Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design

Combining discrete and continuous data is an important capability for generative models. We present Discrete Flow Models (DFMs), a new flow-based model of discrete data that provides the missing link in enabling flow-based generative models to be applied to multimodal continuous and discrete data problems. Our key insight is that the discrete equivalent of continuous space flow matching can be realized using Continuous Time Markov Chains. DFMs benefit from a simple derivation that includes discrete diffusion models as a specific instance while allowing improved performance over existing diffusion-based approaches. We utilize our DFMs method to build a multimodal flow-based modeling framework. We apply this capability to the task of protein co-design, wherein we learn a model for jointly generating protein structure and sequence. Our approach achieves state-of-the-art co-design performance while allowing the same multimodal model to be used for flexible generation of the sequence or structure.

Rethinking Variational Inference for Probabilistic Programs with Stochastic Support

We introduce Support Decomposition Variational Inference (SDVI), a new variational inference (VI) approach for probabilistic programs with stochastic support. Existing approaches to this problem rely on designing a single global variational guide on a variable-by-variable basis, while maintaining the stochastic control flow of the original program. SDVI instead breaks the program down into sub-programs with static support, before automatically building separate sub-guides for each. This decomposition significantly aids in the construction of suitable variational families, enabling, in turn, substantial improvements in inference performance.

Beyond Bayesian Model Averaging over Paths in Probabilistic Programs with Stochastic Support

The posterior in probabilistic programs with stochastic support decomposes as a weighted sum of the local posterior distributions associated with each possible program path. We show that making predictions with this full posterior implicitly performs a Bayesian model averaging (BMA) over paths. This is potentially problematic, as model misspecification can cause the BMA weights to prematurely collapse onto a single path, leading to sub-optimal predictions in turn. To remedy this issue, we propose alternative mechanisms for path weighting: one based on stacking and one based on ideas from PAC-Bayes. We show how both can be implemented as a cheap post-processing step on top of existing inference engines. In our experiments, we find them to be more robust and lead to better predictions compared to the default BMA weights.

In-Context Learning in Large Language Models Learns Label Relationships but Is Not Conventional Learning

The performance of Large Language Models (LLMs) on downstream tasks often improves significantly when including examples of the input-label relationship in the context. However, there is currently no consensus about how this in-context learning (ICL) ability of LLMs works: for example, while Xie et al. (2021) liken ICL to a general-purpose learning algorithm, Min et al. (2022b) argue ICL does not even learn label relationships from in-context examples. In this paper, we study (1) how labels of in-context examples affect predictions, (2) how label relationships learned during pre-training interact with input-label examples provided in-context, and (3) how ICL aggregates label information across in-context examples. Our findings suggests LLMs usually incorporate information from in-context labels, but that pre-training and in-context label relationships are treated differently, and that the model does not consider all in-context information equally. Our results give insights into understanding and aligning LLM behavior.

SelfCheck: Using LLMs to Zero-Shot Check Their Own Step-by-Step Reasoning

The recent progress in large language models (LLMs), especially the invention of chain-of-thoughts (CoT) prompting, makes it possible to solve reasoning problems. However, even the strongest LLMs are still struggling with more complicated problems that require non-linear thinking and multi-step reasoning. In this work, we explore whether LLMs have the ability to recognize their own errors, without resorting to external resources. In particular, we investigate whether they can be used to identify individual errors within a step-by-step reasoning. To this end, we propose a zero-shot verification scheme to recognize such errors. We then use this verification scheme to improve question-answering performance, by using it to perform weighted voting on different generated answers. We test the method on three math datasets-GSM8K, MathQA, and MATH-and find that it successfully recognizes errors and, in turn, increases final predictive performance.

On the Expected Size of Conformal Prediction Sets

While conformal predictors reap the benefits of rigorous statistical guarantees for their error frequency, the size of their corresponding prediction sets is critical to their practical utility. Unfortunately, there is currently a lack of finite-sample analysis and guarantees for their prediction set sizes. To address this shortfall, we theoretically quantify the expected size of the prediction set under the split conformal prediction framework. As this precise formulation cannot usually be calculated directly, we further derive point estimates and high probability intervals that can be easily computed, providing a practical method for characterizing the expected prediction set size across different possible realizations of the test and calibration data. Additionally, we corroborate the efficacy of our results with experiments on real-world datasets, for both regression and classification problems.

Trans-Dimensional Generative Modeling via Jump Diffusion Models

We propose a new class of generative models that naturally handle data of varying dimensionality by jointly modeling the state and dimension of each datapoint. The generative process is formulated as a jump diffusion process that makes jumps between different dimensional spaces. We first define a dimension destroying forward noising process, before deriving the dimension creating time-reversed generative process along with a novel evidence lower bound training objective for learning to approximate it. Simulating our learned approximation to the time-reversed generative process then provides an effective way of sampling data of varying dimensionality by jointly generating state values and dimensions. We demonstrate our approach on molecular and video datasets of varying dimensionality, reporting better compatibility with test-time diffusion guidance imputation tasks and improved interpolation capabilities versus fixed dimensional models that generate state values and dimensions separately.

Deep Stochastic Processes via Functional Markov Transition Operators

We introduce Markov Neural Processes (MNPs), a new class of Stochastic Processes (SPs) which are constructed by stacking sequences of neural parameterised Markov transition operators in function space. We prove that these Markov transition operators can preserve the exchangeability and consistency of SPs. Therefore, the proposed iterative construction adds substantial flexibility and expressivity to the original framework of Neural Processes (NPs) without compromising consistency or adding restrictions. Our experiments demonstrate clear advantages of MNPs over baseline models on a variety of tasks.

Prediction-Oriented Bayesian Active Learning

Information-theoretic approaches to active learning have traditionally focused on maximising the information gathered about the model parameters, most commonly by optimising the BALD score. We highlight that this can be suboptimal from the perspective of predictive performance. For example, BALD lacks a notion of an input distribution and so is prone to prioritise data of limited relevance. To address this we propose the expected predictive information gain (EPIG), an acquisition function that measures information gain in the space of predictions rather than parameters. We find that using EPIG leads to stronger predictive performance compared with BALD across a range of datasets and models, and thus provides an appealing drop-in replacement.