This tutorial provides an in-depth guide on inference-time guidance and alignment methods for optimizing downstream reward functions in diffusion models. While diffusion models are renowned for their generative modeling capabilities, practical applications in fields such as biology often require sample generation that maximizes specific metrics (e.g., stability, affinity in proteins, closeness to target structures). In these scenarios, diffusion models can be adapted not only to generate realistic samples but also to explicitly maximize desired measures at inference time without fine-tuning. This tutorial explores the foundational aspects of such inference-time algorithms. We review these methods from a unified perspective, demonstrating that current techniques -- such as Sequential Monte Carlo (SMC)-based guidance, value-based sampling, and classifier guidance -- aim to approximate soft optimal denoising processes (a.k.a. policies in RL) that combine pre-trained denoising processes with value functions serving as look-ahead functions that predict from intermediate states to terminal rewards. Within this framework, we present several novel algorithms not yet covered in the literature. Furthermore, we discuss (1) fine-tuning methods combined with inference-time techniques, (2) inference-time algorithms based on search algorithms such as Monte Carlo tree search, which have received limited attention in current research, and (3) connections between inference-time algorithms in language models and diffusion models. The code of this tutorial on protein design is available at https://github.com/masa-ue/AlignInversePro

A machine learning tasks from observations must encounter and process uncertainty and novelty, especially when it is expected to maintain performance when observing new information and to choose the best fitting hypothesis to the currently observed information. In this context, some key questions arise: what is information, how much information did the observations provide, how much information is required to identify the data-generating process, how many observations remain to get that information, and how does a predictor determine that it has observed novel information? This paper strengthens existing answers to these questions by formalizing the notion of "identifiable information" that arises from the language used to express the relationship between distinct states. Model identifiability and sample complexity are defined via computation of an indicator function over a set of hypotheses. Their properties and asymptotic statistics are described for data-generating processes ranging from deterministic processes to ergodic stationary stochastic processes. This connects the notion of identifying information in finite steps with asymptotic statistics and PAC-learning. The indicator function's computation naturally formalizes novel information and its identification from observations with respect to a hypothesis set. We also proved that computable PAC-Bayes learners' sample complexity distribution is determined by its moments in terms of the the prior probability distribution over a fixed finite hypothesis set.

Conflicting objectives present a considerable challenge in interleaving multi-task learning, necessitating the need for meticulous design and balance to ensure effective learning of a representative latent data space across all tasks without mutual negative impact. Our proposed model, Deep Disentangled Interleaving Variational Encoding (Deep-DIVE) learns disentangled features from the original input to form clusters in the embedding space and unifies these features via the cross-attention mechanism in the fusion stage. We theoretically prove that combining the objectives for reconstruction and forecasting fully captures the lower bound and mathematically derive a loss function for disentanglement using Naïve Bayes. Experiments on two public datasets show that DeepDIVE disentangles the original input and yields forecast accuracies better than the original VAE and comparable to existing state-of-the-art baselines. In multi-objective deep learning, gradients from different objectives can conflict, when the different loss terms induce competing gradient directions during training of the network. Balancing these gradients to ensure stable and effective learning is a significant challenge prompting the development of methods to mitigate this issue, such as Liu et al. (2021); Yu et al. (2020); Sener & Koltun (2018) which solve an additional optmization problem before each gradient update step, to manipulate conflicting gradients before the update.

Graph convolution networks (GCNs) for recommendations have emerged as an important research topic due to their ability to exploit higher-order neighbors. Despite their success, most of them suffer from the popularity bias brought by a small number of active users and popular items. Also, a real-world user-item bipartite graph contains many noisy interactions, which may hamper the sensitive GCNs. Most existing works typically perform graph augmentation to create multiple views of the original graph by randomly dropping edges/nodes or relying on predefined rules, and these augmented views always serve as an auxiliary task by maximizing their correspondence. However, we argue that the graph structures generated from these vanilla approaches may be suboptimal, and maximizing their correspondence will force the representation to capture information irrelevant for the recommendation task.

Causal structure learning from time series data is a major scientific challenge. Existing algorithms assume that measurements occur sufficiently quickly; more precisely, they assume that the system and measurement timescales are approximately equal. In many scientific domains, however, measurements occur at a significantly slower rate than the underlying system changes. Moreover, the size of the mismatch between timescales is often unknown. This paper provides three distinct causal structure learning algorithms, all of which discover all dynamic graphs that could explain the observed measurement data as arising from undersampling at some rate. That is, these algorithms all learn causal structure without assuming any particular relation between the measurement and system timescales; they are thus rate-agnostic.

A growing body of work has begun to study intervention design for efficient structure learning of causal directed acyclic graphs (DAGs). A typical setting is a \emph{causally sufficient} setting, i.e. a system with no latent confounders, selection bias, or feedback, when the essential graph of the observational equivalence class (EC) is given as an input and interventions are assumed to be noiseless. Most existing works focus on \textit{worst-case} or \textit{average-case} lower bounds for the number of interventions required to orient a DAG. These worst-case lower bounds only establish that the largest clique in the essential graph \textit{could} make it difficult to learn the true DAG. In this work, we develop a \textit{universal} lower bound for single-node interventions that establishes that the largest clique is \textit{always} a fundamental impediment to structure learning.

Discovering ideal Graph Neural Networks (GNNs) architectures for different tasks is labor intensive and time consuming. To save human efforts, Neural Architecture Search (NAS) recently has been used to automatically discover adequate GNN architectures for certain tasks in order to achieve competitive or even better performance compared with manually designed architectures. However, existing works utilizing NAS to search GNN structures fail to answer the question: how NAS is able to select the desired GNN architectures? In this paper, we investigate this question to solve the problem, for the first time. We conduct a measurement study with experiments to discover that gradient based NAS methods tend to select proper architectures based on the usefulness of different types of information with respect to the target task.

We develop a latent variable model and an efficient spectral algorithm motivated by the recent emergence of very large data sets of chromatin marks from multiple human cell types. A natural model for chromatin data in one cell type is a Hidden Markov Model (HMM); we model the relationship between multiple cell types by connecting their hidden states by a fixed tree of known structure. The main challenge with learning parameters of such models is that iterative methods such as EM are very slow, while naive spectral methods result in time and space complexity exponential in the number of cell types. We exploit properties of the tree structure of the hidden states to provide spectral algorithms that are more computationally efficient for current biological datasets. We provide sample complexity bounds for our algorithm and evaluate it experimentally on biological data from nine human cell types.

We introduce the Locally Linear Latent Variable Model (LL-LVM), a probabilistic model for non-linear manifold discovery that describes a joint distribution over observations, their manifold coordinates and locally linear maps conditioned on a set of neighbourhood relationships. The model allows straightforward variational optimisation of the posterior distribution on coordinates and locally linear maps from the latent space to the observation space given the data. Thus, the LL-LVM encapsulates the local-geometry preserving intuitions that underlie non-probabilistic methods such as locally linear embedding (LLE). Its probabilistic semantics make it easy to evaluate the quality of hypothesised neighbourhood relationships, select the intrinsic dimensionality of the manifold, construct out-of-sample extensions and to combine the manifold model with additional probabilistic models that capture the structure of coordinates within the manifold.

Learning structures between groups of variables from data with missing values is an important task in the real world, yet difficult to solve. One typical scenario is discovering the structure among topics in the education domain to identify learning pathways. Here, the observations are student performances for questions under each topic which contain missing values. However, most existing methods focus on learning structures between a few individual variables from the complete data. In this work, we propose VISL, a novel scalable structure learning approach that can simultaneously infer structures between groups of variables under missing data and perform missing value imputations with deep learning. Particularly, we propose a generative model with a structured latent space and a graph neural network-based architecture, scaling to a large number of variables.