faithful summarization dataset SummDSC via multiple-dimensional evaluation. We experimentally validate the effectiveness of our approach, which leads to an improvement in multiple factual consistency metrics compared to baselines.

Permute-and-Flip: An optimally robust and watermarkable decoder for LLMs

In this paper, we propose a new decoding method called Permute-and-Flip (PF) decoder. It enjoys robustness properties similar to the standard sampling decoder, but is provably up to 2x better in its quality-robustness tradeoff than sampling and never worse than any other decoder. We also design a cryptographic watermarking scheme analogous to Aaronson's Gumbel watermark, but naturally tailored for PF decoder. The watermarking scheme does not change the distribution to sample, while allowing arbitrarily low false positive rate and high recall whenever the generated text has high entropy. Our experiments show that the PF decoder (and its watermarked counterpart) significantly outperform(s) naive sampling (and it's Gumbel watermarked counterpart) in terms of perplexity, while retaining the same robustness (and detectability), hence making it a promising new approach for LLM decoding. The code is available at https://github.com/XuandongZhao/pf-decoding

Mamba-UNet: UNet-Like Pure Visual Mamba for Medical Image Segmentation

In recent advancements in medical image analysis, Convolutional Neural Networks (CNN) and Vision Transformers (ViT) have set significant benchmarks. While the former excels in capturing local features through its convolution operations, the latter achieves remarkable global context understanding by leveraging self-attention mechanisms. However, both architectures exhibit limitations in efficiently modeling long-range dependencies within medical images, which is a critical aspect for precise segmentation. Inspired by the Mamba architecture, known for its proficiency in handling long sequences and global contextual information with enhanced computational efficiency as a State Space Model (SSM), we propose Mamba-UNet, a novel architecture that synergizes the U-Net in medical image segmentation with Mamba's capability. Mamba-UNet adopts a pure Visual Mamba (VMamba)-based encoder-decoder structure, infused with skip connections to preserve spatial information across different scales of the network. This design facilitates a comprehensive feature learning process, capturing intricate details and broader semantic contexts within medical images. We introduce a novel integration mechanism within the VMamba blocks to ensure seamless connectivity and information flow between the encoder and decoder paths, enhancing the segmentation performance. We conducted experiments on publicly available MRI cardiac multi-structures segmentation dataset. The results show that Mamba-UNet outperforms UNet, Swin-UNet in medical image segmentation under the same hyper-parameter setting. The source code and baseline implementations are available.

EasyInstruct: An Easy-to-use Instruction Processing Framework for Large Language Models

In recent years, instruction tuning has gained increasing attention and emerged as a crucial technique to enhance the capabilities of Large Language Models (LLMs). To construct high-quality instruction datasets, many instruction processing approaches have been proposed, aiming to achieve a delicate balance between data quantity and data quality. Nevertheless, due to inconsistencies that persist among various instruction processing methods, there is no standard open-source instruction processing implementation framework available for the community, which hinders practitioners from further developing and advancing. To facilitate instruction processing research and development, we present EasyInstruct, an easy-to-use instruction processing framework for LLMs, which modularizes instruction generation, selection, and prompting, while also considering their combination and interaction. EasyInstruct is publicly released and actively maintained at https://github.com/zjunlp/EasyInstruct, along with a running demo App at https://huggingface.co/spaces/zjunlp/EasyInstruct for quick-start, calling for broader research centered on instruction data.

Progress and Opportunities of Foundation Models in Bioinformatics

Bioinformatics has witnessed a paradigm shift with the increasing integration of artificial intelligence (AI), particularly through the adoption of foundation models (FMs). These AI techniques have rapidly advanced, addressing historical challenges in bioinformatics such as the scarcity of annotated data and the presence of data noise. FMs are particularly adept at handling large-scale, unlabeled data, a common scenario in biological contexts due to the time-consuming and costly nature of experimentally determining labeled data. This characteristic has allowed FMs to excel and achieve notable results in various downstream validation tasks, demonstrating their ability to represent diverse biological entities effectively. Undoubtedly, FMs have ushered in a new era in computational biology, especially in the realm of deep learning. The primary goal of this survey is to conduct a systematic investigation and summary of FMs in bioinformatics, tracing their evolution, current research status, and the methodologies employed. Central to our focus is the application of FMs to specific biological problems, aiming to guide the research community in choosing appropriate FMs for their research needs. We delve into the specifics of the problem at hand including sequence analysis, structure prediction, function annotation, and multimodal integration, comparing the structures and advancements against traditional methods. Furthermore, the review analyses challenges and limitations faced by FMs in biology, such as data noise, model explainability, and potential biases. Finally, we outline potential development paths and strategies for FMs in future biological research, setting the stage for continued innovation and application in this rapidly evolving field. This comprehensive review serves not only as an academic resource but also as a roadmap for future explorations and applications of FMs in biology.

KS-Lottery: Finding Certified Lottery Tickets for Multilingual Language Models

The lottery ticket hypothesis posits the existence of ``winning tickets'' within a randomly initialized neural network. Do winning tickets exist for LLMs in fine-tuning scenarios? How can we find such winning tickets? In this paper, we propose KS-Lottery, a method to identify a small subset of LLM parameters highly effective in multilingual fine-tuning. Our key idea is to use Kolmogorov-Smirnov Test to analyze the distribution shift of parameters before and after fine-tuning. We further theoretically prove that KS-Lottery can find the certified winning tickets in the embedding layer, fine-tuning on the found parameters is guaranteed to perform as well as full fine-tuning. Comparing KS-Lottery with other parameter-efficient tuning algorithms on translation tasks, the experimental results show that KS-Lottery finds a much smaller set of parameters for fine-tuning while achieving the comparable performance as full fine-tuning LLM. Surprisingly, we find that fine-tuning 18 tokens' embedding of LLaMA suffices to reach the fine-tuning translation performance. Code and model will be released to the public.