Ribonucleic acid (RNA) plays a variety of crucial roles in fundamental biological processes. Recently, RNA has become an interesting drug target, emphasizing the need to improve our understanding of its structures and functions. Over the years, sequencing technologies have produced an enormous amount of unlabeled RNA data, which hides important knowledge and potential. Motivated by the successes of protein language models, we introduce RiboNucleic Acid Language Model (RiNALMo) to help unveil the hidden code of RNA. RiNALMo is the largest RNA language model to date with $650$ million parameters pre-trained on $36$ million non-coding RNA sequences from several available databases. RiNALMo is able to extract hidden knowledge and capture the underlying structure information implicitly embedded within the RNA sequences. RiNALMo achieves state-of-the-art results on several downstream tasks. Notably, we show that its generalization capabilities can overcome the inability of other deep learning methods for secondary structure prediction to generalize on unseen RNA families. The code has been made publicly available on https://github.com/lbcb-sci/RiNALMo.
This paper investigates the gap in representation powers of Recurrent Neural Networks (RNNs) and Transformers in the context of solving algorithmic problems. We focus on understanding whether RNNs, known for their memory efficiency in handling long sequences, can match the performance of Transformers, particularly when enhanced with Chain-of-Thought (CoT) prompting. Our theoretical analysis reveals that CoT improves RNNs but is insufficient to close the gap with Transformers. A key bottleneck lies in the inability of RNNs to perfectly retrieve information from the context, even with CoT: for several tasks that explicitly or implicitly require this capability, such as associative recall and determining if a graph is a tree, we prove that RNNs are not expressive enough to solve the tasks while Transformers can solve them with ease. Conversely, we prove that adopting techniques to enhance the in-context retrieval capability of RNNs, including Retrieval-Augmented Generation (RAG) and adding a single Transformer layer, can elevate RNNs to be capable of solving all polynomial-time solvable problems with CoT, hence closing the representation gap with Transformers.
Existing question answering (QA) datasets are no longer challenging to most powerful Large Language Models (LLMs). Traditional QA benchmarks like TriviaQA, NaturalQuestions, ELI5 and HotpotQA mainly study ``known unknowns'' with clear indications of both what information is missing, and how to find it to answer the question. Hence, good performance on these benchmarks provides a false sense of security. A yet unmet need of the NLP community is a bank of non-factoid, multi-perspective questions involving a great deal of unclear information needs, i.e. ``unknown uknowns''. We claim we can find such questions in search engine logs, which is surprising because most question-intent queries are indeed factoid. We present Researchy Questions, a dataset of search engine queries tediously filtered to be non-factoid, ``decompositional'' and multi-perspective. We show that users spend a lot of ``effort'' on these questions in terms of signals like clicks and session length, and that they are also challenging for GPT-4. We also show that ``slow thinking'' answering techniques, like decomposition into sub-questions shows benefit over answering directly. We release $\sim$ 100k Researchy Questions, along with the Clueweb22 URLs that were clicked.
Large Language Model (LLM) systems are inherently compositional, with individual LLM serving as the core foundation with additional layers of objects such as plugins, sandbox, and so on. Along with the great potential, there are also increasing concerns over the security of such probabilistic intelligent systems. However, existing studies on LLM security often focus on individual LLM, but without examining the ecosystem through the lens of LLM systems with other objects (e.g., Frontend, Webtool, Sandbox, and so on). In this paper, we systematically analyze the security of LLM systems, instead of focusing on the individual LLMs. To do so, we build on top of the information flow and formulate the security of LLM systems as constraints on the alignment of the information flow within LLM and between LLM and other objects. Based on this construction and the unique probabilistic nature of LLM, the attack surface of the LLM system can be decomposed into three key components: (1) multi-layer security analysis, (2) analysis of the existence of constraints, and (3) analysis of the robustness of these constraints. To ground this new attack surface, we propose a multi-layer and multi-step approach and apply it to the state-of-art LLM system, OpenAI GPT4. Our investigation exposes several security issues, not just within the LLM model itself but also in its integration with other components. We found that although the OpenAI GPT4 has designed numerous safety constraints to improve its safety features, these safety constraints are still vulnerable to attackers. To further demonstrate the real-world threats of our discovered vulnerabilities, we construct an end-to-end attack where an adversary can illicitly acquire the user's chat history, all without the need to manipulate the user's input or gain direct access to OpenAI GPT4. Our demo is in the link: https://fzwark.github.io/LLM-System-Attack-Demo/
Out-of-distribution detection is a crucial technique for deploying machine learning models in the real world to handle the unseen scenarios. In this paper, we propose a simple but effective Neural Activation Prior (NAP) for out-of-distribution detection (OOD). Our neural activation prior is based on a key observation that, for a channel before the global pooling layer of a fully trained neural network, the probability of a few of its neurons being activated with a larger response by an in-distribution (ID) sample is significantly higher than that by an OOD sample. An intuitive explanation is each channel in a model fully trained on ID dataset would play a role in detecting a certain pattern in the samples within the ID dataset, and a few neurons can be activated with a large response when the pattern is detected in an input sample. Thus, a new scoring function based on this prior is proposed to highlight the role of these strongly activated neurons in OOD detection. This approach is plug-and-play and does not lead to any performance degradation on in-distribution data classification and requires no extra training or statistics from training or external datasets. Notice that previous methods primarily rely on post-global-pooling features of the neural networks, while the within-channel distribution information we leverage would be discarded by the global pooling operator. Consequently, our method is orthogonal to existing approaches and can be effectively combined with them in various applications. Experimental results show that our method achieves the state-of-the-art performance on CIFAR-10, CIFAR-100 and ImageNet datasets, which demonstrates the power of the proposed prior.
Designing protein sequences with specific biological functions and structural stability is crucial in biology and chemistry. Generative models already demonstrated their capabilities for reliable protein design. However, previous models are limited to the unconditional generation of protein sequences and lack the controllable generation ability that is vital to biological tasks. In this work, we propose TaxDiff, a taxonomic-guided diffusion model for controllable protein sequence generation that combines biological species information with the generative capabilities of diffusion models to generate structurally stable proteins within the sequence space. Specifically, taxonomic control information is inserted into each layer of the transformer block to achieve fine-grained control. The combination of global and local attention ensures the sequence consistency and structural foldability of taxonomic-specific proteins. Extensive experiments demonstrate that TaxDiff can consistently achieve better performance on multiple protein sequence generation benchmarks in both taxonomic-guided controllable generation and unconditional generation. Remarkably, the sequences generated by TaxDiff even surpass those produced by direct-structure-generation models in terms of confidence based on predicted structures and require only a quarter of the time of models based on the diffusion model. The code for generating proteins and training new versions of TaxDiff is available at:https://github.com/Linzy19/TaxDiff.
Sunlight and shadow play critical roles in how urban spaces are utilized, thrive, and grow. While access to sunlight is essential to the success of urban environments, shadows can provide shaded places to stay during the hot seasons, mitigate heat island effect, and increase pedestrian comfort levels. Properly quantifying sunlight access and shadows in large urban environments is key in tackling some of the important challenges facing cities today. In this paper, we propose Deep Umbra, a novel computational framework that enables the quantification of sunlight access and shadows at a global scale. Our framework is based on a conditional generative adversarial network that considers the physical form of cities to compute high-resolution spatial information of accumulated sunlight access for the different seasons of the year. We use data from seven different cities to train our model, and show, through an extensive set of experiments, its low overall RMSE (below 0.1) as well as its extensibility to cities that were not part of the training set. Additionally, we contribute a set of case studies and a comprehensive dataset with sunlight access information for more than 100 cities across six continents of the world. Deep Umbra is available at https://urbantk.org/shadows.
Food touches our lives through various endeavors, including flavor, nourishment, health, and sustainability. Recipes are cultural capsules transmitted across generations via unstructured text. Automated protocols for recognizing named entities, the building blocks of recipe text, are of immense value for various applications ranging from information extraction to novel recipe generation. Named entity recognition is a technique for extracting information from unstructured or semi-structured data with known labels. Starting with manually-annotated data of 6,611 ingredient phrases, we created an augmented dataset of 26,445 phrases cumulatively. Simultaneously, we systematically cleaned and analyzed ingredient phrases from RecipeDB, the gold-standard recipe data repository, and annotated them using the Stanford NER. Based on the analysis, we sampled a subset of 88,526 phrases using a clustering-based approach while preserving the diversity to create the machine-annotated dataset. A thorough investigation of NER approaches on these three datasets involving statistical, fine-tuning of deep learning-based language models and few-shot prompting on large language models (LLMs) provides deep insights. We conclude that few-shot prompting on LLMs has abysmal performance, whereas the fine-tuned spaCy-transformer emerges as the best model with macro-F1 scores of 95.9%, 96.04%, and 95.71% for the manually-annotated, augmented, and machine-annotated datasets, respectively.
Polarimetric synthetic aperture radar (PolSAR) images encompass valuable information that can facilitate extensive land cover interpretation and generate diverse output products. Extracting meaningful features from PolSAR data poses challenges distinct from those encountered in optical imagery. Deep learning (DL) methods offer effective solutions for overcoming these challenges in PolSAR feature extraction. Convolutional neural networks (CNNs) play a crucial role in capturing PolSAR image characteristics by leveraging kernel capabilities to consider local information and the complex-valued nature of PolSAR data. In this study, a novel three-branch fusion of complex-valued CNN, named the Shallow to Deep Feature Fusion Network (SDF2Net), is proposed for PolSAR image classification. To validate the performance of the proposed method, classification results are compared against multiple state-of-the-art approaches using the airborne synthetic aperture radar (AIRSAR) datasets of Flevoland and San Francisco, as well as the ESAR Oberpfaffenhofen dataset. The results indicate that the proposed approach demonstrates improvements in overallaccuracy, with a 1.3% and 0.8% enhancement for the AIRSAR datasets and a 0.5% improvement for the ESAR dataset. Analyses conducted on the Flevoland data underscore the effectiveness of the SDF2Net model, revealing a promising overall accuracy of 96.01% even with only a 1% sampling ratio.
Deep learning-based methods monopolize the latest research in the field of thermal infrared (TIR) object tracking. However, relying solely on deep learning models to obtain better tracking results requires carefully selecting feature information that is beneficial to representing the target object and designing a reasonable template update strategy, which undoubtedly increases the difficulty of model design. Thus, recent TIR tracking methods face many challenges in complex scenarios. This paper introduces a novel Deep Bayesian Filtering (DBF) method to enhance TIR tracking in these challenging situations. DBF is distinctive in its dual-model structure: the system and observation models. The system model leverages motion data to estimate the potential positions of the target object based on two-dimensional Brownian motion, thus generating a prior probability. Following this, the observation model comes into play upon capturing the TIR image. It serves as a classifier and employs infrared information to ascertain the likelihood of these estimated positions, creating a likelihood probability. According to the guidance of the two models, the position of the target object can be determined, and the template can be dynamically updated. Experimental analysis across several benchmark datasets reveals that DBF achieves competitive performance, surpassing most existing TIR tracking methods in complex scenarios.