Chris Wendler

Mathieu Chevalley, Jacob Sackett-Sanders, Yusuf Roohani et al.

In drug discovery, mapping interactions between genes within cellular systems is a crucial early step. Such maps are not only foundational for understanding the molecular mechanisms underlying disease biology but also pivotal for formulating hypotheses about potential targets for new medicines. Recognizing the need to elevate the construction of these gene-gene interaction networks, especially from large-scale, real-world datasets of perturbed single cells, the CausalBench Challenge was initiated. This challenge aimed to inspire the machine learning community to enhance state-of-the-art methods, emphasizing better utilization of expansive genetic perturbation data. Using the framework provided by the CausalBench benchmark, participants were tasked with refining the current methodologies or proposing new ones. This report provides an analysis and summary of the methods submitted during the challenge to give a partial image of the state of the art at the time of the challenge. Notably, the winning solutions significantly improved performance compared to previous baselines, establishing a new state of the art for this critical task in biology and medicine.

Bastian Seifert, Chris Wendler, Markus Püschel

We present a novel form of Fourier analysis, and associated signal processing concepts, for signals (or data) indexed by edge-weighted directed acyclic graphs (DAGs). This means that our Fourier basis yields an eigendecomposition of a suitable notion of shift and convolution operators that we define. DAGs are the common model to capture causal relationships between data values and in this case our proposed Fourier analysis relates data with its causes under a linearity assumption that we define. The definition of the Fourier transform requires the transitive closure of the weighted DAG for which several forms are possible depending on the interpretation of the edge weights. Examples include level of influence, distance, or pollution distribution. Our framework is different from prior GSP: it is specific to DAGs and leverages, and extends, the classical theory of Moebius inversion from combinatorics. For a prototypical application we consider DAGs modeling dynamic networks in which edges change over time. Specifically, we model the spread of an infection on such a DAG obtained from real-world contact tracing data and learn the infection signal from samples assuming sparsity in the Fourier domain.

Romeo Valentin, Claudio Ferrari, Jérémy Scheurer et al.

We present our submission for the configuration task of the Machine Learning for Combinatorial Optimization (ML4CO) NeurIPS 2021 competition. The configuration task is to predict a good configuration of the open-source solver SCIP to solve a mixed integer linear program (MILP) efficiently. We pose this task as a supervised learning problem: First, we compile a large dataset of the solver performance for various configurations and all provided MILP instances. Second, we use this data to train a graph neural network that learns to predict a good configuration for a specific instance. The submission was tested on the three problem benchmarks of the competition and improved solver performance over the default by 12% and 35% and 8% across the hidden test instances. We ranked 3rd out of 15 on the global leaderboard and won the student leaderboard. We make our code publicly available at \url{https://github.com/RomeoV/ml4co-competition} .

Viacheslav Surkov, Chris Wendler, Antonio Mari et al.

For large language models (LLMs), sparse autoencoders (SAEs) have been shown to decompose intermediate representations that often are not interpretable directly into sparse sums of interpretable features, facilitating better control and subsequent analysis. However, similar analyses and approaches have been lacking for text-to-image models. We investigate the possibility of using SAEs to learn interpretable features for SDXL Turbo, a few-step text-to-image diffusion model. To this end, we train SAEs on the updates performed by transformer blocks within SDXL Turbo's denoising U-net in its 1-step setting. Interestingly, we find that they generalize to 4-step SDXL Turbo and even to the multi-step SDXL base model (i.e., a different model) without additional training. In addition, we show that their learned features are interpretable, causally influence the generation process, and reveal specialization among the blocks. We do so by creating RIEBench, a representation-based image editing benchmark, for editing images while they are generated by turning on and off individual SAE features. This allows us to track which transformer blocks' features are the most impactful depending on the edit category. Our work is the first investigation of SAEs for interpretability in text-to-image diffusion models and our results establish SAEs as a promising approach for understanding and manipulating the internal mechanisms of text-to-image models.

Saibo Geng, Berkay Döner, Chris Wendler et al.

Constrained decoding, a technique for enforcing constraints on language model outputs, offers a way to control text generation without retraining or architectural modifications. Its application is, however, typically restricted to models that give users access to next-token distributions (usually via softmax logits), which poses a limitation with blackbox large language models (LLMs). This paper introduces sketch-guided constrained decoding (SGCD), a novel approach to constrained decoding for blackbox LLMs, which operates without access to the logits of the blackbox LLM. SGCD utilizes a locally hosted auxiliary model to refine the output of an unconstrained blackbox LLM, effectively treating this initial output as a "sketch" for further elaboration. This approach is complementary to traditional logit-based techniques and enables the application of constrained decoding in settings where full model transparency is unavailable. We demonstrate the efficacy of SGCD through experiments in closed information extraction and constituency parsing, showing how it enhances the utility and flexibility of blackbox LLMs for complex NLP tasks.

Panagiotis Misiakos, Chris Wendler, Markus Püschel

We present a novel perspective and algorithm for learning directed acyclic graphs (DAGs) from data generated by a linear structural equation model (SEM). First, we show that a linear SEM can be viewed as a linear transform that, in prior work, computes the data from a dense input vector of random valued root causes (as we will call them) associated with the nodes. Instead, we consider the case of (approximately) few root causes and also introduce noise in the measurement of the data. Intuitively, this means that the DAG data is produced by few data-generating events whose effect percolates through the DAG. We prove identifiability in this new setting and show that the true DAG is the global minimizer of the $L^0$-norm of the vector of root causes. For data with few root causes, with and without noise, we show superior performance compared to prior DAG learning methods.

Chris Wendler, Andisheh Amrollahi, Bastian Seifert et al.

Many applications of machine learning on discrete domains, such as learning preference functions in recommender systems or auctions, can be reduced to estimating a set function that is sparse in the Fourier domain. In this work, we present a new family of algorithms for learning Fourier-sparse set functions. They require at most $nk - k \log_2 k + k$ queries (set function evaluations), under mild conditions on the Fourier coefficients, where $n$ is the size of the ground set and $k$ the number of non-zero Fourier coefficients. In contrast to other work that focused on the orthogonal Walsh-Hadamard transform, our novel algorithms operate with recently introduced non-orthogonal Fourier transforms that offer different notions of Fourier-sparsity. These naturally arise when modeling, e.g., sets of items forming substitutes and complements. We demonstrate effectiveness on several real-world applications.

Markus Püschel, Chris Wendler

Set functions are functions (or signals) indexed by the powerset (set of all subsets) of a finite set N. They are fundamental and ubiquitous in many application domains and have been used, for example, to formally describe or quantify loss functions for semantic image segmentation, the informativeness of sensors in sensor networks the utility of sets of items in recommender systems, cooperative games in game theory, or bidders in combinatorial auctions. In particular, the subclass of submodular functions occurs in many optimization and machine learning problems. In this paper, we derive discrete-set signal processing (SP), a novel shift-invariant linear signal processing framework for set functions. Discrete-set SP considers different notions of shift obtained from set union and difference operations. For each shift it provides associated notions of shift-invariant filters, convolution, Fourier transform, and frequency response. We provide intuition for our framework using the concept of generalized coverage function that we define, identify multivariate mutual information as a special case of a discrete-set spectrum, and motivate frequency ordering. Our work brings a new set of tools for analyzing and processing set functions, and, in particular, for dealing with their exponential nature. We show two prototypical applications and experiments: compression in submodular function optimization and sampling for preference elicitation in combinatorial auctions.

Chris Wendler, Dan Alistarh, Markus Püschel

We present a novel class of convolutional neural networks (CNNs) for set functions, i.e., data indexed with the powerset of a finite set. The convolutions are derived as linear, shift-equivariant functions for various notions of shifts on set functions. The framework is fundamentally different from graph convolutions based on the Laplacian, as it provides not one but several basic shifts, one for each element in the ground set. Prototypical experiments with several set function classification tasks on synthetic datasets and on datasets derived from real-world hypergraphs demonstrate the potential of our new powerset CNNs.