Toward AI-Driven Digital Organism: Multiscale Foundation Models for Predicting, Simulating and Programming Biology at All Levels

We present an approach of using AI to model and simulate biology and life. Why is it important? Because at the core of medicine, pharmacy, public health, longevity, agriculture and food security, environmental protection, and clean energy, it is biology at work. Biology in the physical world is too complex to manipulate and always expensive and risky to tamper with. In this perspective, we layout an engineering viable approach to address this challenge by constructing an AI-Driven Digital Organism (AIDO), a system of integrated multiscale foundation models, in a modular, connectable, and holistic fashion to reflect biological scales, connectedness, and complexities. An AIDO opens up a safe, affordable and high-throughput alternative platform for predicting, simulating and programming biology at all levels from molecules to cells to individuals. We envision that an AIDO is poised to trigger a new wave of better-guided wet-lab experimentation and better-informed first-principle reasoning, which can eventually help us better decode and improve life.

VideoGLaMM: A Large Multimodal Model for Pixel-Level Visual Grounding in Videos

Fine-grained alignment between videos and text is challenging due to complex spatial and temporal dynamics in videos. Existing video-based Large Multimodal Models (LMMs) handle basic conversations but struggle with precise pixel-level grounding in videos. To address this, we introduce VideoGLaMM, a LMM designed for fine-grained pixel-level grounding in videos based on user-provided textual inputs. Our design seamlessly connects three key components: a Large Language Model, a dual vision encoder that emphasizes both spatial and temporal details, and a spatio-temporal decoder for accurate mask generation. This connection is facilitated via tunable V-L and L-V adapters that enable close Vision-Language (VL) alignment. The architecture is trained to synchronize both spatial and temporal elements of video content with textual instructions. To enable fine-grained grounding, we curate a multimodal dataset featuring detailed visually-grounded conversations using a semiautomatic annotation pipeline, resulting in a diverse set of 38k video-QA triplets along with 83k objects and 671k masks. We evaluate VideoGLaMM on three challenging tasks: Grounded Conversation Generation, Visual Grounding, and Referring Video Segmentation. Experimental results show that our model consistently outperforms existing approaches across all three tasks.

Reducing Hyperparameter Tuning Costs in ML, Vision and Language Model Training Pipelines via Memoization-Awareness

The training or fine-tuning of machine learning, vision, and language models is often implemented as a pipeline: a sequence of stages encompassing data preparation, model training and evaluation. In this paper, we exploit pipeline structures to reduce the cost of hyperparameter tuning for model training/fine-tuning, which is particularly valuable for language models given their high costs in GPU-days. We propose a "memoization-aware" Bayesian Optimization (BO) algorithm, EEIPU, that works in tandem with a pipeline caching system, allowing it to evaluate significantly more hyperparameter candidates per GPU-day than other tuning algorithms. The result is better-quality hyperparameters in the same amount of search time, or equivalently, reduced search time to reach the same hyperparameter quality. In our benchmarks on machine learning (model ensembles), vision (convolutional architecture) and language (T5 architecture) pipelines, we compare EEIPU against recent BO algorithms: EEIPU produces an average of $103\%$ more hyperparameter candidates (within the same budget), and increases the validation metric by an average of $108\%$ more than other algorithms (where the increase is measured starting from the end of warm-up iterations).

Atlas-Chat: Adapting Large Language Models for Low-Resource Moroccan Arabic Dialect

We introduce Atlas-Chat, the first-ever collection of large language models specifically developed for dialectal Arabic. Focusing on Moroccan Arabic, also known as Darija, we construct our instruction dataset by consolidating existing Darija language resources, creating novel datasets both manually and synthetically, and translating English instructions with stringent quality control. Atlas-Chat-9B and 2B models, fine-tuned on the dataset, exhibit superior ability in following Darija instructions and performing standard NLP tasks. Notably, our models outperform both state-of-the-art and Arabic-specialized LLMs like LLaMa, Jais, and AceGPT, e.g., achieving a 13% performance boost over a larger 13B model on DarijaMMLU, in our newly introduced evaluation suite for Darija covering both discriminative and generative tasks. Furthermore, we perform an experimental analysis of various fine-tuning strategies and base model choices to determine optimal configurations. All our resources are publicly accessible, and we believe our work offers comprehensive design methodologies of instruction-tuning for low-resource language variants, which are often neglected in favor of data-rich languages by contemporary LLMs.

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities

The cell is arguably the smallest unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells. Here we propose a vision of AI-powered Virtual Cells, where robust representations of cells and cellular systems under different conditions are directly learned from growing biological data across measurements and scales. We discuss desired capabilities of AI Virtual Cells, including generating universal representations of biological entities across scales, and facilitating interpretable in silico experiments to predict and understand their behavior using Virtual Instruments. We further address the challenges, opportunities and requirements to realize this vision including data needs, evaluation strategies, and community standards and engagement to ensure biological accuracy and broad utility. We envision a future where AI Virtual Cells help identify new drug targets, predict cellular responses to perturbations, as well as scale hypothesis exploration. With open science collaborations across the biomedical ecosystem that includes academia, philanthropy, and the biopharma and AI industries, a comprehensive predictive understanding of cell mechanisms and interactions is within reach.

PSM: Learning Probabilistic Embeddings for Multi-scale Zero-Shot Soundscape Mapping

A soundscape is defined by the acoustic environment a person perceives at a location. In this work, we propose a framework for mapping soundscapes across the Earth. Since soundscapes involve sound distributions that span varying spatial scales, we represent locations with multi-scale satellite imagery and learn a joint representation among this imagery, audio, and text. To capture the inherent uncertainty in the soundscape of a location, we design the representation space to be probabilistic. We also fuse ubiquitous metadata (including geolocation, time, and data source) to enable learning of spatially and temporally dynamic representations of soundscapes. We demonstrate the utility of our framework by creating large-scale soundscape maps integrating both audio and text with temporal control. To facilitate future research on this task, we also introduce a large-scale dataset, GeoSound, containing over $300k$ geotagged audio samples paired with both low- and high-resolution satellite imagery. We demonstrate that our method outperforms the existing state-of-the-art on both GeoSound and the existing SoundingEarth dataset. Our dataset and code is available at https://github.com/mvrl/PSM.

What is Your Data Worth to GPT? LLM-Scale Data Valuation with Influence Functions

Large language models (LLMs) are trained on a vast amount of human-written data, but data providers often remain uncredited. In response to this issue, data valuation (or data attribution), which quantifies the contribution or value of each data to the model output, has been discussed as a potential solution. Nevertheless, applying existing data valuation methods to recent LLMs and their vast training datasets has been largely limited by prohibitive compute and memory costs. In this work, we focus on influence functions, a popular gradient-based data valuation method, and significantly improve its scalability with an efficient gradient projection strategy called LoGra that leverages the gradient structure in backpropagation. We then provide a theoretical motivation of gradient projection approaches to influence functions to promote trust in the data valuation process. Lastly, we lower the barrier to implementing data valuation systems by introducing LogIX, a software package that can transform existing training code into data valuation code with minimal effort. In our data valuation experiments, LoGra achieves competitive accuracy against more expensive baselines while showing up to 6,500x improvement in throughput and 5x reduction in GPU memory usage when applied to Llama3-8B-Instruct and the 1B-token dataset.

Efficient Test-Time Adaptation of Vision-Language Models

Test-time adaptation with pre-trained vision-language models has attracted increasing attention for tackling distribution shifts during the test time. Though prior studies have achieved very promising performance, they involve intensive computation which is severely unaligned with test-time adaptation. We design TDA, a training-free dynamic adapter that enables effective and efficient test-time adaptation with vision-language models. TDA works with a lightweight key-value cache that maintains a dynamic queue with few-shot pseudo labels as values and the corresponding test-sample features as keys. Leveraging the key-value cache, TDA allows adapting to test data gradually via progressive pseudo label refinement which is super-efficient without incurring any backpropagation. In addition, we introduce negative pseudo labeling that alleviates the adverse impact of pseudo label noises by assigning pseudo labels to certain negative classes when the model is uncertain about its pseudo label predictions. Extensive experiments over two benchmarks demonstrate TDA's superior effectiveness and efficiency as compared with the state-of-the-art. The code has been released in \url{https://kdiaaa.github.io/tda/}.

FreGS: 3D Gaussian Splatting with Progressive Frequency Regularization

3D Gaussian splatting has achieved very impressive performance in real-time novel view synthesis. However, it often suffers from over-reconstruction during Gaussian densification where high-variance image regions are covered by a few large Gaussians only, leading to blur and artifacts in the rendered images. We design a progressive frequency regularization (FreGS) technique to tackle the over-reconstruction issue within the frequency space. Specifically, FreGS performs coarse-to-fine Gaussian densification by exploiting low-to-high frequency components that can be easily extracted with low-pass and high-pass filters in the Fourier space. By minimizing the discrepancy between the frequency spectrum of the rendered image and the corresponding ground truth, it achieves high-quality Gaussian densification and alleviates the over-reconstruction of Gaussian splatting effectively. Experiments over multiple widely adopted benchmarks (e.g., Mip-NeRF360, Tanks-and-Temples and Deep Blending) show that FreGS achieves superior novel view synthesis and outperforms the state-of-the-art consistently.

Follow My Instruction and Spill the Beans: Scalable Data Extraction from Retrieval-Augmented Generation Systems

Retrieval-Augmented Generation (RAG) improves pre-trained models by incorporating external knowledge at test time to enable customized adaptation. We study the risk of datastore leakage in Retrieval-In-Context RAG Language Models (LMs). We show that an adversary can exploit LMs' instruction-following capabilities to easily extract text data verbatim from the datastore of RAG systems built with instruction-tuned LMs via prompt injection. The vulnerability exists for a wide range of modern LMs that span Llama2, Mistral/Mixtral, Vicuna, SOLAR, WizardLM, Qwen1.5, and Platypus2, and the exploitability exacerbates as the model size scales up. Extending our study to production RAG models GPTs, we design an attack that can cause datastore leakage with a 100% success rate on 25 randomly selected customized GPTs with at most 2 queries, and we extract text data verbatim at a rate of 41% from a book of 77,000 words and 3% from a corpus of 1,569,000 words by prompting the GPTs with only 100 queries generated by themselves.