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Title: Interactive Visual Exploration of Latent Space (IVELS) for peptide auto-encoder model selection

Paper content:
We present a tool for Interactive Visual Exploration of Latent Space (IVELS) for model selection.
Evaluating generative models of discrete sequences from a  continuous  latent  space  is  a  challenging  problem,  since  their  optimization involves multiple competing objective terms.
We introduce a model-selection pipeline  to  compare  and  filter  models  throughout  consecutive  stages  of  more complex and expensive metrics.
We present the pipeline in an interactive visual tool to enable the exploration of the metrics, analysis of the learned latent space, and selection of the best model for a given task.
We focus specifically on the variational auto-encoder family in a case study of modeling peptide sequences, which are short sequences of amino acids.
This task is especially interesting due to the presence of multiple attributes we want to model.
We demonstrate how an interactive visual comparison can assist in evaluating how well an unsupervised auto-encoder meaningfully captures the attributes of interest in its latent space.
Unsupervised representation learning and generation of text from a continuous space is an important topic in natural language processing.
This problem has been successfully addressed by variational auto-encoders (VAE) BID16 and variations, which we will introduce in Section 2. The same methods are also relevant to areas like drug discovery, as the therapeutic small molecules and macromolecules (nucleic acids, peptides, proteins) can be represented as discrete linear sequences, analogous to text strings.
Our case study of interest is modeling peptide sequences.In the VAE formulation, we define the sequence representation as a latent variable modeling problem of inputs x and latent variables z, where the joint distribution p(x, z) is factored as p(z)p θ (x|z) and the inference of the hidden variable z for a given input x is approximated through an inference network q φ (z|x).
The auto-encoder training typically aims to minimize two competing objectives:
(a) reconstruction of the input and
(b) regularization in the latent space.
Term
(b) acts as a proxy to two real desiderata:
(i) "meaningful" representations in latent space, and
(ii) the ability to sample new datapoints from p(x) through p(z)p θ (x|z).
These competing goals and objectives form a fundamental trade-off, and as a consequence, there is no easy way to measure the success of an auto-encoder model.
Instead, measuring success requires careful consideration of multiple different metrics.
The discussion of the metrics is in Section 2.2, and they will be incorporated in the IVELS tool (Section 5.1 and 5.2).For
generating discrete sequences while controlling user-specific attributes, for example peptide sequences with specific functionality, it is crucial to consider conditional generation. The
most Figure 1 : Overview of the IVELS tool. In
every stage, we can filter the models to select the ones with satisfactory performance. In
the first stage, models can be compared using the static metrics that are typically computed during training (left). In
the second stage, we investigate the activity vs noise of the learned latent space (top right) and evaluate whether we can linearly separate attributes (not shown). During
the third stage, the tool enables interactive exploration of the attributes in a 2D projection of the latent space (bottom right). straightforward
approach would be limiting the training set to those sequences with the desired attributes. However, this would
require large quantities of data labeled with exactly those attributes, which is often not available. Moreover, the usage
of those models that are trained on a specific set of labeled data will likely be restricted to that domain. In contrast, unlabeled
sequence data is often freely available. Therefore, a reasonable
approach for model training is to train a VAE on a large corpus without requiring attribute labels, then leveraging the structure in the latent space for conditional generation based on attributes which are introduced post-hoc. As a prerequisite for this
goal, we focus on how q φ (z|x) encodes the data with specific attributes. We introduce the encoding
of the data subset corresponding to a specific attribute, i.e. the subset marginal posterior, in Section 3. This will be important in the IVELS tool (Section 5.3 and 5.4). Now that we introduced our
models (VAE family), the importance of conditioning on attributes, and our case study of interest (peptide generation), we turn to the focus of our paper. To assist in the model selection
process, we present a visual tool for interactive exploration and selection of auto-encoder models. Instead of selecting models by one
single unified metric, the tool enables a machine learning practitioner to interactively compare different models, visualize several metrics of interest, and explore the latent space of the encoder. This exploration is building around
distributions in the latent space of data subsets, where the subsets are defined by the attributes of interest. We will quantify whether a linear classifier
can discriminate attributes in the latent space, and enable visual exploration of the attributes with 2D projections. The setup allows the definition of new ad-hoc
attributes and sets to assist users in understanding the learned latent space. The tool is described in Section 5.In Section
6, we discuss some observations we made using IVELS as it relates to (1) our specific domain of peptide modeling and (2) different variations of VAE models.
We presented a tool for Interactive Visual Exploration of Latent Space (IVELS) for model selection focused on auto-encoder models for peptide sequences.
Even though we present the tool with this use case, the principle is generally useful for models which do not have a single metric to compare and evaluate.
With some adaptation to the model and metrics, this tool could be extended to evaluate other latent variable models, either for sequences or images, speech synthesis models, etc.
In all those scenarios, having a usable, visual and interactive tool for model architects and model trainers will enable efficient exploration and selection of different model variations.
The results from this evaluation can further guide the generation of samples with the desired attribute(s).

assistant: text: We present a visual tool to interactively explore the latent space of an auto-encoder for peptide sequences and their attributes.