arXiv subjects

Eric P. Xing

Publications and source records attributed to Eric P. Xing.

At least 55 records · Page 3Linked to original sources

arXiv2025

Causal Representation Learning from Multimodal Biomedical Observations

Prevalent in biomedical applications (e.g., human phenotype research), multimodal datasets can provide valuable insights into the underlying physiological mechanisms. However, current machine learning (ML) models designed to analyze these datasets often lack interpretability and identifiability guarantees, which are essential for biomedical research. Recent advances in causal representation learning have shown promise in identifying interpretable latent causal variables with formal theoretical guarantees. Unfortunately, most current work on multimodal distributions either relies on restrictive parametric assumptions or yields only coarse identification results, limiting their applicability to biomedical research that favors a detailed understanding of the mechanisms. In this work, we aim to develop flexible identification conditions for multimodal data and principled methods to facilitate the understanding of biomedical datasets. Theoretically, we consider a nonparametric latent distribution (c.f., parametric assumptions in previous work) that allows for causal relationships across potentially different modalities. We establish identifiability guarantees for each latent component, extending the subspace identification results from previous work. Our key theoretical contribution is the structural sparsity of causal connections between modalities, which, as we will discuss, is natural for a large collection of biomedical systems. Empirically, we present a practical framework to instantiate our theoretical insights. We demonstrate the effectiveness of our approach through extensive experiments on both numerical and synthetic datasets. Results on a real-world human phenotype dataset are consistent with established biomedical research, validating our theoretical and methodological framework.

cs.LG↗

arXiv2025

Transformers to SSMs: Distilling Quadratic Knowledge to Subquadratic Models

Transformer architectures have become a dominant paradigm for domains like language modeling but suffer in many inference settings due to their quadratic-time self-attention. Recently proposed subquadratic architectures, such as Mamba, have shown promise, but have been pretrained with substantially less computational resources than the strongest Transformer models. In this work, we present a method that is able to distill a pretrained Transformer architecture into alternative architectures such as state space models (SSMs). The key idea to our approach is that we can view both Transformers and SSMs as applying different forms of mixing matrices over the token sequences. We can thus progressively distill the Transformer architecture by matching different degrees of granularity in the SSM: first matching the mixing matrices themselves, then the hidden units at each block, and finally the end-to-end predictions. Our method, called MOHAWK, is able to distill a Mamba-2 variant based on the Phi-1.5 architecture (Phi-Mamba) using only 3B tokens and a hybrid version (Hybrid Phi-Mamba) using 5B tokens. Despite using less than 1% of the training data typically used to train models from scratch, Phi-Mamba boasts substantially stronger performance compared to all past open-source non-Transformer models. MOHAWK allows models like SSMs to leverage computational resources invested in training Transformer-based architectures, highlighting a new avenue for building such models.

cs.LG↗

arXiv2025

Scaling Structure Aware Virtual Screening to Billions of Molecules with SPRINT

Virtual screening of small molecules against protein targets can accelerate drug discovery and development by predicting drug-target interactions (DTIs). However, structure-based methods like molecular docking are too slow to allow for broad proteome-scale screens, limiting their application in screening for off-target effects or new molecular mechanisms. Recently, vector-based methods using protein language models (PLMs) have emerged as a complementary approach that bypasses explicit 3D structure modeling. Here, we develop SPRINT, a vector-based approach for screening entire chemical libraries against whole proteomes for DTIs and novel mechanisms of action. SPRINT improves on prior work by using a self-attention based architecture and structure-aware PLMs to learn drug-target co-embeddings for binder prediction, search, and retrieval. SPRINT achieves SOTA enrichment factors in virtual screening on LIT-PCBA, DTI classification benchmarks, and binding affinity prediction benchmarks, while providing interpretability in the form of residue-level attention maps. In addition to being both accurate and interpretable, SPRINT is ultra-fast: querying the whole human proteome against the ENAMINE Real Database (6.7B drugs) for the 100 most likely binders per protein takes 16 minutes. SPRINT promises to enable virtual screening at an unprecedented scale, opening up new opportunities for in silico drug repurposing and development. SPRINT is available on the web as ColabScreen: https://bit.ly/colab-screen

q-bio.BM↗

arXiv2025

Fast Matrix Multiplications for Lookup Table-Quantized LLMs

The deployment of large language models (LLMs) is often constrained by memory bandwidth, where the primary bottleneck is the cost of transferring model parameters from the GPU's global memory to its registers. When coupled with custom kernels that fuse the dequantization and matmul operations, weight-only quantization can thus enable faster inference by reducing the amount of memory movement. However, developing high-performance kernels for weight-quantized LLMs presents substantial challenges, especially when the weights are compressed to non-evenly-divisible bit widths (e.g., 3 bits) with non-uniform, lookup table (LUT) quantization. This paper describes FLUTE, a flexible lookup table engine for LUT-quantized LLMs, which uses offline restructuring of the quantized weight matrix to minimize bit manipulations associated with unpacking, and vectorization and duplication of the lookup table to mitigate shared memory bandwidth constraints. At batch sizes < 32 and quantization group size of 128 (typical in LLM inference), the FLUTE kernel can be 2-4x faster than existing GEMM kernels. As an application of FLUTE, we explore a simple extension to lookup table-based NormalFloat quantization and apply it to quantize LLaMA3 to various configurations, obtaining competitive quantization performance against strong baselines while obtaining an end-to-end throughput increase of 1.5 to 2 times.

cs.LG↗

arXiv2025

Towards Understanding Extrapolation: a Causal Lens

Canonical work handling distribution shifts typically necessitates an entire target distribution that lands inside the training distribution. However, practical scenarios often involve only a handful of target samples, potentially lying outside the training support, which requires the capability of extrapolation. In this work, we aim to provide a theoretical understanding of when extrapolation is possible and offer principled methods to achieve it without requiring an on-support target distribution. To this end, we formulate the extrapolation problem with a latent-variable model that embodies the minimal change principle in causal mechanisms. Under this formulation, we cast the extrapolation problem into a latent-variable identification problem. We provide realistic conditions on shift properties and the estimation objectives that lead to identification even when only one off-support target sample is available, tackling the most challenging scenarios. Our theory reveals the intricate interplay between the underlying manifold's smoothness and the shift properties. We showcase how our theoretical results inform the design of practical adaptation algorithms. Through experiments on both synthetic and real-world data, we validate our theoretical findings and their practical implications.

cs.LG↗

arXiv2025

Learning Discrete Concepts in Latent Hierarchical Models

Learning concepts from natural high-dimensional data (e.g., images) holds potential in building human-aligned and interpretable machine learning models. Despite its encouraging prospect, formalization and theoretical insights into this crucial task are still lacking. In this work, we formalize concepts as discrete latent causal variables that are related via a hierarchical causal model that encodes different abstraction levels of concepts embedded in high-dimensional data (e.g., a dog breed and its eye shapes in natural images). We formulate conditions to facilitate the identification of the proposed causal model, which reveals when learning such concepts from unsupervised data is possible. Our conditions permit complex causal hierarchical structures beyond latent trees and multi-level directed acyclic graphs in prior work and can handle high-dimensional, continuous observed variables, which is well-suited for unstructured data modalities such as images. We substantiate our theoretical claims with synthetic data experiments. Further, we discuss our theory's implications for understanding the underlying mechanisms of latent diffusion models and provide corresponding empirical evidence for our theoretical insights.

cs.LG↗

arXiv2024

Web2Code: A Large-scale Webpage-to-Code Dataset and Evaluation Framework for Multimodal LLMs

Multimodal large language models (MLLMs) have shown impressive success across modalities such as image, video, and audio in a variety of understanding and generation tasks. However, current MLLMs are surprisingly poor at understanding webpage screenshots and generating their corresponding HTML code. To address this problem, we propose $\texttt{Web2Code}$, a benchmark consisting of a new large-scale webpage-to-code dataset for instruction tuning and an evaluation framework for the webpage understanding and HTML code translation abilities of MLLMs. For dataset construction, we leverage pretrained LLMs to enhance existing webpage-to-code datasets as well as generate a diverse pool of new webpages rendered into images. Specifically, the inputs are webpage images and instructions, while the responses are the webpage's HTML code. We further include diverse natural language QA pairs about the webpage content in the responses to enable a more comprehensive understanding of the web content. To evaluate model performance in these tasks, we develop an evaluation framework for testing MLLMs' abilities in webpage understanding and web-to-code generation. Extensive experiments show that our proposed dataset is beneficial not only to our proposed tasks but also in the general visual domain. We hope our work will contribute to the development of general MLLMs suitable for web-based content generation and task automation. Our data and code are available at https://github.com/MBZUAI-LLM/web2code.

cs.CV↗

arXiv2024

Patient-Specific Models of Treatment Effects Explain Heterogeneity in Tuberculosis

Tuberculosis (TB) is a major global health challenge, and is compounded by co-morbidities such as HIV, diabetes, and anemia, which complicate treatment outcomes and contribute to heterogeneous patient responses. Traditional models of TB often overlook this heterogeneity by focusing on broad, pre-defined patient groups, thereby missing the nuanced effects of individual patient contexts. We propose moving beyond coarse subgroup analyses by using contextualized modeling, a multi-task learning approach that encodes patient context into personalized models of treatment effects, revealing patient-specific treatment benefits. Applied to the TB Portals dataset with multi-modal measurements for over 3,000 TB patients, our model reveals structured interactions between co-morbidities, treatments, and patient outcomes, identifying anemia, age of onset, and HIV as influential for treatment efficacy. By enhancing predictive accuracy in heterogeneous populations and providing patient-specific insights, contextualized models promise to enable new approaches to personalized treatment.

cs.LG↗

arXiv2024

Dynamic Rewarding with Prompt Optimization Enables Tuning-free Self-Alignment of Language Models

Aligning Large Language Models (LLMs) traditionally relies on costly training and human preference annotations. Self-alignment seeks to reduce these expenses by enabling models to align themselves. To further lower costs and achieve alignment without any expensive tuning or annotations, we introduce a new tuning-free approach for self-alignment, Dynamic Rewarding with Prompt Optimization (DRPO). Our approach leverages a search-based optimization framework that allows LLMs to iteratively self-improve and craft the optimal alignment instructions, all without additional training or human intervention. The core of DRPO is a dynamic rewarding mechanism, which identifies and rectifies model-specific alignment weaknesses, allowing LLMs to adapt efficiently to diverse alignment challenges. Empirical evaluations on eight recent LLMs, both open- and closed-sourced, demonstrate that DRPO significantly enhances alignment performance, with base models outperforming their SFT/RLHF-tuned counterparts. Moreover, the prompts automatically optimized by DRPO surpass those curated by human experts, further validating the effectiveness of our approach. Our findings highlight the great potential of current LLMs to achieve adaptive self-alignment through inference-time optimization, complementing tuning-based alignment methods.

cs.CL↗

arXiv2024

Crystal: Illuminating LLM Abilities on Language and Code

Large Language Models (LLMs) specializing in code generation (which are also often referred to as code LLMs), e.g., StarCoder and Code Llama, play increasingly critical roles in various software development scenarios. It is also crucial for code LLMs to possess both code generation and natural language abilities for many specific applications, such as code snippet retrieval using natural language or code explanations. The intricate interaction between acquiring language and coding skills complicates the development of strong code LLMs. Furthermore, there is a lack of thorough prior studies on the LLM pretraining strategy that mixes code and natural language. In this work, we propose a pretraining strategy to enhance the integration of natural language and coding capabilities within a single LLM. Specifically, it includes two phases of training with appropriately adjusted code/language ratios. The resulting model, Crystal, demonstrates remarkable capabilities in both domains. Specifically, it has natural language and coding performance comparable to that of Llama 2 and Code Llama, respectively. Crystal exhibits better data efficiency, using 1.4 trillion tokens compared to the more than 2 trillion tokens used by Llama 2 and Code Llama. We verify our pretraining strategy by analyzing the training process and observe consistent improvements in most benchmarks. We also adopted a typical application adaptation phase with a code-centric data mixture, only to find that it did not lead to enhanced performance or training efficiency, underlining the importance of a carefully designed data recipe. To foster research within the community, we commit to open-sourcing every detail of the pretraining, including our training datasets, code, loggings and 136 checkpoints throughout the training.

cs.SE↗

arXiv2024

LQ-LoRA: Low-rank Plus Quantized Matrix Decomposition for Efficient Language Model Finetuning

We propose a simple approach for memory-efficient adaptation of pretrained language models. Our approach uses an iterative algorithm to decompose each pretrained matrix into a high-precision low-rank component and a memory-efficient quantized component. During finetuning, the quantized component remains fixed and only the low-rank component is updated. We present an integer linear programming formulation of the quantization component which enables dynamic configuration of quantization parameters (e.g., bit-width, block size) for each matrix given an overall target memory budget. We further explore a data-aware version of the algorithm which uses an approximation of the Fisher information matrix to weight the reconstruction objective during matrix decomposition. Experiments on finetuning RoBERTa and LLaMA-2 (7B and 70B) demonstrate that our low-rank plus quantized matrix decomposition approach (LQ-LoRA) outperforms strong QLoRA and GPTQ-LoRA baselines and enables aggressive quantization to sub-3 bits with only minor performance degradations. When finetuned on a language modeling calibration dataset, LQ-LoRA can also be used for model compression; in this setting our 2.75-bit LLaMA-2-70B model (which has 2.85 bits on average when including the low-rank components and requires 27GB of GPU memory) performs respectably compared to the 16-bit baseline.

cs.CL↗

arXiv2024

On Optimizing the Communication of Model Parallelism

We study a novel and important communication pattern in large-scale model-parallel deep learning (DL), which we call cross-mesh resharding. This pattern emerges when the two paradigms of model parallelism - intra-operator and inter-operator parallelism - are combined to support large models on large clusters. In cross-mesh resharding, a sharded tensor needs to be sent from a source device mesh to a destination device mesh, on which the tensor may be distributed with the same or different layouts. We formalize this as a many-to-many multicast communication problem, and show that existing approaches either are sub-optimal or do not generalize to different network topologies or tensor layouts, which result from different model architectures and parallelism strategies. We then propose two contributions to address cross-mesh resharding: an efficient broadcast-based communication system, and an "overlapping-friendly" pipeline schedule. On microbenchmarks, our overall system outperforms existing ones by up to 10x across various tensor and mesh layouts. On end-to-end training of two large models, GPT-3 and U-Transformer, we improve throughput by 10% and 50%, respectively.

cs.LG↗

arXiv2024

Pandora: Towards General World Model with Natural Language Actions and Video States

World models simulate future states of the world in response to different actions. They facilitate interactive content creation and provides a foundation for grounded, long-horizon reasoning. Current foundation models do not fully meet the capabilities of general world models: large language models (LLMs) are constrained by their reliance on language modality and their limited understanding of the physical world, while video models lack interactive action control over the world simulations. This paper makes a step towards building a general world model by introducing Pandora, a hybrid autoregressive-diffusion model that simulates world states by generating videos and allows real-time control with free-text actions. Pandora achieves domain generality, video consistency, and controllability through large-scale pretraining and instruction tuning. Crucially, Pandora bypasses the cost of training-from-scratch by integrating a pretrained LLM (7B) and a pretrained video model, requiring only additional lightweight finetuning. We illustrate extensive outputs by Pandora across diverse domains (indoor/outdoor, natural/urban, human/robot, 2D/3D, etc.). The results indicate great potential of building stronger general world models with larger-scale training.

cs.CV↗

arXiv2024

Unified Generation, Reconstruction, and Representation: Generalized Diffusion with Adaptive Latent Encoding-Decoding

The vast applications of deep generative models are anchored in three core capabilities -- generating new instances, reconstructing inputs, and learning compact representations -- across various data types, such as discrete text/protein sequences and continuous images. Existing model families, like variational autoencoders (VAEs), generative adversarial networks (GANs), autoregressive models, and (latent) diffusion models, generally excel in specific capabilities and data types but fall short in others. We introduce Generalized Encoding-Decoding Diffusion Probabilistic Models (EDDPMs) which integrate the core capabilities for broad applicability and enhanced performance. EDDPMs generalize the Gaussian noising-denoising in standard diffusion by introducing parameterized encoding-decoding. Crucially, EDDPMs are compatible with the well-established diffusion model objective and training recipes, allowing effective learning of the encoder-decoder parameters jointly with diffusion. By choosing appropriate encoder/decoder (e.g., large language models), EDDPMs naturally apply to different data types. Extensive experiments on text, proteins, and images demonstrate the flexibility to handle diverse data and tasks and the strong improvement over various existing models.

cs.LG↗

arXiv2024

Contextualized Policy Recovery: Modeling and Interpreting Medical Decisions with Adaptive Imitation Learning

Interpretable policy learning seeks to estimate intelligible decision policies from observed actions; however, existing models force a tradeoff between accuracy and interpretability, limiting data-driven interpretations of human decision-making processes. Fundamentally, existing approaches are burdened by this tradeoff because they represent the underlying decision process as a universal policy, when in fact human decisions are dynamic and can change drastically under different contexts. Thus, we develop Contextualized Policy Recovery (CPR), which re-frames the problem of modeling complex decision processes as a multi-task learning problem, where each context poses a unique task and complex decision policies can be constructed piece-wise from many simple context-specific policies. CPR models each context-specific policy as a linear map, and generates new policy models $\textit{on-demand}$ as contexts are updated with new observations. We provide two flavors of the CPR framework: one focusing on exact local interpretability, and one retaining full global interpretability. We assess CPR through studies on simulated and real data, achieving state-of-the-art performance on predicting antibiotic prescription in intensive care units ($+22\%$ AUROC vs. previous SOTA) and predicting MRI prescription for Alzheimer's patients ($+7.7\%$ AUROC vs. previous SOTA). With this improvement, CPR closes the accuracy gap between interpretable and black-box methods, allowing high-resolution exploration and analysis of context-specific decision models.

cs.LG↗

arXiv2024

DISTFLASHATTN: Distributed Memory-efficient Attention for Long-context LLMs Training

FlashAttention (Dao, 2023) effectively reduces the quadratic peak memory usage to linear in training transformer-based large language models (LLMs) on a single GPU. In this paper, we introduce DISTFLASHATTN, a distributed memory-efficient attention mechanism optimized for long-context LLMs training. We propose three key techniques: token-level workload balancing, overlapping key-value communication, and a rematerialization-aware gradient checkpointing algorithm. We evaluate DISTFLASHATTN on Llama-7B and variants with sequence lengths from 32K to 512K. DISTFLASHATTN achieves 8x longer sequences, 4.45 - 5.64x speedup compared to Ring Self-Attention, 2 - 8x longer sequences, 1.24 - 2.01x speedup compared to Megatron-LM with FlashAttention. It achieves 1.67x and 1.26 - 1.88x speedup compared to recent Ring Attention and DeepSpeed-Ulysses. Code is available at https://github.com/RulinShao/LightSeq.

cs.LG↗

arXiv2024

LMSYS-Chat-1M: A Large-Scale Real-World LLM Conversation Dataset

Studying how people interact with large language models (LLMs) in real-world scenarios is increasingly important due to their widespread use in various applications. In this paper, we introduce LMSYS-Chat-1M, a large-scale dataset containing one million real-world conversations with 25 state-of-the-art LLMs. This dataset is collected from 210K unique IP addresses in the wild on our Vicuna demo and Chatbot Arena website. We offer an overview of the dataset's content, including its curation process, basic statistics, and topic distribution, highlighting its diversity, originality, and scale. We demonstrate its versatility through four use cases: developing content moderation models that perform similarly to GPT-4, building a safety benchmark, training instruction-following models that perform similarly to Vicuna, and creating challenging benchmark questions. We believe that this dataset will serve as a valuable resource for understanding and advancing LLM capabilities. The dataset is publicly available at https://huggingface.co/datasets/lmsys/lmsys-chat-1m.

cs.CL↗

arXiv2024

MobiLlama: Towards Accurate and Lightweight Fully Transparent GPT

"Bigger the better" has been the predominant trend in recent Large Language Models (LLMs) development. However, LLMs do not suit well for scenarios that require on-device processing, energy efficiency, low memory footprint, and response efficiency. These requisites are crucial for privacy, security, and sustainable deployment. This paper explores the "less is more" paradigm by addressing the challenge of designing accurate yet efficient Small Language Models (SLMs) for resource constrained devices. Our primary contribution is the introduction of an accurate and fully transparent open-source 0.5 billion (0.5B) parameter SLM, named MobiLlama, catering to the specific needs of resource-constrained computing with an emphasis on enhanced performance with reduced resource demands. MobiLlama is a SLM design that initiates from a larger model and applies a careful parameter sharing scheme to reduce both the pre-training and the deployment cost. Our work strives to not only bridge the gap in open-source SLMs but also ensures full transparency, where complete training data pipeline, training code, model weights, and over 300 checkpoints along with evaluation codes is available at : https://github.com/mbzuai-oryx/MobiLlama.

cs.CL↗