Manifold-Constrained Nucleus-Level Denoising Diffusion Model for Structure-Based Drug Design

Artificial intelligence models have shown great potential in structure-based drug design, generating ligands with high binding affinities. However, existing models have often overlooked a crucial physical constraint: atoms must maintain a minimum pairwise distance to avoid separation violation, a phenomenon governed by the balance of attractive and repulsive forces. To mitigate such separation violations, we propose NucleusDiff. It models the interactions between atomic nuclei and their surrounding electron clouds by enforcing the distance constraint between the nuclei and manifolds. We quantitatively evaluate NucleusDiff using the CrossDocked2020 dataset and a COVID-19 therapeutic target, demonstrating that NucleusDiff reduces violation rate by up to 100.00% and enhances binding affinity by up to 22.16%, surpassing state-of-the-art models for structure-based drug design. We also provide qualitative analysis through manifold sampling, visually confirming the effectiveness of NucleusDiff in reducing separation violations and improving binding affinities.

Can Large Language Models Understand Symbolic Graphics Programs?

Assessing the capabilities of large language models (LLMs) is often challenging, in part, because it is hard to find tasks to which they have not been exposed during training. We take one step to address this challenge by turning to a new task: focusing on symbolic graphics programs, which are a popular representation for graphics content that procedurally generates visual data. LLMs have shown exciting promise towards program synthesis, but do they understand symbolic graphics programs? Unlike conventional programs, symbolic graphics programs can be translated to graphics content. Here, we characterize an LLM's understanding of symbolic programs in terms of their ability to answer questions related to the graphics content. This task is challenging as the questions are difficult to answer from the symbolic programs alone -- yet, they would be easy to answer from the corresponding graphics content as we verify through a human experiment. To understand symbolic programs, LLMs may need to possess the ability to imagine how the corresponding graphics content would look without directly accessing the rendered visual content. We use this task to evaluate LLMs by creating a large benchmark for the semantic understanding of symbolic graphics programs. This benchmark is built via program-graphics correspondence, hence requiring minimal human efforts. We evaluate current LLMs on our benchmark to elucidate a preliminary assessment of their ability to reason about visual scenes from programs. We find that this task distinguishes existing LLMs and models considered good at reasoning perform better. Lastly, we introduce Symbolic Instruction Tuning (SIT) to improve this ability. Specifically, we query GPT4-o with questions and images generated by symbolic programs. Such data are then used to finetune an LLM. We also find that SIT data can improve the general instruction following ability of LLMs.

Representational Alignment Supports Effective Machine Teaching

A good teacher should not only be knowledgeable; but should be able to communicate in a way that the student understands -- to share the student's representation of the world. In this work, we integrate insights from machine teaching and pragmatic communication with the burgeoning literature on representational alignment to characterize a utility curve defining a relationship between representational alignment and teacher capability for promoting student learning. To explore the characteristics of this utility curve, we design a supervised learning environment that disentangles representational alignment from teacher accuracy. We conduct extensive computational experiments with machines teaching machines, complemented by a series of experiments in which machines teach humans. Drawing on our findings that improved representational alignment with a student improves student learning outcomes (i.e., task accuracy), we design a classroom matching procedure that assigns students to teachers based on the utility curve. If we are to design effective machine teachers, it is not enough to build teachers that are accurate -- we want teachers that can align, representationally, to their students too.

Verbalized Machine Learning: Revisiting Machine Learning with Language Models

Motivated by the large progress made by large language models (LLMs), we introduce the framework of verbalized machine learning (VML). In contrast to conventional machine learning models that are typically optimized over a continuous parameter space, VML constrains the parameter space to be human-interpretable natural language. Such a constraint leads to a new perspective of function approximation, where an LLM with a text prompt can be viewed as a function parameterized by the text prompt. Guided by this perspective, we revisit classical machine learning problems, such as regression and classification, and find that these problems can be solved by an LLM-parameterized learner and optimizer. The major advantages of VML include (1) easy encoding of inductive bias: prior knowledge about the problem and hypothesis class can be encoded in natural language and fed into the LLM-parameterized learner; (2) automatic model class selection: the optimizer can automatically select a concrete model class based on data and verbalized prior knowledge, and it can update the model class during training; and (3) interpretable learner updates: the LLM-parameterized optimizer can provide explanations for why each learner update is performed. We conduct several studies to empirically evaluate the effectiveness of VML, and hope that VML can serve as a stepping stone to stronger interpretability and trustworthiness in ML.

ChatHuman: Language-driven 3D Human Understanding with Retrieval-Augmented Tool Reasoning

Numerous methods have been proposed to detect, estimate, and analyze properties of people in images, including the estimation of 3D pose, shape, contact, human-object interaction, emotion, and more. Each of these methods works in isolation instead of synergistically. Here we address this problem and build a language-driven human understanding system -- ChatHuman, which combines and integrates the skills of many different methods. To do so, we finetune a Large Language Model (LLM) to select and use a wide variety of existing tools in response to user inputs. In doing so, ChatHuman is able to combine information from multiple tools to solve problems more accurately than the individual tools themselves and to leverage tool output to improve its ability to reason about humans. The novel features of ChatHuman include leveraging academic publications to guide the application of 3D human-related tools, employing a retrieval-augmented generation model to generate in-context-learning examples for handling new tools, and discriminating and integrating tool results to enhance 3D human understanding. Our experiments show that ChatHuman outperforms existing models in both tool selection accuracy and performance across multiple 3D human-related tasks. ChatHuman is a step towards consolidating diverse methods for human analysis into a single, powerful, system for 3D human reasoning.

Re-Thinking Inverse Graphics With Large Language Models

Inverse graphics -- the task of inverting an image into physical variables that, when rendered, enable reproduction of the observed scene -- is a fundamental challenge in computer vision and graphics. Disentangling an image into its constituent elements, such as the shape, color, and material properties of the objects of the 3D scene that produced it, requires a comprehensive understanding of the environment. This requirement limits the ability of existing carefully engineered approaches to generalize across domains. Inspired by the zero-shot ability of large language models (LLMs) to generalize to novel contexts, we investigate the possibility of leveraging the broad world knowledge encoded in such models in solving inverse-graphics problems. To this end, we propose the Inverse-Graphics Large Language Model (IG-LLM), an inverse-graphics framework centered around an LLM, that autoregressively decodes a visual embedding into a structured, compositional 3D-scene representation. We incorporate a frozen pre-trained visual encoder and a continuous numeric head to enable end-to-end training. Through our investigation, we demonstrate the potential of LLMs to facilitate inverse graphics through next-token prediction, without the use of image-space supervision. Our analysis opens up new possibilities for precise spatial reasoning about images that exploit the visual knowledge of LLMs. We will release our code and data to ensure the reproducibility of our investigation and to facilitate future research at https://ig-llm.is.tue.mpg.de/

Your Finetuned Large Language Model is Already a Powerful Out-of-distribution Detector

We revisit the likelihood ratio between a pretrained large language model (LLM) and its finetuned variant as a criterion for out-of-distribution (OOD) detection. The intuition behind such a criterion is that, the pretrained LLM has the prior knowledge about OOD data due to its large amount of training data, and once finetuned with the in-distribution data, the LLM has sufficient knowledge to distinguish their difference. Leveraging the power of LLMs, we show that, for the first time, the likelihood ratio can serve as an effective OOD detector. Moreover, we apply the proposed LLM-based likelihood ratio to detect OOD questions in question-answering (QA) systems, which can be used to improve the performance of specialized LLMs for general questions. Given that likelihood can be easily obtained by the loss functions within contemporary neural network frameworks, it is straightforward to implement this approach in practice. Since both the pretrained LLMs and its various finetuned models are available, our proposed criterion can be effortlessly incorporated for OOD detection without the need for further training. We conduct comprehensive evaluation across on multiple settings, including far OOD, near OOD, spam detection, and QA scenarios, to demonstrate the effectiveness of the method.

Easy-to-Hard Generalization: Scalable Alignment Beyond Human Supervision

Current AI alignment methodologies rely on human-provided demonstrations or judgments, and the learned capabilities of AI systems would be upper-bounded by human capabilities as a result. This raises a challenging research question: How can we keep improving the systems when their capabilities have surpassed the levels of humans? This paper answers this question in the context of tackling hard reasoning tasks (e.g., level 4-5 MATH problems) via learning from human annotations on easier tasks (e.g., level 1-3 MATH problems), which we term as \textit{easy-to-hard generalization}. Our key insight is that an evaluator (reward model) trained on supervisions for easier tasks can be effectively used for scoring candidate solutions of harder tasks and hence facilitating easy-to-hard generalization over different levels of tasks. Based on this insight, we propose a novel approach to scalable alignment, which firstly trains the process-supervised reward models on easy problems (e.g., level 1-3), and then uses them to evaluate the performance of policy models on hard problems. We show that such \textit{easy-to-hard generalization from evaluators} can enable \textit{easy-to-hard generalizations in generators} either through re-ranking or reinforcement learning (RL). Notably, our process-supervised 7b RL model achieves an accuracy of 34.0\% on MATH500, despite only using human supervision on easy problems. Our approach suggests a promising path toward AI systems that advance beyond the frontier of human supervision.

A Compact Representation for Bayesian Neural Networks By Removing Permutation Symmetry

Bayesian neural networks (BNNs) are a principled approach to modeling predictive uncertainties in deep learning, which are important in safety-critical applications. Since exact Bayesian inference over the weights in a BNN is intractable, various approximate inference methods exist, among which sampling methods such as Hamiltonian Monte Carlo (HMC) are often considered the gold standard. While HMC provides high-quality samples, it lacks interpretable summary statistics because its sample mean and variance is meaningless in neural networks due to permutation symmetry. In this paper, we first show that the role of permutations can be meaningfully quantified by a number of transpositions metric. We then show that the recently proposed rebasin method allows us to summarize HMC samples into a compact representation that provides a meaningful explicit uncertainty estimate for each weight in a neural network, thus unifying sampling methods with variational inference. We show that this compact representation allows us to compare trained BNNs directly in weight space across sampling methods and variational inference, and to efficiently prune neural networks trained without explicit Bayesian frameworks by exploiting uncertainty estimates from HMC.

GraphDreamer: Compositional 3D Scene Synthesis from Scene Graphs

As pretrained text-to-image diffusion models become increasingly powerful, recent efforts have been made to distill knowledge from these text-to-image pretrained models for optimizing a text-guided 3D model. Most of the existing methods generate a holistic 3D model from a plain text input. This can be problematic when the text describes a complex scene with multiple objects, because the vectorized text embeddings are inherently unable to capture a complex description with multiple entities and relationships. Holistic 3D modeling of the entire scene further prevents accurate grounding of text entities and concepts. To address this limitation, we propose GraphDreamer, a novel framework to generate compositional 3D scenes from scene graphs, where objects are represented as nodes and their interactions as edges. By exploiting node and edge information in scene graphs, our method makes better use of the pretrained text-to-image diffusion model and is able to fully disentangle different objects without image-level supervision. To facilitate modeling of object-wise relationships, we use signed distance fields as representation and impose a constraint to avoid inter-penetration of objects. To avoid manual scene graph creation, we design a text prompt for ChatGPT to generate scene graphs based on text inputs. We conduct both qualitative and quantitative experiments to validate the effectiveness of GraphDreamer in generating high-fidelity compositional 3D scenes with disentangled object entities.