CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent's effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between beginner biological researchers and CRISPR genome engineering techniques, and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks.

Diffusion Model for Data-Driven Black-Box Optimization

Generative AI has redefined artificial intelligence, enabling the creation of innovative content and customized solutions that drive business practices into a new era of efficiency and creativity. In this paper, we focus on diffusion models, a powerful generative AI technology, and investigate their potential for black-box optimization over complex structured variables. Consider the practical scenario where one wants to optimize some structured design in a high-dimensional space, based on massive unlabeled data (representing design variables) and a small labeled dataset. We study two practical types of labels: 1) noisy measurements of a real-valued reward function and 2) human preference based on pairwise comparisons. The goal is to generate new designs that are near-optimal and preserve the designed latent structures. Our proposed method reformulates the design optimization problem into a conditional sampling problem, which allows us to leverage the power of diffusion models for modeling complex distributions. In particular, we propose a reward-directed conditional diffusion model, to be trained on the mixed data, for sampling a near-optimal solution conditioned on high predicted rewards. Theoretically, we establish sub-optimality error bounds for the generated designs. The sub-optimality gap nearly matches the optimal guarantee in off-policy bandits, demonstrating the efficiency of reward-directed diffusion models for black-box optimization. Moreover, when the data admits a low-dimensional latent subspace structure, our model efficiently generates high-fidelity designs that closely respect the latent structure. We provide empirical experiments validating our model in decision-making and content-creation tasks.

Embodied LLM Agents Learn to Cooperate in Organized Teams

Large Language Models (LLMs) have emerged as integral tools for reasoning, planning, and decision-making, drawing upon their extensive world knowledge and proficiency in language-related tasks. LLMs thus hold tremendous potential for natural language interaction within multi-agent systems to foster cooperation. However, LLM agents tend to over-report and comply with any instruction, which may result in information redundancy and confusion in multi-agent cooperation. Inspired by human organizations, this paper introduces a framework that imposes prompt-based organization structures on LLM agents to mitigate these problems. Through a series of experiments with embodied LLM agents and human-agent collaboration, our results highlight the impact of designated leadership on team efficiency, shedding light on the leadership qualities displayed by LLM agents and their spontaneous cooperative behaviors. Further, we harness the potential of LLMs to propose enhanced organizational prompts, via a Criticize-Reflect process, resulting in novel organization structures that reduce communication costs and enhance team efficiency.

Assessing the Brittleness of Safety Alignment via Pruning and Low-Rank Modifications

Large language models (LLMs) show inherent brittleness in their safety mechanisms, as evidenced by their susceptibility to jailbreaking and even non-malicious fine-tuning. This study explores this brittleness of safety alignment by leveraging pruning and low-rank modifications. We develop methods to identify critical regions that are vital for safety guardrails, and that are disentangled from utility-relevant regions at both the neuron and rank levels. Surprisingly, the isolated regions we find are sparse, comprising about $3\%$ at the parameter level and $2.5\%$ at the rank level. Removing these regions compromises safety without significantly impacting utility, corroborating the inherent brittleness of the model's safety mechanisms. Moreover, we show that LLMs remain vulnerable to low-cost fine-tuning attacks even when modifications to the safety-critical regions are restricted. These findings underscore the urgent need for more robust safety strategies in LLMs.

A 5' UTR Language Model for Decoding Untranslated Regions of mRNA and Function Predictions

The 5' UTR, a regulatory region at the beginning of an mRNA molecule, plays a crucial role in regulating the translation process and impacts the protein expression level. Language models have showcased their effectiveness in decoding the functions of protein and genome sequences. Here, we introduced a language model for 5' UTR, which we refer to as the UTR-LM. The UTR-LM is pre-trained on endogenous 5' UTRs from multiple species and is further augmented with supervised information including secondary structure and minimum free energy. We fine-tuned the UTR-LM in a variety of downstream tasks. The model outperformed the best-known benchmark by up to 42% for predicting the Mean Ribosome Loading, and by up to 60% for predicting the Translation Efficiency and the mRNA Expression Level. The model also applies to identifying unannotated Internal Ribosome Entry Sites within the untranslated region and improves the AUPR from 0.37 to 0.52 compared to the best baseline. Further, we designed a library of 211 novel 5' UTRs with high predicted values of translation efficiency and evaluated them via a wet-lab assay. Experiment results confirmed that our top designs achieved a 32.5% increase in protein production level relative to well-established 5' UTR optimized for therapeutics.

A Variational Auto-Encoder Enabled Multi-Band Channel Prediction Scheme for Indoor Localization

Indoor localization is getting increasing demands for various cutting-edged technologies, like Virtual/Augmented reality and smart home. Traditional model-based localization suffers from significant computational overhead, so fingerprint localization is getting increasing attention, which needs lower computation cost after the fingerprint database is built. However, the accuracy of indoor localization is limited by the complicated indoor environment which brings the multipath signal refraction. In this paper, we provided a scheme to improve the accuracy of indoor fingerprint localization from the frequency domain by predicting the channel state information (CSI) values from another transmitting channel and spliced the multi-band information together to get more precise localization results. We tested our proposed scheme on COST 2100 simulation data and real time orthogonal frequency division multiplexing (OFDM) WiFi data collected from an office scenario.

Deep Reinforcement Learning for Efficient and Fair Allocation of Health Care Resources

Scarcity of health care resources could result in the unavoidable consequence of rationing. For example, ventilators are often limited in supply, especially during public health emergencies or in resource-constrained health care settings, such as amid the pandemic of COVID-19. Currently, there is no universally accepted standard for health care resource allocation protocols, resulting in different governments prioritizing patients based on various criteria and heuristic-based protocols. In this study, we investigate the use of reinforcement learning for critical care resource allocation policy optimization to fairly and effectively ration resources. We propose a transformer-based deep Q-network to integrate the disease progression of individual patients and the interaction effects among patients during the critical care resource allocation. We aim to improve both fairness of allocation and overall patient outcomes. Our experiments demonstrate that our method significantly reduces excess deaths and achieves a more equitable distribution under different levels of ventilator shortage, when compared to existing severity-based and comorbidity-based methods in use by different governments. Our source code is included in the supplement and will be released on Github upon publication.

Reward-Directed Conditional Diffusion: Provable Distribution Estimation and Reward Improvement

We explore the methodology and theory of reward-directed generation via conditional diffusion models. Directed generation aims to generate samples with desired properties as measured by a reward function, which has broad applications in generative AI, reinforcement learning, and computational biology. We consider the common learning scenario where the data set consists of unlabeled data along with a smaller set of data with noisy reward labels. Our approach leverages a learned reward function on the smaller data set as a pseudolabeler. From a theoretical standpoint, we show that this directed generator can effectively learn and sample from the reward-conditioned data distribution. Additionally, our model is capable of recovering the latent subspace representation of data. Moreover, we establish that the model generates a new population that moves closer to a user-specified target reward value, where the optimality gap aligns with the off-policy bandit regret in the feature subspace. The improvement in rewards obtained is influenced by the interplay between the strength of the reward signal, the distribution shift, and the cost of off-support extrapolation. We provide empirical results to validate our theory and highlight the relationship between the strength of extrapolation and the quality of generated samples.

Scaling In-Context Demonstrations with Structured Attention

The recent surge of large language models (LLMs) highlights their ability to perform in-context learning, i.e., "learning" to perform a task from a few demonstrations in the context without any parameter updates. However, their capabilities of in-context learning are limited by the model architecture: 1) the use of demonstrations is constrained by a maximum sentence length due to positional embeddings; 2) the quadratic complexity of attention hinders users from using more demonstrations efficiently; 3) LLMs are shown to be sensitive to the order of the demonstrations. In this work, we tackle these challenges by proposing a better architectural design for in-context learning. We propose SAICL (Structured Attention for In-Context Learning), which replaces the full-attention by a structured attention mechanism designed for in-context learning, and removes unnecessary dependencies between individual demonstrations, while making the model invariant to the permutation of demonstrations. We evaluate SAICL in a meta-training framework and show that SAICL achieves comparable or better performance than full attention while obtaining up to 3.4x inference speed-up. SAICL also consistently outperforms a strong Fusion-in-Decoder (FiD) baseline which processes each demonstration independently. Finally, thanks to its linear nature, we demonstrate that SAICL can easily scale to hundreds of demonstrations with continuous performance gains with scaling.

Visual Adversarial Examples Jailbreak Large Language Models

Recently, there has been a surge of interest in introducing vision into Large Language Models (LLMs). The proliferation of large Visual Language Models (VLMs), such as Flamingo, BLIP-2, and GPT-4, signifies an exciting convergence of advancements in both visual and language foundation models. Yet, the risks associated with this integrative approach are largely unexamined. In this paper, we shed light on the security and safety implications of this trend. First, we underscore that the continuous and high-dimensional nature of the additional visual input space intrinsically makes it a fertile ground for adversarial attacks. This unavoidably expands the attack surfaces of LLMs. Second, we highlight that the broad functionality of LLMs also presents visual attackers with a wider array of achievable adversarial objectives, extending the implications of security failures beyond mere misclassification. To elucidate these risks, we study adversarial examples in the visual input space of a VLM. Specifically, against MiniGPT-4, which incorporates safety mechanisms that can refuse harmful instructions, we present visual adversarial examples that can circumvent the safety mechanisms and provoke harmful behaviors of the model. Remarkably, we discover that adversarial examples, even if optimized on a narrow, manually curated derogatory corpus against specific social groups, can universally jailbreak the model's safety mechanisms. A single such adversarial example can generally undermine MiniGPT-4's safety, enabling it to heed a wide range of harmful instructions and produce harmful content far beyond simply imitating the derogatory corpus used in optimization. Unveiling these risks, we accentuate the urgent need for comprehensive risk assessments, robust defense strategies, and the implementation of responsible practices for the secure and safe utilization of VLMs.