Daily Papers

The cascade of 2D geometric transformations were exploited to model relations between entities in a knowledge graph (KG), leading to an effective KG embedding (KGE) model, CompoundE. Furthermore, the rotation in the 3D space was proposed as a new KGE model, Rotate3D, by leveraging its non-commutative property. Inspired by CompoundE and Rotate3D, we leverage 3D compound geometric transformations, including translation, rotation, scaling, reflection, and shear and propose a family of KGE models, named CompoundE3D, in this work. CompoundE3D allows multiple design variants to match rich underlying characteristics of a KG. Since each variant has its own advantages on a subset of relations, an ensemble of multiple variants can yield superior performance. The effectiveness and flexibility of CompoundE3D are experimentally verified on four popular link prediction datasets.

In a compound AI system, components such as an LLM call, a retriever, a code interpreter, or tools are interconnected. The system's behavior is primarily driven by parameters such as instructions or tool definitions. Recent advancements enable end-to-end optimization of these parameters using an LLM. Notably, leveraging an LLM as an optimizer is particularly efficient because it avoids gradient computation and can generate complex code and instructions. This paper presents a survey of the principles and emerging trends in LLM-based optimization of compound AI systems. It covers archetypes of compound AI systems, approaches to LLM-based end-to-end optimization, and insights into future directions and broader impacts. Importantly, this survey uses concepts from program analysis to provide a unified view of how an LLM optimizer is prompted to optimize a compound AI system. The exhaustive list of paper is provided at https://github.com/linyuhongg/LLM-based-Optimization-of-Compound-AI-Systems.

In many domains, autoregressive models can attain high likelihood on the task of predicting the next observation. However, this maximum-likelihood (MLE) objective does not necessarily match a downstream use-case of autoregressively generating high-quality sequences. The MLE objective weights sequences proportionally to their frequency under the data distribution, with no guidance for the model's behaviour out of distribution (OOD): leading to compounding error during autoregressive generation. In order to address this compounding error problem, we formulate sequence generation as an imitation learning (IL) problem. This allows us to minimize a variety of divergences between the distribution of sequences generated by an autoregressive model and sequences from a dataset, including divergences with weight on OOD generated sequences. The IL framework also allows us to incorporate backtracking by introducing a backspace action into the generation process. This further mitigates the compounding error problem by allowing the model to revert a sampled token if it takes the sequence OOD. Our resulting method, SequenceMatch, can be implemented without adversarial training or major architectural changes. We identify the SequenceMatch-chi^2 divergence as a more suitable training objective for autoregressive models which are used for generation. We show that empirically, SequenceMatch training leads to improvements over MLE on text generation with language models.

State-of-the-art machine learning methods exhibit limited compositional generalization. At the same time, there is a lack of realistic benchmarks that comprehensively measure this ability, which makes it challenging to find and evaluate improvements. We introduce a novel method to systematically construct such benchmarks by maximizing compound divergence while guaranteeing a small atom divergence between train and test sets, and we quantitatively compare this method to other approaches for creating compositional generalization benchmarks. We present a large and realistic natural language question answering dataset that is constructed according to this method, and we use it to analyze the compositional generalization ability of three machine learning architectures. We find that they fail to generalize compositionally and that there is a surprisingly strong negative correlation between compound divergence and accuracy. We also demonstrate how our method can be used to create new compositionality benchmarks on top of the existing SCAN dataset, which confirms these findings.

A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing, reducing the failure rate, and streamlining clinical trials. In this work, we make an initial attempt towards enabling ChatGPT-like capabilities on drug molecule graphs, by developing a prototype system DrugChat. DrugChat works in a similar way as ChatGPT. Users upload a compound molecule graph and ask various questions about this compound. DrugChat will answer these questions in a multi-turn, interactive manner. The DrugChat system consists of a graph neural network (GNN), a large language model (LLM), and an adaptor. The GNN takes a compound molecule graph as input and learns a representation for this graph. The adaptor transforms the graph representation produced by the GNN into another representation that is acceptable to the LLM. The LLM takes the compound representation transformed by the adaptor and users' questions about this compound as inputs and generates answers. All these components are trained end-to-end. To train DrugChat, we collected instruction tuning datasets which contain 10,834 drug compounds and 143,517 question-answer pairs. The code and data is available at https://github.com/UCSD-AI4H/drugchat

Partial correlations quantify linear association between two variables adjusting for the influence of the remaining variables. They form the backbone for graphical models and are readily obtained from the inverse of the covariance matrix. For compositional data, the covariance structure is specified from log ratios of variables, so unless we try to "open" the data via a normalization, this implies changes in the definition and interpretation of partial correlations. In the present work, we elucidate how results derived by Aitchison (1986) lead to a natural definition of partial correlation that has a number of advantages over current measures of association. For this, we show that the residuals of log-ratios between a variable with a reference, when adjusting for all remaining variables including the reference, are reference-independent. Since the reference itself can be controlled for, correlations between residuals are defined for the variables directly without the necessity to recur to ratios except when specifying which variables are partialled out. Thus, perhaps surprisingly, partial correlations do not have the problems commonly found with measures of pairwise association on compositional data. They are well-defined between two variables, are properly scaled, and allow for negative association. By design, they are subcompositionally incoherent, but they share this property with conventional partial correlations (where results change when adjusting for the influence of fewer variables). We discuss the equivalence with normalization-based approaches whenever the normalizing variables are controlled for. We also discuss the partial variances and correlations we obtain from a previously studied data set of Roman glass cups.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

The interdiffusion coefficients are estimated either following the Wagner's method expressed with respect to the composition (mol or atomic fraction) normalized variable after considering the molar volume variation or the den Broeder's method expressed with respect to the concentration (composition divided by the molar volume) normalized variable. On the other hand, the relations for estimation of the intrinsic diffusion coefficients of components as established by van Loo and integrated diffusion coefficients in a phase with narrow homogeneity range as established by Wagner are currently available with respect to the composition normalized variable only. In this study, we have first derived the relation proposed by den Broeder following the line of treatment proposed by Wagner. Further, the relations for estimation of the intrinsic diffusion coefficients of the components and integrated interdiffusion coefficient are established with respect to the concentration normalized variable, which were not available earlier. The veracity of these methods is examined based on the estimation of data in Ni-Pd, Ni-Al and Cu-Sn systems. Our analysis indicates that both the approaches are logically correct and there is small difference in the estimated data in these systems although a higher difference could be found in other systems. The integrated interdiffusion coefficients with respect to the concentration (or concentration normalized variable) can only be estimated considering the ideal molar volume variation. This might be drawback in certain practical systems.

Combination therapies have become the standard of care for diseases such as cancer, tuberculosis, malaria and HIV. However, the combinatorial set of available multi-drug treatments creates a challenge in identifying effective combination therapies available in a situation. To assist medical professionals in identifying beneficial drug-combinations, we construct an expert-annotated dataset for extracting information about the efficacy of drug combinations from the scientific literature. Beyond its practical utility, the dataset also presents a unique NLP challenge, as the first relation extraction dataset consisting of variable-length relations. Furthermore, the relations in this dataset predominantly require language understanding beyond the sentence level, adding to the challenge of this task. We provide a promising baseline model and identify clear areas for further improvement. We release our dataset, code, and baseline models publicly to encourage the NLP community to participate in this task.

In this paper, a mathematical model is developed to describe the evolution of the concentration of compounds through a gas chromatography column. The model couples mass balances and kinetic equations for all components. Both single and multiple-component cases are considered with constant or variable velocity. Non-dimensionalisation indicates the small effect of diffusion. The system where diffusion is neglected is analysed using Laplace transforms. In the multiple-component case, it is demonstrated that the competition between the compounds is negligible and the equations may be decoupled. This reduces the problem to solving a single integral equation to determine the concentration profile for all components (since they are scaled versions of each other). For a given analyte, we then only two parameters need to be fitted to the data. To verify this approach, the full governing equations are also solved numerically using the finite difference method and a global adaptive quadrature method to integrate the Laplace transformation. Comparison with the Laplace solution verifies the high degree of accuracy of the simpler Laplace form. The Laplace solution is then verified against experimental data from BTEX chromatography. This novel method, which involves solving a single equation and fitting parameters in pairs for individual components, is highly efficient. It is significantly faster and simpler than the full numerical solution and avoids the computationally expensive methods that would normally be used to fit all curves at the same time.

In the field of quantitative trading, it is common practice to transform raw historical stock data into indicative signals for the market trend. Such signals are called alpha factors. Alphas in formula forms are more interpretable and thus favored by practitioners concerned with risk. In practice, a set of formulaic alphas is often used together for better modeling precision, so we need to find synergistic formulaic alpha sets that work well together. However, most traditional alpha generators mine alphas one by one separately, overlooking the fact that the alphas would be combined later. In this paper, we propose a new alpha-mining framework that prioritizes mining a synergistic set of alphas, i.e., it directly uses the performance of the downstream combination model to optimize the alpha generator. Our framework also leverages the strong exploratory capabilities of reinforcement learning~(RL) to better explore the vast search space of formulaic alphas. The contribution to the combination models' performance is assigned to be the return used in the RL process, driving the alpha generator to find better alphas that improve upon the current set. Experimental evaluations on real-world stock market data demonstrate both the effectiveness and the efficiency of our framework for stock trend forecasting. The investment simulation results show that our framework is able to achieve higher returns compared to previous approaches.

This paper studies the impact of artificial intelligence on innovation, exploiting the randomized introduction of a new materials discovery technology to 1,018 scientists in the R&D lab of a large U.S. firm. AI-assisted researchers discover 44% more materials, resulting in a 39% increase in patent filings and a 17% rise in downstream product innovation. These compounds possess more novel chemical structures and lead to more radical inventions. However, the technology has strikingly disparate effects across the productivity distribution: while the bottom third of scientists see little benefit, the output of top researchers nearly doubles. Investigating the mechanisms behind these results, I show that AI automates 57% of "idea-generation" tasks, reallocating researchers to the new task of evaluating model-produced candidate materials. Top scientists leverage their domain knowledge to prioritize promising AI suggestions, while others waste significant resources testing false positives. Together, these findings demonstrate the potential of AI-augmented research and highlight the complementarity between algorithms and expertise in the innovative process. Survey evidence reveals that these gains come at a cost, however, as 82% of scientists report reduced satisfaction with their work due to decreased creativity and skill underutilization.

As large language models (LLMs) become increasingly advanced, their ability to exhibit compositional generalization -- the capacity to combine learned skills in novel ways not encountered during training -- has garnered significant attention. This type of generalization, particularly in scenarios beyond training data, is also of great interest in the study of AI safety and alignment. A recent study introduced the SKILL-MIX evaluation, where models are tasked with composing a short paragraph demonstrating the use of a specified k-tuple of language skills. While small models struggled with composing even with k=3, larger models like GPT-4 performed reasonably well with k=5 and 6. In this paper, we employ a setup akin to SKILL-MIX to evaluate the capacity of smaller models to learn compositional generalization from examples. Utilizing a diverse set of language skills -- including rhetorical, literary, reasoning, theory of mind, and common sense -- GPT-4 was used to generate text samples that exhibit random subsets of k skills. Subsequent fine-tuning of 7B and 13B parameter models on these combined skill texts, for increasing values of k, revealed the following findings: (1) Training on combinations of k=2 and 3 skills results in noticeable improvements in the ability to compose texts with k=4 and 5 skills, despite models never having seen such examples during training. (2) When skill categories are split into training and held-out groups, models significantly improve at composing texts with held-out skills during testing despite having only seen training skills during fine-tuning, illustrating the efficacy of the training approach even with previously unseen skills. This study also suggests that incorporating skill-rich (potentially synthetic) text into training can substantially enhance the compositional capabilities of models.

Large pretrained models such as GPT-3 have had tremendous impact on modern natural language processing by leveraging self-supervised learning to learn salient representations that can be used to readily finetune on a wide variety of downstream tasks. We investigate the possibility of transferring such advances to molecular machine learning by building a chemical foundation model, ChemBERTa-2, using the language of SMILES. While labeled data for molecular prediction tasks is typically scarce, libraries of SMILES strings are readily available. In this work, we build upon ChemBERTa by optimizing the pretraining process. We compare multi-task and self-supervised pretraining by varying hyperparameters and pretraining dataset size, up to 77M compounds from PubChem. To our knowledge, the 77M set constitutes one of the largest datasets used for molecular pretraining to date. We find that with these pretraining improvements, we are competitive with existing state-of-the-art architectures on the MoleculeNet benchmark suite. We analyze the degree to which improvements in pretraining translate to improvement on downstream tasks.

The data used to pretrain large language models has a decisive impact on a model's downstream performance, which has led to a large body of work on data selection methods that aim to automatically determine the most suitable data to use for pretraining. Existing data selection methods suffer from slow and computationally expensive processes, a problem amplified by the increasing size of models and of pretraining datasets. Data mixing, on the other hand, reduces the complexity of data selection by grouping data points together and determining sampling probabilities across entire groups. However, data mixing proportions are typically fixed before training and therefore cannot adapt to changing training dynamics. To address these limitations, we develop an efficient algorithm for Online Data Mixing (ODM) that combines elements from both data selection and data mixing. Based on multi-armed bandit algorithms, our online approach optimizes the data mixing proportions during training. Remarkably, our method trains a model that reaches the final perplexity of the next best method with 19\% fewer training iterations, and improves performance on the 5-shot MMLU benchmark by 1.9% relative accuracy, while adding negligible wall-clock time during pretraining.

Pretrained models are the standard starting point for training. This approach consistently outperforms the use of a random initialization. However, pretraining is a costly endeavour that few can undertake. In this paper, we create better base models at hardly any cost, by fusing multiple existing fine tuned models into one. Specifically, we fuse by averaging the weights of these models. We show that the fused model results surpass the pretrained model ones. We also show that fusing is often better than intertraining. We find that fusing is less dependent on the target task. Furthermore, weight decay nullifies intertraining effects but not those of fusing.

In the early 2000s, renowned chef Heston Blumenthal formulated his "food pairing" hypothesis, positing that if foods share many flavor compounds, then they tend to taste good when eaten together. In 2011, Ahn et al. conducted a study using a dataset of recipes, ingredients, and flavor compounds, finding that, in Western cuisine, ingredients in recipes often share more flavor compounds than expected by chance, indicating a natural tendency towards food pairing. Building upon Ahn's research, our work applies state-of-the-art collaborative filtering techniques to the dataset, providing a tool that can recommend new foods to add in recipes, retrieve missing ingredients and advise against certain combinations. We create our recommender in two ways, by taking into account ingredients appearances in recipes or shared flavor compounds between foods. While our analysis confirms the existence of food pairing, the recipe-based recommender performs significantly better than the flavor-based one, leading to the conclusion that food pairing is just one of the principles to take into account when creating recipes. Furthermore, and more interestingly, we find that food pairing in data is mostly due to trivial couplings of very similar ingredients, leading to a reconsideration of its current role in recipes, from being an already existing feature to a key to open up new scenarios in gastronomy. Our flavor-based recommender can thus leverage this novel concept and provide a new tool to lead culinary innovation.

Learning neural subset selection tasks, such as compound selection in AI-aided drug discovery, have become increasingly pivotal across diverse applications. The existing methodologies in the field primarily concentrate on constructing models that capture the relationship between utility function values and subsets within their respective supersets. However, these approaches tend to overlook the valuable information contained within the superset when utilizing neural networks to model set functions. In this work, we address this oversight by adopting a probabilistic perspective. Our theoretical findings demonstrate that when the target value is conditioned on both the input set and subset, it is essential to incorporate an invariant sufficient statistic of the superset into the subset of interest for effective learning. This ensures that the output value remains invariant to permutations of the subset and its corresponding superset, enabling identification of the specific superset from which the subset originated. Motivated by these insights, we propose a simple yet effective information aggregation module designed to merge the representations of subsets and supersets from a permutation invariance perspective. Comprehensive empirical evaluations across diverse tasks and datasets validate the enhanced efficacy of our approach over conventional methods, underscoring the practicality and potency of our proposed strategies in real-world contexts.

Recent developments in natural language representations have been accompanied by large and expensive models that leverage vast amounts of general-domain text through self-supervised pre-training. Due to the cost of applying such models to down-stream tasks, several model compression techniques on pre-trained language representations have been proposed (Sun et al., 2019; Sanh, 2019). However, surprisingly, the simple baseline of just pre-training and fine-tuning compact models has been overlooked. In this paper, we first show that pre-training remains important in the context of smaller architectures, and fine-tuning pre-trained compact models can be competitive to more elaborate methods proposed in concurrent work. Starting with pre-trained compact models, we then explore transferring task knowledge from large fine-tuned models through standard knowledge distillation. The resulting simple, yet effective and general algorithm, Pre-trained Distillation, brings further improvements. Through extensive experiments, we more generally explore the interaction between pre-training and distillation under two variables that have been under-studied: model size and properties of unlabeled task data. One surprising observation is that they have a compound effect even when sequentially applied on the same data. To accelerate future research, we will make our 24 pre-trained miniature BERT models publicly available.

Pretraining data of large language models composes multiple domains (e.g., web texts, academic papers, codes), whose mixture proportions crucially impact the competence of outcome models. While existing endeavors rely on heuristics or qualitative strategies to tune the proportions, we discover the quantitative predictability of model performance regarding the mixture proportions in function forms, which we refer to as the data mixing laws. Fitting such functions on sample mixtures unveils model performance on unseen mixtures before actual runs, thus guiding the selection of an ideal data mixture. Furthermore, we propose nested use of the scaling laws of training steps, model sizes, and our data mixing law to enable predicting the performance of large models trained on massive data under various mixtures with only small-scale training. Moreover, experimental results verify that our method effectively optimizes the training mixture of a 1B model trained for 100B tokens in RedPajama, reaching a performance comparable to the one trained for 48% more steps on the default mixture. Extending the application of data mixing laws to continual training accurately predicts the critical mixture proportion that avoids catastrophic forgetting and outlooks the potential for dynamic data schedules

This paper proposes a method for the automatic creation of variables (in the case of regression) that complement the information contained in the initial input vector. The method works as a pre-processing step in which the continuous values of the variable to be regressed are discretized into a set of intervals which are then used to define value thresholds. Then classifiers are trained to predict whether the value to be regressed is less than or equal to each of these thresholds. The different outputs of the classifiers are then concatenated in the form of an additional vector of variables that enriches the initial vector of the regression problem. The implemented system can thus be considered as a generic pre-processing tool. We tested the proposed enrichment method with 5 types of regressors and evaluated it in 33 regression datasets. Our experimental results confirm the interest of the approach.

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 on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e.g., the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e.g., drugs or antibiotics). In such underspecified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

Doctors typically write in incomprehensible handwriting, making it difficult for both the general public and some pharmacists to understand the medications they have prescribed. It is not ideal for them to write the prescription quietly and methodically because they will be dealing with dozens of patients every day and will be swamped with work.As a result, their handwriting is illegible. This may result in reports or prescriptions consisting of short forms and cursive writing that a typical person or pharmacist won't be able to read properly, which will cause prescribed medications to be misspelled. However, some individuals are accustomed to writing prescriptions in regional languages because we all live in an area with a diversity of regional languages. It makes analyzing the content much more challenging. So, in this project, we'll use a recognition system to build a tool that can translate the handwriting of physicians in any language. This system will be made into an application which is fully autonomous in functioning. As the user uploads the prescription image the program will pre-process the image by performing image pre-processing, and word segmentations initially before processing the image for training. And it will be done for every language we require the model to detect. And as of the deduction model will be made using deep learning techniques including CNN, RNN, and LSTM, which are utilized to train the model. To match words from various languages that will be written in the system, Unicode will be used. Furthermore, fuzzy search and market basket analysis are employed to offer an end result that will be optimized from the pharmaceutical database and displayed to the user as a structured output.

We characterize the cut patterns that can be produced by "orthogonal fold & cut": folding an axis-aligned rectangular sheet of paper along horizontal and vertical creases, and then making a single straight cut (at any angle). Along the way, we solve a handful of related problems: orthogonal fold & punch, 1D fold & cut, signed 1D fold & cut, and 1D interval fold & cut.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and 8times289M). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

Model fusing has always been an important topic, especially in an era where large language models (LLM) and multi-modal language models (MLM) with different architectures, parameter sizes and training pipelines, are being created all the time. In this work, we propose a post-hoc framework, aiming at fusing heterogeneous models off-the-shell, which we call likelihood composition, and the basic idea is to compose multiple models' likelihood distribution when doing a multi-choice visual-question-answering task. Here the core concept, likelihood, is actually the log-probability of the candidate answer. In likelihood composition, we introduce some basic operations: debias, highlight, majority-vote and ensemble. By combining (composing) these basic elements, we get the mixed composition methods: mix-composition. Through conducting comprehensive experiments on 9 VQA datasets and 10 MLMs, we prove the effectiveness of mix-composition compared with simple ensemble or majority-vote methods. In this framework, people can propose new basic composition methods and combine them to get the new mixed composition methods. We hope our proposed likelihood composition can provide a new perspective of fusing heterogeneous models and inspire the exploration under this framework.

Knowledge of mixtures' phase equilibria is crucial in nature and technical chemistry. Phase equilibria calculations of mixtures require activity coefficients. However, experimental data on activity coefficients is often limited due to high cost of experiments. For an accurate and efficient prediction of activity coefficients, machine learning approaches have been recently developed. However, current machine learning approaches still extrapolate poorly for activity coefficients of unknown molecules. In this work, we introduce the SMILES-to-Properties-Transformer (SPT), a natural language processing network to predict binary limiting activity coefficients from SMILES codes. To overcome the limitations of available experimental data, we initially train our network on a large dataset of synthetic data sampled from COSMO-RS (10 Million data points) and then fine-tune the model on experimental data (20 870 data points). This training strategy enables SPT to accurately predict limiting activity coefficients even for unknown molecules, cutting the mean prediction error in half compared to state-of-the-art models for activity coefficient predictions such as COSMO-RS, UNIFAC, and improving on recent machine learning approaches.

We provide a distillation scaling law that estimates distilled model performance based on a compute budget and its allocation between the student and teacher. Our findings reduce the risks associated with using distillation at scale; compute allocation for both the teacher and student models can now be done to maximize student performance. We provide compute optimal distillation recipes for when 1) a teacher exists, or 2) a teacher needs training. If many students are to be distilled, or a teacher already exists, distillation outperforms supervised pretraining until a compute level which grows predictably with student size. If one student is to be distilled and a teacher also needs training, supervised learning should be done instead. Additionally, we provide insights across our large scale study of distillation, which increase our understanding of distillation and inform experimental design.

Conceptual combination is a cognitive process that merges basic concepts, enabling the creation of complex expressions. During this process, the properties of combination (e.g., the whiteness of a peeled apple) can be inherited from basic concepts, newly emerge, or be canceled. However, previous studies have evaluated a limited set of properties and have not examined the generative process. To address this gap, we introduce the Conceptual Combination with Property Type dataset (CCPT), which consists of 12.3K annotated triplets of noun phrases, properties, and property types. Using CCPT, we establish three types of tasks to evaluate LLMs for conceptual combination thoroughly. Our key findings are threefold: (1) Our automatic metric grading property emergence and cancellation closely corresponds with human judgments. (2) LLMs, including OpenAI's o1, struggle to generate noun phrases which possess given emergent properties. (3) Our proposed method, inspired by cognitive psychology model that explains how relationships between concepts are formed, improves performances in all generative tasks. The dataset and experimental code are available at https://github.com/seokwon99/CCPT.git.

AI is undergoing a paradigm shift, with breakthroughs achieved by systems orchestrating multiple large language models (LLMs) and other complex components. As a result, developing principled and automated optimization methods for compound AI systems is one of the most important new challenges. Neural networks faced a similar challenge in its early days until backpropagation and automatic differentiation transformed the field by making optimization turn-key. Inspired by this, we introduce TextGrad, a powerful framework performing automatic ``differentiation'' via text. TextGrad backpropagates textual feedback provided by LLMs to improve individual components of a compound AI system. In our framework, LLMs provide rich, general, natural language suggestions to optimize variables in computation graphs, ranging from code snippets to molecular structures. TextGrad follows PyTorch's syntax and abstraction and is flexible and easy-to-use. It works out-of-the-box for a variety of tasks, where the users only provide the objective function without tuning components or prompts of the framework. We showcase TextGrad's effectiveness and generality across a diverse range of applications, from question answering and molecule optimization to radiotherapy treatment planning. Without modifying the framework, TextGrad improves the zero-shot accuracy of GPT-4o in Google-Proof Question Answering from 51% to 55%, yields 20% relative performance gain in optimizing LeetCode-Hard coding problem solutions, improves prompts for reasoning, designs new druglike small molecules with desirable in silico binding, and designs radiation oncology treatment plans with high specificity. TextGrad lays a foundation to accelerate the development of the next-generation of AI systems.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

This paper introduces a novel training methodology that enables a small Transformer model to generalize the addition of two-digit numbers to numbers with unseen lengths of digits. The proposed approach employs an autoregressive generation technique, processing from right to left, which mimics a common manual method for adding large numbers. To the best of my knowledge, this methodology has not been previously explored in the literature. All results are reproducible, and the corresponding R code is available at: https://github.com/AGPatriota/ALGA-R/.

Complex chemical structures, like drugs, are usually defined by SMILES strings as a sequence of molecules and bonds. These SMILES strings are used in different complex machine learning-based drug-related research and representation works. Escaping from complex representation, in this work, we pose a single question: What if we treat drug SMILES as conventional sentences and engage in text classification for drug classification? Our experiments affirm the possibility with very competitive scores. The study explores the notion of viewing each atom and bond as sentence components, employing basic NLP methods to categorize drug types, proving that complex problems can also be solved with simpler perspectives. The data and code are available here: https://github.com/azminewasi/Drug-Classification-NLP.