On How AI Needs to Change to Advance the Science of Drug Discovery

Research around AI for Science has seen significant success since the rise of deep learning models over the past decade, even with longstanding challenges such as protein structure prediction. However, this fast development inevitably made their flaws apparent -- especially in domains of reasoning where understanding the cause-effect relationship is important. One such domain is drug discovery, in which such understanding is required to make sense of data otherwise plagued by spurious correlations. Said spuriousness only becomes worse with the ongoing trend of ever-increasing amounts of data in the life sciences and thereby restricts researchers in their ability to understand disease biology and create better therapeutics. Therefore, to advance the science of drug discovery with AI it is becoming necessary to formulate the key problems in the language of causality, which allows the explication of modelling assumptions needed for identifying true cause-effect relationships. In this attention paper, we present causal drug discovery as the craft of creating models that ground the process of drug discovery in causal reasoning.Comment: Main paper: 6 pages, References: 1.5 pages. Main paper: 3 figure

On the Tractability of Neural Causal Inference

Roth (1996) proved that any form of marginal inference with probabilistic graphical models (e.g. Bayesian Networks) will at least be NP-hard. Introduced and extensively investigated in the past decade, the neural probabilistic circuits known as sum-product network (SPN) offers linear time complexity. On another note, research around neural causal models (NCM) recently gained traction, demanding a tighter integration of causality for machine learning. To this end, we present a theoretical investigation of if, when, how and under what cost tractability occurs for different NCM. We prove that SPN-based causal inference is generally tractable, opposed to standard MLP-based NCM. We further introduce a new tractable NCM-class that is efficient in inference and fully expressive in terms of Pearl's Causal Hierarchy. Our comparative empirical illustration on simulations and standard benchmarks validates our theoretical proofs.Comment: Main paper: 8 pages, References: 2 pages, Appendix: 5 pages. Figures: 5 main, 2 appendi

Causal Parrots: Large Language Models May Talk Causality But Are Not Causal

Some argue scale is all what is needed to achieve AI, covering even causal models. We make it clear that large language models (LLMs) cannot be causal and give reason onto why sometimes we might feel otherwise. To this end, we define and exemplify a new subgroup of Structural Causal Model (SCM) that we call meta SCM which encode causal facts about other SCM within their variables. We conjecture that in the cases where LLM succeed in doing causal inference, underlying was a respective meta SCM that exposed correlations between causal facts in natural language on whose data the LLM was ultimately trained. If our hypothesis holds true, then this would imply that LLMs are like parrots in that they simply recite the causal knowledge embedded in the data. Our empirical analysis provides favoring evidence that current LLMs are even weak `causal parrots.'Comment: Published in Transactions in Machine Learning Research (TMLR) (08/2023). Main paper: 17 pages, References: 3 pages, Appendix: 7 pages. Figures: 5 main, 3 appendix. Tables: 3 mai

Pearl Causal Hierarchy on Image Data: Intricacies & Challenges

Many researchers have voiced their support towards Pearl's counterfactual theory of causation as a stepping stone for AI/ML research's ultimate goal of intelligent systems. As in any other growing subfield, patience seems to be a virtue since significant progress on integrating notions from both fields takes time, yet, major challenges such as the lack of ground truth benchmarks or a unified perspective on classical problems such as computer vision seem to hinder the momentum of the research movement. This present work exemplifies how the Pearl Causal Hierarchy (PCH) can be understood on image data by providing insights on several intricacies but also challenges that naturally arise when applying key concepts from Pearlian causality to the study of image data.Comment: Main paper: 9 pages, References: 2 pages. Main paper: 7 figure

Can Linear Programs Have Adversarial Examples? A Causal Perspective

The recent years have been marked by extended research on adversarial attacks, especially on deep neural networks. With this work we intend on posing and investigating the question of whether the phenomenon might be more general in nature, that is, adversarial-style attacks outside classification. Specifically, we investigate optimization problems starting with Linear Programs (LPs). We start off by demonstrating the shortcoming of a naive mapping between the formalism of adversarial examples and LPs, to then reveal how we can provide the missing piece -- intriguingly, through the Pearlian notion of Causality. Characteristically, we show the direct influence of the Structural Causal Model (SCM) onto the subsequent LP optimization, which ultimately exposes a notion of confounding in LPs (inherited by said SCM) that allows for adversarial-style attacks. We provide both the general proof formally alongside existential proofs of such intriguing LP-parameterizations based on SCM for three combinatorial problems, namely Linear Assignment, Shortest Path and a real world problem of energy systems.Comment: Main paper: 9 pages, References: 2 page, Supplement: 2 pages. Main paper: 2 figures, 3 tables, Supplement: 1 figure, 1 tabl

Tearing Apart NOTEARS: Controlling the Graph Prediction via Variance Manipulation

Simulations are ubiquitous in machine learning. Especially in graph learning, simulations of Directed Acyclic Graphs (DAG) are being deployed for evaluating new algorithms. In the literature, it was recently argued that continuous-optimization approaches to structure discovery such as NOTEARS might be exploiting the sortability of the variable's variances in the available data due to their use of least square losses. Specifically, since structure discovery is a key problem in science and beyond, we want to be invariant to the scale being used for measuring our data (e.g. meter versus centimeter should not affect the causal direction inferred by the algorithm). In this work, we further strengthen this initial, negative empirical suggestion by both proving key results in the multivariate case and corroborating with further empirical evidence. In particular, we show that we can control the resulting graph with our targeted variance attacks, even in the case where we can only partially manipulate the variances of the data.Comment: Main paper: 5.5 pages, References: 1 page, Supplement: 2 pages. Main paper: 3 figures, Supplement: 1 figure, 1 tabl

Machines Explaining Linear Programs

There has been a recent push in making machine learning models more interpretable so that their performance can be trusted. Although successful, these methods have mostly focused on the deep learning methods while the fundamental optimization methods in machine learning such as linear programs (LP) have been left out. Even if LPs can be considered as whitebox or clearbox models, they are not easy to understand in terms of relationships between inputs and outputs. As a linear program only provides the optimal solution to an optimization problem, further explanations are often helpful. In this work, we extend the attribution methods for explaining neural networks to linear programs. These methods explain the model by providing relevance scores for the model inputs, to show the influence of each input on the output. Alongside using classical gradient-based attribution methods we also propose a way to adapt perturbation-based attribution methods to LPs. Our evaluations of several different linear and integer problems showed that attribution methods can generate useful explanations for linear programs. However, we also demonstrate that using a neural attribution method directly might come with some drawbacks, as the properties of these methods on neural networks do not necessarily transfer to linear programs. The methods can also struggle if a linear program has more than one optimal solution, as a solver just returns one possible solution. Our results can hopefully be used as a good starting point for further research in this direction.Comment: Main paper: 9.5 pages, References: 2.5 pages, Supplement: 6 pages. Main paper: 5 figures, 4 tables, Supplement: 3 figures, 6 table

Towards a Solution to Bongard Problems: A Causal Approach

To date, Bongard Problems (BP) remain one of the few fortresses of AI history yet to be raided by the powerful models of the current era. We present a systematic analysis using modern techniques from the intersection of causality and AI/ML in a humble effort of reviving research around BPs. Specifically, we first compile the BPs into a Markov decision process, then secondly pose causal assumptions on the data generating process arguing for their applicability to BPs, and finally apply reinforcement learning techniques for solving the BPs subject to the causal assumptions.Comment: Main paper: 5.5 pages, References: 1 page, Supplement: 1 page. Main paper: 5 figures, Supplement: 3 figure