15 accepted papers
In GFlowNets and variational inference, it has been shown that the mean square error between target and model log probabilities is an effective, low variance, surrogate loss for training generative models. This loss has the property that when evaluated \emph{on-policy} its gradients correspond to th…
In drug discovery, highly automated high-throughput laboratories are used to screen a large number of compounds in search of effective drugs. These experiments are expensive, so one might hope to reduce their cost by only experimenting on a subset of the compounds, and predicting the outcomes of the…
Large language models (LLMs) have recently been proposed as general-purpose agents for experimental design, with claims that they can perform in-context experimental design. We evaluate this hypothesis using open-source instruction-tuned LLMs applied to genetic perturbation and molecular property di
Sparse dictionary learning (DL) has emerged as a powerful approach to extract semantically meaningful concepts from the internals of large language models (LLMs) trained mainly in the text domain. In this work, we explore whether DL can extract meaningful concepts from less human-interpretable scien…
Deriving insights from experimentally generated datasets requires methods that can account for random and systematic measurement errors and remove them in order to accurately represent the underlying effects of the conditions being tested. Here we present a framework for pretraining on large-scale m…
Causal representation learning has showed a variety of settings in which we can disentangle latent variables with identifiability guarantees (up to some reasonable equivalence class). Common to all of these approaches is the assumption that (1) the latent variables are represented as $d$-dimensional…
Multimodal representation learning techniques typically require paired samples to learn shared representations, but collecting paired samples can be challenging in fields like biology, where measurement devices often destroy the samples. This paper presents an approach to address the challenge of al…
Scientific hypotheses typically concern specific aspects of complex, imperfectly understood or entirely unknown mechanisms, such as the effect of gene expression levels on phenotypes or how microbial communities influence environmental health. Such queries are inherently causal (rather than purely a…
One of the grand challenges of cell biology is inferring the gene regulatory network (GRN) which describes interactions between genes and their products that control gene expression and cellular function. We can treat this as a causal discovery problem but with two non-standard challenges: (1) regul…
Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus…
A key goal of unsupervised representation learning is ``inverting'' a data generating process to recover its latent properties. Existing work that provably achieves this goal relies on strong assumptions on relationships between the latent variables (e.g., independence conditional on auxiliary info…
Formulating real-world optimization problems often begins with making predictions from historical data (e.g., an optimizer that aims to recommend fast routes relies upon travel-time predictions). Typically, learning the prediction model used to generate the optimization problem and solving that prob…
The theory of representation learning aims to build methods that provably invert the data generating process with minimal domain knowledge or any source of supervision. Most prior approaches require strong distributional assumptions on the latent variables and weak supervision (auxiliary information…
We use deep learning to model interactions across two or more sets of objects, such as user{–}movie ratings or protein{–}drug bindings. The canonical representation of such interactions is a matrix (or tensor) with an exchangeability property: the encoding’s meaning is not changed by permuting rows…
Counterfactual prediction requires understanding causal relationships between so-called treatment and outcome variables. This paper provides a recipe for augmenting deep learning methods to accurately characterize such relationships in the presence of instrument variables (IVs) – sources of treatmen…