Daily Papers

Vector Symbolic Architectures (VSAs) give a way to represent a complex object as a single fixed-length vector, so that similar objects have similar vector representations. These vector representations then become easy to use for machine learning or nearest-neighbor search. We review a previously proposed VSA method, MBAT (Matrix Binding of Additive Terms), which uses multiplication by random matrices for binding related terms. However, multiplying by such matrices introduces instabilities which can harm performance. Making the random matrices be orthogonal matrices provably fixes this problem. With respect to larger scale applications, we see how to apply MBAT vector representations for any data expressed in JSON. JSON is used in numerous programming languages to express complex data, but its native format appears highly unsuited for machine learning. Expressing JSON as a fixed-length vector makes it readily usable for machine learning and nearest-neighbor search. Creating such JSON vectors also shows that a VSA needs to employ binding operations that are non-commutative. VSAs are now ready to try with full-scale practical applications, including healthcare, pharmaceuticals, and genomics. Keywords: MBAT (Matrix Binding of Additive Terms), VSA (Vector Symbolic Architecture), HDC (Hyperdimensional Computing), Distributed Representations, Binding, Orthogonal Matrices, Recurrent Connections, Machine Learning, Search, JSON, VSA Applications

We introduce Codex, a GPT language model fine-tuned on publicly available code from GitHub, and study its Python code-writing capabilities. A distinct production version of Codex powers GitHub Copilot. On HumanEval, a new evaluation set we release to measure functional correctness for synthesizing programs from docstrings, our model solves 28.8% of the problems, while GPT-3 solves 0% and GPT-J solves 11.4%. Furthermore, we find that repeated sampling from the model is a surprisingly effective strategy for producing working solutions to difficult prompts. Using this method, we solve 70.2% of our problems with 100 samples per problem. Careful investigation of our model reveals its limitations, including difficulty with docstrings describing long chains of operations and with binding operations to variables. Finally, we discuss the potential broader impacts of deploying powerful code generation technologies, covering safety, security, and economics.

Vector Symbolic Architectures (VSAs) have emerged as a novel framework for enabling interpretable machine learning algorithms equipped with the ability to reason and explain their decision processes. The basic idea is to represent discrete information through high dimensional random vectors. Complex data structures can be built up with operations over vectors such as the "binding" operation involving element-wise vector multiplication, which associates data together. The reverse task of decomposing the associated elements is a combinatorially hard task, with an exponentially large search space. The main algorithm for performing this search is the resonator network, inspired by Hopfield network-based memory search operations. In this work, we introduce a new variant of the resonator network, based on self-attention based update rules in the iterative search problem. This update rule, based on the Hopfield network with log-sum-exp energy function and norm-bounded states, is shown to substantially improve the performance and rate of convergence. As a result, our algorithm enables a larger capacity for associative memory, enabling applications in many tasks like perception based pattern recognition, scene decomposition, and object reasoning. We substantiate our algorithm with a thorough evaluation and comparisons to baselines.

Hyperdimensional computing (HDC) is a biologically-inspired framework which represents symbols with high-dimensional vectors, and uses vector operations to manipulate them. The ensemble of a particular vector space and a prescribed set of vector operations (including one addition-like for "bundling" and one outer-product-like for "binding") form a *vector symbolic architecture* (VSA). While VSAs have been employed in numerous applications and have been studied empirically, many theoretical questions about VSAs remain open. We analyze the *representation capacities* of four common VSAs: MAP-I, MAP-B, and two VSAs based on sparse binary vectors. "Representation capacity' here refers to bounds on the dimensions of the VSA vectors required to perform certain symbolic tasks, such as testing for set membership i in S and estimating set intersection sizes |X cap Y| for two sets of symbols X and Y, to a given degree of accuracy. We also analyze the ability of a novel variant of a Hopfield network (a simple model of associative memory) to perform some of the same tasks that are typically asked of VSAs. In addition to providing new bounds on VSA capacities, our analyses establish and leverage connections between VSAs, "sketching" (dimensionality reduction) algorithms, and Bloom filters.

Although text-to-image (T2I) models exhibit remarkable generation capabilities, they frequently fail to accurately bind semantically related objects or attributes in the input prompts; a challenge termed semantic binding. Previous approaches either involve intensive fine-tuning of the entire T2I model or require users or large language models to specify generation layouts, adding complexity. In this paper, we define semantic binding as the task of associating a given object with its attribute, termed attribute binding, or linking it to other related sub-objects, referred to as object binding. We introduce a novel method called Token Merging (ToMe), which enhances semantic binding by aggregating relevant tokens into a single composite token. This ensures that the object, its attributes and sub-objects all share the same cross-attention map. Additionally, to address potential confusion among main objects with complex textual prompts, we propose end token substitution as a complementary strategy. To further refine our approach in the initial stages of T2I generation, where layouts are determined, we incorporate two auxiliary losses, an entropy loss and a semantic binding loss, to iteratively update the composite token to improve the generation integrity. We conducted extensive experiments to validate the effectiveness of ToMe, comparing it against various existing methods on the T2I-CompBench and our proposed GPT-4o object binding benchmark. Our method is particularly effective in complex scenarios that involve multiple objects and attributes, which previous methods often fail to address. The code will be publicly available at https://github.com/hutaihang/ToMe.

We extend JAX with the capability to automatically differentiate higher-order functions (functionals and operators). By representing functions as a generalization of arrays, we seamlessly use JAX's existing primitive system to implement higher-order functions. We present a set of primitive operators that serve as foundational building blocks for constructing several key types of functionals. For every introduced primitive operator, we derive and implement both linearization and transposition rules, aligning with JAX's internal protocols for forward and reverse mode automatic differentiation. This enhancement allows for functional differentiation in the same syntax traditionally use for functions. The resulting functional gradients are themselves functions ready to be invoked in python. We showcase this tool's efficacy and simplicity through applications where functional derivatives are indispensable. The source code of this work is released at https://github.com/sail-sg/autofd .

Though end-to-end neural approaches have recently been dominating NLP tasks in both performance and ease-of-use, they lack interpretability and robustness. We propose Binder, a training-free neural-symbolic framework that maps the task input to a program, which (1) allows binding a unified API of language model (LM) functionalities to a programming language (e.g., SQL, Python) to extend its grammar coverage and thus tackle more diverse questions, (2) adopts an LM as both the program parser and the underlying model called by the API during execution, and (3) requires only a few in-context exemplar annotations. Specifically, we employ GPT-3 Codex as the LM. In the parsing stage, with only a few in-context exemplars, Codex is able to identify the part of the task input that cannot be answerable by the original programming language, correctly generate API calls to prompt Codex to solve the unanswerable part, and identify where to place the API calls while being compatible with the original grammar. In the execution stage, Codex can perform versatile functionalities (e.g., commonsense QA, information extraction) given proper prompts in the API calls. Binder achieves state-of-the-art results on WikiTableQuestions and TabFact datasets, with explicit output programs that benefit human debugging. Note that previous best systems are all finetuned on tens of thousands of task-specific samples, while Binder only uses dozens of annotations as in-context exemplars without any training. Our code is available at https://github.com/HKUNLP/Binder .

Knot diagrams are among the most common visual tools in topology. Computer programs now make it possible to draw, manipulate and render them digitally, which proves to be useful in knot theory teaching and research. Still, an openly available tool to manipulate knot diagrams in a real-time, interactive way is yet to be developed. We introduce a method of operating on the geometry of the knot diagram itself without any underlying three-dimensional structure that can underpin such an application. This allows us to directly interact with vector graphics knot diagrams while at the same time computing knot invariants in ways proposed by previous work. An implementation of this method is provided.

A key component of understanding hand-object interactions is the ability to identify the active object -- the object that is being manipulated by the human hand. In order to accurately localize the active object, any method must reason using information encoded by each image pixel, such as whether it belongs to the hand, the object, or the background. To leverage each pixel as evidence to determine the bounding box of the active object, we propose a pixel-wise voting function. Our pixel-wise voting function takes an initial bounding box as input and produces an improved bounding box of the active object as output. The voting function is designed so that each pixel inside of the input bounding box votes for an improved bounding box, and the box with the majority vote is selected as the output. We call the collection of bounding boxes generated inside of the voting function, the Relational Box Field, as it characterizes a field of bounding boxes defined in relationship to the current bounding box. While our voting function is able to improve the bounding box of the active object, one round of voting is typically not enough to accurately localize the active object. Therefore, we repeatedly apply the voting function to sequentially improve the location of the bounding box. However, since it is known that repeatedly applying a one-step predictor (i.e., auto-regressive processing with our voting function) can cause a data distribution shift, we mitigate this issue using reinforcement learning (RL). We adopt standard RL to learn the voting function parameters and show that it provides a meaningful improvement over a standard supervised learning approach. We perform experiments on two large-scale datasets: 100DOH and MECCANO, improving AP50 performance by 8% and 30%, respectively, over the state of the art.

We explore the effects of various plasticity functions on assemblies of neurons. To bridge the gap between experimental and computational theories we make use of a conceptual framework, the Assembly Calculus, which is a formal system for the description of brain function based on assemblies of neurons. The Assembly Calculus includes operations for projecting, associating, and merging assemblies of neurons. Our research is focused on simulating different plasticity functions with Assembly Calculus. Our main contribution is the modification and evaluation of the projection operation. We experiment with Oja's and Spike Time-Dependent Plasticity (STDP) rules and test the effect of various hyper-parameters.

Extracting causal relationships from observed correlations is a growing area in probabilistic reasoning, originating with the seminal work of Pearl and others from the early 1990s. This paper develops a new, categorically oriented view based on a clear distinction between syntax (string diagrams) and semantics (stochastic matrices), connected via interpretations as structure-preserving functors. A key notion in the identification of causal effects is that of an intervention, whereby a variable is forcefully set to a particular value independent of any prior propensities. We represent the effect of such an intervention as an endofunctor which performs `string diagram surgery' within the syntactic category of string diagrams. This diagram surgery in turn yields a new, interventional distribution via the interpretation functor. While in general there is no way to compute interventional distributions purely from observed data, we show that this is possible in certain special cases using a calculational tool called comb disintegration. We demonstrate the use of this technique on a well-known toy example, where we predict the causal effect of smoking on cancer in the presence of a confounding common cause. After developing this specific example, we show this technique provides simple sufficient conditions for computing interventions which apply to a wide variety of situations considered in the causal inference literature.

The ability to automatically detect and track surgical instruments in endoscopic videos can enable transformational interventions. Assessing surgical performance and efficiency, identifying skilled tool use and choreography, and planning operational and logistical aspects of OR resources are just a few of the applications that could benefit. Unfortunately, obtaining the annotations needed to train machine learning models to identify and localize surgical tools is a difficult task. Annotating bounding boxes frame-by-frame is tedious and time-consuming, yet large amounts of data with a wide variety of surgical tools and surgeries must be captured for robust training. Moreover, ongoing annotator training is needed to stay up to date with surgical instrument innovation. In robotic-assisted surgery, however, potentially informative data like timestamps of instrument installation and removal can be programmatically harvested. The ability to rely on tool installation data alone would significantly reduce the workload to train robust tool-tracking models. With this motivation in mind we invited the surgical data science community to participate in the challenge, SurgToolLoc 2022. The goal was to leverage tool presence data as weak labels for machine learning models trained to detect tools and localize them in video frames with bounding boxes. We present the results of this challenge along with many of the team's efforts. We conclude by discussing these results in the broader context of machine learning and surgical data science. The training data used for this challenge consisting of 24,695 video clips with tool presence labels is also being released publicly and can be accessed at https://console.cloud.google.com/storage/browser/isi-surgtoolloc-2022.

One of the central tasks in software maintenance is being able to understand and develop code changes. Thus, given a natural language description of the desired new operation of a function, an agent (human or AI) might be asked to generate the set of edits to that function to implement the desired new operation; likewise, given a set of edits to a function, an agent might be asked to generate a changed description, of that function's new workings. Thus, there is an incentive to train a neural model for change-related tasks. Motivated by this, we offer a new, "natural", large dataset of coupled changes to code and documentation mined from actual high-quality GitHub projects, where each sample represents a single commit where the code and the associated docstring were changed together. We present the methodology for gathering the dataset, and some sample, challenging (but realistic) tasks where our dataset provides opportunities for both learning and evaluation. We find that current models (specifically Llama-3.1 405B, Mixtral 8times22B) do find these maintenance-related tasks challenging.

Intermediate reasoning or acting steps have successfully improved large language models (LLMs) for handling various downstream natural language processing (NLP) tasks. When applying LLMs for code generation, recent works mainly focus on directing the models to articulate intermediate natural-language reasoning steps, as in chain-of-thought (CoT) prompting, and then output code with the natural language or other structured intermediate steps. However, such output is not suitable for code translation or generation tasks since the standard CoT has different logical structures and forms of expression with the code. In this work, we introduce the universal code (UniCode) as the intermediate representation. It is a description of algorithm steps using a mix of conventions of programming languages, such as assignment operator, conditional operator, and loop. Hence, we collect an instruction dataset UniCoder-Instruct to train our model UniCoder on multi-task learning objectives. UniCoder-Instruct comprises natural-language questions, code solutions, and the corresponding universal code. The alignment between the intermediate universal code representation and the final code solution significantly improves the quality of the generated code. The experimental results demonstrate that UniCoder with the universal code significantly outperforms the previous prompting methods by a large margin, showcasing the effectiveness of the structural clues in pseudo-code.

The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor generalization due to limited supervised data. In this paper, we propose to learn protein-ligand binding representation in a self-supervised learning manner. Different from existing pre-training approaches which treat proteins and ligands individually, we emphasize to discern the intricate binding patterns from fine-grained interactions. Specifically, this self-supervised learning problem is formulated as a prediction of the conclusive binding complex structure given a pocket and ligand with a Transformer based interaction module, which naturally emulates the binding process. To ensure the representation of rich binding information, we introduce two pre-training tasks, i.e.~atomic pairwise distance map prediction and mask ligand reconstruction, which comprehensively model the fine-grained interactions from both structure and feature space. Extensive experiments have demonstrated the superiority of our method across various binding tasks, including protein-ligand affinity prediction, virtual screening and protein-ligand docking.

In this work, we propose a concise neural operator architecture for operator learning. Drawing an analogy with a conventional fully connected neural network, we define the neural operator as follows: the output of the i-th neuron in a nonlinear operator layer is defined by mathcal O_i(u) = sigmaleft( sum_j mathcal W_{ij} u + mathcal B_{ij}right). Here, mathcal W_{ij} denotes the bounded linear operator connecting j-th input neuron to i-th output neuron, and the bias mathcal B_{ij} takes the form of a function rather than a scalar. Given its new universal approximation property, the efficient parameterization of the bounded linear operators between two neurons (Banach spaces) plays a critical role. As a result, we introduce MgNO, utilizing multigrid structures to parameterize these linear operators between neurons. This approach offers both mathematical rigor and practical expressivity. Additionally, MgNO obviates the need for conventional lifting and projecting operators typically required in previous neural operators. Moreover, it seamlessly accommodates diverse boundary conditions. Our empirical observations reveal that MgNO exhibits superior ease of training compared to other CNN-based models, while also displaying a reduced susceptibility to overfitting when contrasted with spectral-type neural operators. We demonstrate the efficiency and accuracy of our method with consistently state-of-the-art performance on different types of partial differential equations (PDEs).

Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on heavy candidate sampling coupled with scoring, ranking, and fine-tuning steps. We challenge this paradigm with EquiBind, an SE(3)-equivariant geometric deep learning model performing direct-shot prediction of both i) the receptor binding location (blind docking) and ii) the ligand's bound pose and orientation. EquiBind achieves significant speed-ups and better quality compared to traditional and recent baselines. Further, we show extra improvements when coupling it with existing fine-tuning techniques at the cost of increased running time. Finally, we propose a novel and fast fine-tuning model that adjusts torsion angles of a ligand's rotatable bonds based on closed-form global minima of the von Mises angular distance to a given input atomic point cloud, avoiding previous expensive differential evolution strategies for energy minimization.

Unified multi-model representation spaces are the foundation of multimodal understanding and generation. However, the billions of model parameters and catastrophic forgetting problems make it challenging to further enhance pre-trained unified spaces. In this work, we propose FreeBind, an idea that treats multimodal representation spaces as basic units, and freely augments pre-trained unified space by integrating knowledge from extra expert spaces via "space bonds". Specifically, we introduce two kinds of basic space bonds: 1) Space Displacement Bond and 2) Space Combination Bond. Based on these basic bonds, we design Complex Sequential & Parallel Bonds to effectively integrate multiple spaces simultaneously. Benefiting from the modularization concept, we further propose a coarse-to-fine customized inference strategy to flexibly adjust the enhanced unified space for different purposes. Experimentally, we bind ImageBind with extra image-text and audio-text expert spaces, resulting in three main variants: ImageBind++, InternVL_IB, and InternVL_IB++. These resulting spaces outperform ImageBind on 5 audio-image-text downstream tasks across 9 datasets. Moreover, via customized inference, it even surpasses the advanced audio-text and image-text expert spaces.

Mechanistic interpretability seeks to understand the internal mechanisms of machine learning models, where localization -- identifying the important model components -- is a key step. Activation patching, also known as causal tracing or interchange intervention, is a standard technique for this task (Vig et al., 2020), but the literature contains many variants with little consensus on the choice of hyperparameters or methodology. In this work, we systematically examine the impact of methodological details in activation patching, including evaluation metrics and corruption methods. In several settings of localization and circuit discovery in language models, we find that varying these hyperparameters could lead to disparate interpretability results. Backed by empirical observations, we give conceptual arguments for why certain metrics or methods may be preferred. Finally, we provide recommendations for the best practices of activation patching going forwards.

Recently, human-computer interaction with various modalities has shown promising applications, like GPT-4o and Gemini. Given the foundational role of multimodal joint representation in understanding and generation pipelines, high-quality omni joint representations would be a step toward co-processing more diverse multimodal information. In this work, we present OmniBind, large-scale multimodal joint representation models ranging in scale from 7 billion to 30 billion parameters, which support 3D, audio, image, and language inputs. Due to the scarcity of data pairs across all modalities, instead of training large models from scratch, we propose remapping and binding the spaces of various pre-trained specialist models together. This approach enables "scaling up" by indirectly increasing the model parameters and the amount of seen data. To effectively integrate various spaces, we dynamically assign weights to different spaces by learning routers with two objectives: cross-modal overall alignment and language representation decoupling. Notably, since binding and routing spaces both only require lightweight networks, OmniBind is extremely training-efficient. Learning the largest 30B model requires merely unpaired unimodal data and approximately 3 days on a single 8-4090 node. Extensive experiments demonstrate the versatility and superiority of OmniBind as an omni representation model, highlighting its great potential for diverse applications, such as any-query and composable multimodal understanding.

Optics and lenses are abstract categorical gadgets that model systems with bidirectional data flow. In this paper we observe that the denotational definition of optics - identifying two optics as equivalent by observing their behaviour from the outside - is not suitable for operational, software oriented approaches where optics are not merely observed, but built with their internal setups in mind. We identify operational differences between denotationally isomorphic categories of cartesian optics and lenses: their different composition rule and corresponding space-time tradeoffs, positioning them at two opposite ends of a spectrum. With these motivations we lift the existing categorical constructions and their relationships to the 2-categorical level, showing that the relevant operational concerns become visible. We define the 2-category 2-Optic(C) whose 2-cells explicitly track optics' internal configuration. We show that the 1-category Optic(C) arises by locally quotienting out the connected components of this 2-category. We show that the embedding of lenses into cartesian optics gets weakened from a functor to an oplax functor whose oplaxator now detects the different composition rule. We determine the difficulties in showing this functor forms a part of an adjunction in any of the standard 2-categories. We establish a conjecture that the well-known isomorphism between cartesian lenses and optics arises out of the lax 2-adjunction between their double-categorical counterparts. In addition to presenting new research, this paper is also meant to be an accessible introduction to the topic.

Background. The rapid and growing popularity of machine learning (ML) applications has led to an increasing interest in MLOps, that is, the practice of continuous integration and deployment (CI/CD) of ML-enabled systems. Aims. Since changes may affect not only the code but also the ML model parameters and the data themselves, the automation of traditional CI/CD needs to be extended to manage model retraining in production. Method. In this paper, we present an initial investigation of the MLOps practices implemented in a set of ML-enabled systems retrieved from GitHub, focusing on GitHub Actions and CML, two solutions to automate the development workflow. Results. Our preliminary results suggest that the adoption of MLOps workflows in open-source GitHub projects is currently rather limited. Conclusions. Issues are also identified, which can guide future research work.

Source code is rarely written in isolation. It depends significantly on the programmatic context, such as the class that the code would reside in. To study this phenomenon, we introduce the task of generating class member functions given English documentation and the programmatic context provided by the rest of the class. This task is challenging because the desired code can vary greatly depending on the functionality the class provides (e.g., a sort function may or may not be available when we are asked to "return the smallest element" in a particular member variable list). We introduce CONCODE, a new large dataset with over 100,000 examples consisting of Java classes from online code repositories, and develop a new encoder-decoder architecture that models the interaction between the method documentation and the class environment. We also present a detailed error analysis suggesting that there is significant room for future work on this task.

Automated surgical instrument localization is an important technology to understand the surgical process and in order to analyze them to provide meaningful guidance during surgery or surgical index after surgery to the surgeon. We introduce a new dataset that reflects the kinematic characteristics of surgical instruments for automated surgical instrument localization of surgical videos. The hSDB(hutom Surgery DataBase)-instrument dataset consists of instrument localization information from 24 cases of laparoscopic cholecystecomy and 24 cases of robotic gastrectomy. Localization information for all instruments is provided in the form of a bounding box for object detection. To handle class imbalance problem between instruments, synthesized instruments modeled in Unity for 3D models are included as training data. Besides, for 3D instrument data, a polygon annotation is provided to enable instance segmentation of the tool. To reflect the kinematic characteristics of all instruments, they are annotated with head and body parts for laparoscopic instruments, and with head, wrist, and body parts for robotic instruments separately. Annotation data of assistive tools (specimen bag, needle, etc.) that are frequently used for surgery are also included. Moreover, we provide statistical information on the hSDB-instrument dataset and the baseline localization performances of the object detection networks trained by the MMDetection library and resulting analyses.

We propose a novel approach for learning interchangeable tokens in language models to obtain an extendable vocabulary that can generalize to new tokens. Our method is designed to address alpha-equivalence, the principle that renaming bound variables in a syntactic expression preserves semantics. This property arises in many formal languages such as temporal logics, in which all proposition symbols represent the same concept but are distinguishable from each other. To handle such tokens, we develop a dual-part embedding approach. The first part is shared across all interchangeable tokens, thereby enforcing that they represent the same core concept. The second part is randomly generated for each token, which enables distinguishability. We evaluate our method in a Transformer encoder-decoder model on two tasks: solving linear temporal logic formulae and copying with extendable vocabulary. Our method demonstrates promising generalization capabilities in addition to introducing a favorable inductive bias for alpha-equivalence.

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose FABind, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. FABind incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed FABind demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

In recent years, instruction-based image editing methods have garnered significant attention in image editing. However, despite encompassing a wide range of editing priors, these methods are helpless when handling editing tasks that are challenging to accurately describe through language. We propose InstructBrush, an inversion method for instruction-based image editing methods to bridge this gap. It extracts editing effects from exemplar image pairs as editing instructions, which are further applied for image editing. Two key techniques are introduced into InstructBrush, Attention-based Instruction Optimization and Transformation-oriented Instruction Initialization, to address the limitations of the previous method in terms of inversion effects and instruction generalization. To explore the ability of instruction inversion methods to guide image editing in open scenarios, we establish a TransformationOriented Paired Benchmark (TOP-Bench), which contains a rich set of scenes and editing types. The creation of this benchmark paves the way for further exploration of instruction inversion. Quantitatively and qualitatively, our approach achieves superior performance in editing and is more semantically consistent with the target editing effects.

We extend Textual Inversion to learn pseudo-words that represent a concept at different resolutions. This allows us to generate images that use the concept with different levels of detail and also to manipulate different resolutions using language. Once learned, the user can generate images at different levels of agreement to the original concept; "A photo of S^*(0)" produces the exact object while the prompt "A photo of S^*(0.8)" only matches the rough outlines and colors. Our framework allows us to generate images that use different resolutions of an image (e.g. details, textures, styles) as separate pseudo-words that can be composed in various ways. We open-soure our code in the following URL: https://github.com/giannisdaras/multires_textual_inversion

Contemporary LLMs pretrained on code are capable of succeeding at a wide variety of programming tasks. However, their performance is very sensitive to syntactic features, such as the names of variables and types, the structure of code, and presence of type hints. We contribute an inference-time technique to make CodeLLMs more robust to syntactic distractors that are semantically irrelevant. Our methodology relies on activation steering, which involves editing internal model activations to steer the model towards the correct prediction. We contribute a novel way to construct steering vectors by taking inspiration from mutation testing, which constructs minimal semantics-breaking code edits. In contrast, we construct steering vectors from semantics-preserving code edits. We apply our approach to the task of type prediction for the gradually typed languages Python and TypeScript. This approach corrects up to 90% of type mispredictions. Finally, we show that steering vectors calculated from Python activations reliably correct type mispredictions in TypeScript, and vice versa. This result suggests that LLMs may be learning to transfer knowledge of types across programming languages.

Recent work shows Large Language Models (LLMs) struggle to understand natural language constraints for various text generation tasks in zero- and few-shot settings. While, in the code domain, there is wide usage of constraints in code format to maintain the integrity of code written in Domain-Specific Languages (DSLs) like JSON and YAML which are widely used for system-level programming tasks in enterprises. Given that LLMs are increasingly used for system-level code tasks, evaluating if they can comprehend these code constraints is crucial. However, no work has been done to evaluate their controllability over code constraints. Hence, we introduce ConCodeEval, a first-of-its-kind benchmark having two novel tasks for code constraints across five representations. Our findings suggest that language models struggle with code constraints. Code languages that perform excellently for normal code tasks do not perform well when the same languages represent fine-grained constraints.

Memory safety violations in low-level code, written in languages like C, continues to remain one of the major sources of software vulnerabilities. One method of removing such violations by construction is to port C code to a safe C dialect. Such dialects rely on programmer-supplied annotations to guarantee safety with minimal runtime overhead. This porting, however, is a manual process that imposes significant burden on the programmer and, hence, there has been limited adoption of this technique. The task of porting not only requires inferring annotations, but may also need refactoring/rewriting of the code to make it amenable to such annotations. In this paper, we use Large Language Models (LLMs) towards addressing both these concerns. We show how to harness LLM capabilities to do complex code reasoning as well as rewriting of large codebases. We also present a novel framework for whole-program transformations that leverages lightweight static analysis to break the transformation into smaller steps that can be carried out effectively by an LLM. We implement our ideas in a tool called MSA that targets the CheckedC dialect. We evaluate MSA on several micro-benchmarks, as well as real-world code ranging up to 20K lines of code. We showcase superior performance compared to a vanilla LLM baseline, as well as demonstrate improvement over a state-of-the-art symbolic (non-LLM) technique.

Code generation, symbolic math reasoning, and other tasks require LLMs to produce outputs that are both syntactically and semantically correct. Constrained LLM generation is a promising direction to enforce adherence to formal grammar, but prior works have empirically observed that strict enforcement of formal constraints often diminishes the reasoning capabilities of LLMs. In this work, we first provide a theoretical explanation for why constraining LLM outputs to very restrictive grammars that only allow syntactically valid final answers reduces the reasoning capabilities of the model. Second, we demonstrate that by augmenting the output grammar with carefully designed additional rules, it is always possible to preserve the reasoning capabilities of the LLM while ensuring syntactic and semantic correctness in its outputs. Building on these theoretical insights, we propose a reasoning-augmented constrained decoding algorithm, CRANE, which effectively balances the correctness of constrained generation with the flexibility of unconstrained generation. Experiments on multiple open-source LLMs and benchmarks show that CRANE significantly outperforms both state-of-the-art constrained decoding strategies and standard unconstrained decoding, showing up to 10% points accuracy improvement over baselines on challenging symbolic reasoning benchmarks GSM-symbolic and FOLIO.

We present a novel Parameter-Efficient Fine-Tuning (PEFT) method, dubbed as Adaptive Freezing of Low Rank Adaptation (AFLoRA). Specifically, for each pre-trained frozen weight tensor, we add a parallel path of trainable low-rank matrices, namely a down-projection and an up-projection matrix, each of which is followed by a feature transformation vector. Based on a novel freezing score, we the incrementally freeze these projection matrices during fine-tuning to reduce the computation and alleviate over-fitting. Our experimental results demonstrate that we can achieve state-of-the-art performance with an average improvement of up to 0.85% as evaluated on GLUE benchmark while yeilding up to 9.5times fewer average trainable parameters. While compared in terms of runtime, AFLoRA can yield up to 1.86times improvement as opposed to similar PEFT alternatives. Besides the practical utility of our approach, we provide insights on the trainability requirements of LoRA paths at different modules and the freezing schedule for the different projection matrices. Code will be released.

Skilled robotic manipulation benefits from complex synergies between non-prehensile (e.g. pushing) and prehensile (e.g. grasping) actions: pushing can help rearrange cluttered objects to make space for arms and fingers; likewise, grasping can help displace objects to make pushing movements more precise and collision-free. In this work, we demonstrate that it is possible to discover and learn these synergies from scratch through model-free deep reinforcement learning. Our method involves training two fully convolutional networks that map from visual observations to actions: one infers the utility of pushes for a dense pixel-wise sampling of end effector orientations and locations, while the other does the same for grasping. Both networks are trained jointly in a Q-learning framework and are entirely self-supervised by trial and error, where rewards are provided from successful grasps. In this way, our policy learns pushing motions that enable future grasps, while learning grasps that can leverage past pushes. During picking experiments in both simulation and real-world scenarios, we find that our system quickly learns complex behaviors amid challenging cases of clutter, and achieves better grasping success rates and picking efficiencies than baseline alternatives after only a few hours of training. We further demonstrate that our method is capable of generalizing to novel objects. Qualitative results (videos), code, pre-trained models, and simulation environments are available at http://vpg.cs.princeton.edu

Input constraints are useful for many software development tasks. For example, input constraints of a function enable the generation of valid inputs, i.e., inputs that follow these constraints, to test the function deeper. API functions of deep learning (DL) libraries have DL specific input constraints, which are described informally in the free form API documentation. Existing constraint extraction techniques are ineffective for extracting DL specific input constraints. To fill this gap, we design and implement a new technique, DocTer, to analyze API documentation to extract DL specific input constraints for DL API functions. DocTer features a novel algorithm that automatically constructs rules to extract API parameter constraints from syntactic patterns in the form of dependency parse trees of API descriptions. These rules are then applied to a large volume of API documents in popular DL libraries to extract their input parameter constraints. To demonstrate the effectiveness of the extracted constraints, DocTer uses the constraints to enable the automatic generation of valid and invalid inputs to test DL API functions. Our evaluation on three popular DL libraries (TensorFlow, PyTorch, and MXNet) shows that the precision of DocTer in extracting input constraints is 85.4%. DocTer detects 94 bugs from 174 API functions, including one previously unknown security vulnerability that is now documented in the CVE database, while a baseline technique without input constraints detects only 59 bugs. Most (63) of the 94 bugs are previously unknown, 54 of which have been fixed or confirmed by developers after we report them. In addition, DocTer detects 43 inconsistencies in documents, 39 of which are fixed or confirmed.

Image manipulation can be considered a special case of image generation where the image to be produced is a modification of an existing image. Image generation and manipulation have been, for the most part, tasks that operate on raw pixels. However, the remarkable progress in learning rich image and object representations has opened the way for tasks such as text-to-image or layout-to-image generation that are mainly driven by semantics. In our work, we address the novel problem of image manipulation from scene graphs, in which a user can edit images by merely applying changes in the nodes or edges of a semantic graph that is generated from the image. Our goal is to encode image information in a given constellation and from there on generate new constellations, such as replacing objects or even changing relationships between objects, while respecting the semantics and style from the original image. We introduce a spatio-semantic scene graph network that does not require direct supervision for constellation changes or image edits. This makes it possible to train the system from existing real-world datasets with no additional annotation effort.

Formulating selective information needs results in queries that implicitly specify set operations, such as intersection, union, and difference. For instance, one might search for "shorebirds that are not sandpipers" or "science-fiction films shot in England". To study the ability of retrieval systems to meet such information needs, we construct QUEST, a dataset of 3357 natural language queries with implicit set operations, that map to a set of entities corresponding to Wikipedia documents. The dataset challenges models to match multiple constraints mentioned in queries with corresponding evidence in documents and correctly perform various set operations. The dataset is constructed semi-automatically using Wikipedia category names. Queries are automatically composed from individual categories, then paraphrased and further validated for naturalness and fluency by crowdworkers. Crowdworkers also assess the relevance of entities based on their documents and highlight attribution of query constraints to spans of document text. We analyze several modern retrieval systems, finding that they often struggle on such queries. Queries involving negation and conjunction are particularly challenging and systems are further challenged with combinations of these operations.

As mathematical computing becomes more democratized in high-level languages, high-performance symbolic-numeric systems are necessary for domain scientists and engineers to get the best performance out of their machine without deep knowledge of code optimization. Naturally, users need different term types either to have different algebraic properties for them, or to use efficient data structures. To this end, we developed Symbolics.jl, an extendable symbolic system which uses dynamic multiple dispatch to change behavior depending on the domain needs. In this work we detail an underlying abstract term interface which allows for speed without sacrificing generality. We show that by formalizing a generic API on actions independent of implementation, we can retroactively add optimized data structures to our system without changing the pre-existing term rewriters. We showcase how this can be used to optimize term construction and give a 113x acceleration on general symbolic transformations. Further, we show that such a generic API allows for complementary term-rewriting implementations. We demonstrate the ability to swap between classical term-rewriting simplifiers and e-graph-based term-rewriting simplifiers. We showcase an e-graph ruleset which minimizes the number of CPU cycles during expression evaluation, and demonstrate how it simplifies a real-world reaction-network simulation to halve the runtime. Additionally, we show a reaction-diffusion partial differential equation solver which is able to be automatically converted into symbolic expressions via multiple dispatch tracing, which is subsequently accelerated and parallelized to give a 157x simulation speedup. Together, this presents Symbolics.jl as a next-generation symbolic-numeric computing environment geared towards modeling and simulation.

Knowledge distillation is one of the primary methods of transferring knowledge from large to small models. However, it requires massive task-specific data, which may not be plausible in many real-world applications. Data augmentation methods such as representation interpolation, token replacement, or augmentation with models are applied to tackle this problem. However, these data augmentation methods either potentially cause shifts in decision boundaries (representation interpolation), are not expressive enough (token replacement), or introduce too much computational overhead (augmentation with models). To this end, we propose AugPro (Augmentation with Projection), an effective and efficient data augmentation method for distillation. Our method builds on top of representation interpolation augmentation methods to maintain the diversity of expressions and converts the augmented data to tokens to avoid shifting decision boundaries. It uses simple operations that come with little computational overhead. The results on multiple GLUE tasks show that our methods can improve distillation performance by a large margin at a low time cost. Codes are available at https://github.com/google-research/google-research/tree/master/augpro.

A supervised learning algorithm searches over a set of functions A to B parametrised by a space P to find the best approximation to some ideal function fcolon A to B. It does this by taking examples (a,f(a)) in Atimes B, and updating the parameter according to some rule. We define a category where these update rules may be composed, and show that gradient descent---with respect to a fixed step size and an error function satisfying a certain property---defines a monoidal functor from a category of parametrised functions to this category of update rules. This provides a structural perspective on backpropagation, as well as a broad generalisation of neural networks.

Lara is a key-value algebra that aims at unifying linear and relational algebra with three types of operation abstraction. The study of Lara's expressive ability reports that it can represent relational algebra and most linear algebra operations. However, several essential computations, such as matrix inversion and determinant, cannot be expressed in Lara. Lara cannot represent global and iterative computation, either. This article proposes IterLara, extending Lara with iterative operators, to provide an algebraic model that unifies operations in general-purpose computing, like big data, AI, scientific computing, and database. We study the expressive ability of Lara and IterLara and prove that IterLara with aggregation functions can represent matrix inversion, determinant. Besides, we demonstrate that IterLara with no limitation of function utility is Turing complete. We also propose the Operation Count (OP) as a metric of computation amount for IterLara and ensure that the OP metric is in accordance with the existing computation metrics.

We present semantic correctness proofs of Automatic Differentiation (AD). We consider a forward-mode AD method on a higher order language with algebraic data types, and we characterise it as the unique structure preserving macro given a choice of derivatives for basic operations. We describe a rich semantics for differentiable programming, based on diffeological spaces. We show that it interprets our language, and we phrase what it means for the AD method to be correct with respect to this semantics. We show that our characterisation of AD gives rise to an elegant semantic proof of its correctness based on a gluing construction on diffeological spaces. We explain how this is, in essence, a logical relations argument. Finally, we sketch how the analysis extends to other AD methods by considering a continuation-based method.

We present a set-theoretic, proof-irrelevant model for Calculus of Constructions (CC) with predicative induction and judgmental equality in Zermelo-Fraenkel set theory with an axiom for countably many inaccessible cardinals. We use Aczel's trace encoding which is universally defined for any function type, regardless of being impredicative. Direct and concrete interpretations of simultaneous induction and mutually recursive functions are also provided by extending Dybjer's interpretations on the basis of Aczel's rule sets. Our model can be regarded as a higher-order generalization of the truth-table methods. We provide a relatively simple consistency proof of type theory, which can be used as the basis for a theorem prover.

Fine-tuning on generalized tasks such as instruction following, code generation, and mathematics has been shown to enhance language models' performance on a range of tasks. Nevertheless, explanations of how such fine-tuning influences the internal computations in these models remain elusive. We study how fine-tuning affects the internal mechanisms implemented in language models. As a case study, we explore the property of entity tracking, a crucial facet of language comprehension, where models fine-tuned on mathematics have substantial performance gains. We identify the mechanism that enables entity tracking and show that (i) in both the original model and its fine-tuned versions primarily the same circuit implements entity tracking. In fact, the entity tracking circuit of the original model on the fine-tuned versions performs better than the full original model. (ii) The circuits of all the models implement roughly the same functionality: Entity tracking is performed by tracking the position of the correct entity in both the original model and its fine-tuned versions. (iii) Performance boost in the fine-tuned models is primarily attributed to its improved ability to handle the augmented positional information. To uncover these findings, we employ: Patch Patching, DCM, which automatically detects model components responsible for specific semantics, and CMAP, a new approach for patching activations across models to reveal improved mechanisms. Our findings suggest that fine-tuning enhances, rather than fundamentally alters, the mechanistic operation of the model.

Convolution is a broadly useful operation with applications including signal processing, machine learning, probability, optics, polynomial multiplication, and efficient parsing. Usually, however, this operation is understood and implemented in more specialized forms, hiding commonalities and limiting usefulness. This paper formulates convolution in the common algebraic framework of semirings and semimodules and populates that framework with various representation types. One of those types is the grand abstract template and itself generalizes to the free semimodule monad. Other representations serve varied uses and performance trade-offs, with implementations calculated from simple and regular specifications. Of particular interest is Brzozowski's method for regular expression matching. Uncovering the method's essence frees it from syntactic manipulations, while generalizing from boolean to weighted membership (such as multisets and probability distributions) and from sets to n-ary relations. The classic trie data structure then provides an elegant and efficient alternative to syntax. Pleasantly, polynomial arithmetic requires no additional implementation effort, works correctly with a variety of representations, and handles multivariate polynomials and power series with ease. Image convolution also falls out as a special case.

User interface understanding with vision-language models has received much attention due to its potential for enabling next-generation software automation. However, existing UI datasets either only provide large-scale context-free element annotations or contextualized functional descriptions for elements at a much smaller scale. In this work, we propose the pipeline for automatically annotating UI elements with detailed functionality descriptions at scale. Specifically, we leverage large language models (LLMs) to infer element functionality by comparing the UI content changes before and after simulated interactions with specific UI elements. To improve annotation quality, we propose LLM-aided rejection and verification, eliminating invalid and incorrect annotations without human labor. We construct an -704k dataset using the proposed pipeline, featuring multi-resolution, multi-device screenshots, diverse data domains, and detailed functionality annotations that have never been provided by previous datasets. Human evaluation shows that the AutoGUI pipeline achieves annotation correctness comparable to trained human annotators. Extensive experimental results show that our -704k dataset remarkably enhances VLM's UI grounding capabilities, exhibits significant scaling effects, and outperforms existing web pre-training data types. We envision AutoGUI as a scalable pipeline for generating massive data to build GUI-oriented VLMs. AutoGUI dataset can be viewed at this anonymous URL: https://autogui-project.github.io/.

Synthesizing inductive loop invariants is fundamental to automating program verification. In this work, we observe that Large Language Models (such as gpt-3.5 or gpt-4) are capable of synthesizing loop invariants for a class of programs in a 0-shot setting, yet require several samples to generate the correct invariants. This can lead to a large number of calls to a program verifier to establish an invariant. To address this issue, we propose a {\it re-ranking} approach for the generated results of LLMs. We have designed a ranker that can distinguish between correct inductive invariants and incorrect attempts based on the problem definition. The ranker is optimized as a contrastive ranker. Experimental results demonstrate that this re-ranking mechanism significantly improves the ranking of correct invariants among the generated candidates, leading to a notable reduction in the number of calls to a verifier.

Singly-TASE operators for the numerical solution of stiff differential equations were proposed by Calvo et al. in J.Sci. Comput. 2023 to reduce the computational cost of Runge-Kutta-TASE (RKTASE) methods when the involved linear systems are solved by some LU factorization. In this paper we propose a modification of these methods to improve the efficiency by considering different TASE operators for each stage of the Runge-Kutta. We prove that the resulting RKTASE methods are equivalent to W-methods (Steihaug and Wolfbrandt, Mathematics of Computation,1979) and this allows us to obtain the order conditions of the proposed Modified Singly-RKTASE methods (MSRKTASE) through the theory developed for the W-methods. We construct new MSRKTASE methods of order two and three and demonstrate their effectiveness through numerical experiments on both linear and nonlinear stiff systems. The results show that the MSRKTASE schemes significantly enhance efficiency and accuracy compared to previous Singly-RKTASE schemes.

We enhance the calculus of string diagrams for monoidal categories with hierarchical features in order to capture closed monoidal (and cartesian closed) structure. Using this new syntax we formulate an automatic differentiation algorithm for (applied) simply typed lambda calculus in the style of [Pearlmutter and Siskind 2008] and we prove for the first time its soundness. To give an efficient yet principled implementation of the AD algorithm we define a sound and complete representation of hierarchical string diagrams as a class of hierarchical hypergraphs we call hypernets.

We explain how the simplicial higher-order unstable homotopy operations defined in [BBS2] may be composed and inserted one in another, thus forming a coherent if complicated algebraic structure.

We introduce Point-Bind, a 3D multi-modality model aligning point clouds with 2D image, language, audio, and video. Guided by ImageBind, we construct a joint embedding space between 3D and multi-modalities, enabling many promising applications, e.g., any-to-3D generation, 3D embedding arithmetic, and 3D open-world understanding. On top of this, we further present Point-LLM, the first 3D large language model (LLM) following 3D multi-modal instructions. By parameter-efficient fine-tuning techniques, Point-LLM injects the semantics of Point-Bind into pre-trained LLMs, e.g., LLaMA, which requires no 3D instruction data, but exhibits superior 3D and multi-modal question-answering capacity. We hope our work may cast a light on the community for extending 3D point clouds to multi-modality applications. Code is available at https://github.com/ZiyuGuo99/Point-Bind_Point-LLM.

Character animation in real-world scenarios necessitates a variety of constraints, such as trajectories, key-frames, interactions, etc. Existing methodologies typically treat single or a finite set of these constraint(s) as separate control tasks. They are often specialized, and the tasks they address are rarely extendable or customizable. We categorize these as solutions to the close-set motion control problem. In response to the complexity of practical motion control, we propose and attempt to solve the open-set motion control problem. This problem is characterized by an open and fully customizable set of motion control tasks. To address this, we introduce a new paradigm, programmable motion generation. In this paradigm, any given motion control task is broken down into a combination of atomic constraints. These constraints are then programmed into an error function that quantifies the degree to which a motion sequence adheres to them. We utilize a pre-trained motion generation model and optimize its latent code to minimize the error function of the generated motion. Consequently, the generated motion not only inherits the prior of the generative model but also satisfies the required constraints. Experiments show that we can generate high-quality motions when addressing a wide range of unseen tasks. These tasks encompass motion control by motion dynamics, geometric constraints, physical laws, interactions with scenes, objects or the character own body parts, etc. All of these are achieved in a unified approach, without the need for ad-hoc paired training data collection or specialized network designs. During the programming of novel tasks, we observed the emergence of new skills beyond those of the prior model. With the assistance of large language models, we also achieved automatic programming. We hope that this work will pave the way for the motion control of general AI agents.

Knowledge editing for large language models can offer an efficient solution to alter a model's behavior without negatively impacting the overall performance. However, the current approach encounters issues with limited generalizability across tasks, necessitating one distinct editor for each task, which significantly hinders the broader applications. To address this, we take the first step to analyze the multi-task generalization issue in knowledge editing. Specifically, we develop an instruction-based editing technique, termed InstructEdit, which facilitates the editor's adaptation to various task performances simultaneously using simple instructions. With only one unified editor for each LLM, we empirically demonstrate that InstructEdit can improve the editor's control, leading to an average 14.86% increase in Reliability in multi-task editing setting. Furthermore, experiments involving holdout unseen task illustrate that InstructEdit consistently surpass previous strong baselines. To further investigate the underlying mechanisms of instruction-based knowledge editing, we analyze the principal components of the editing gradient directions, which unveils that instructions can help control optimization direction with stronger OOD generalization. Code and datasets will be available in https://github.com/zjunlp/EasyEdit.

A large class of inverse problems for PDEs are only well-defined as mappings from operators to functions. Existing operator learning frameworks map functions to functions and need to be modified to learn inverse maps from data. We propose a novel architecture termed Neural Inverse Operators (NIOs) to solve these PDE inverse problems. Motivated by the underlying mathematical structure, NIO is based on a suitable composition of DeepONets and FNOs to approximate mappings from operators to functions. A variety of experiments are presented to demonstrate that NIOs significantly outperform baselines and solve PDE inverse problems robustly, accurately and are several orders of magnitude faster than existing direct and PDE-constrained optimization methods.

Changing how pre-trained models behave -- e.g., improving their performance on a downstream task or mitigating biases learned during pre-training -- is a common practice when developing machine learning systems. In this work, we propose a new paradigm for steering the behavior of neural networks, centered around task vectors. A task vector specifies a direction in the weight space of a pre-trained model, such that movement in that direction improves performance on the task. We build task vectors by subtracting the weights of a pre-trained model from the weights of the same model after fine-tuning on a task. We show that these task vectors can be modified and combined together through arithmetic operations such as negation and addition, and the behavior of the resulting model is steered accordingly. Negating a task vector decreases performance on the target task, with little change in model behavior on control tasks. Moreover, adding task vectors together can improve performance on multiple tasks at once. Finally, when tasks are linked by an analogy relationship of the form ``A is to B as C is to D", combining task vectors from three of the tasks can improve performance on the fourth, even when no data from the fourth task is used for training. Overall, our experiments with several models, modalities and tasks show that task arithmetic is a simple, efficient and effective way of editing models.

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baselines, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel protein sequences; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

We investigate causal computations taking sequences of inputs to sequences of outputs where the nth output depends on the first n inputs only. We model these in category theory via a construction taking a Cartesian category C to another category St(C) with a novel trace-like operation called "delayed trace", which misses yanking and dinaturality axioms of the usual trace. The delayed trace operation provides a feedback mechanism in St(C) with an implicit guardedness guarantee. When C is equipped with a Cartesian differential operator, we construct a differential operator for St(C) using an abstract version of backpropagation through time, a technique from machine learning based on unrolling of functions. This obtains a swath of properties for backpropagation through time, including a chain rule and Schwartz theorem. Our differential operator is also able to compute the derivative of a stateful network without requiring the network to be unrolled.

We propose a new bound for generalization of neural networks using Koopman operators. Whereas most of existing works focus on low-rank weight matrices, we focus on full-rank weight matrices. Our bound is tighter than existing norm-based bounds when the condition numbers of weight matrices are small. Especially, it is completely independent of the width of the network if the weight matrices are orthogonal. Our bound does not contradict to the existing bounds but is a complement to the existing bounds. As supported by several existing empirical results, low-rankness is not the only reason for generalization. Furthermore, our bound can be combined with the existing bounds to obtain a tighter bound. Our result sheds new light on understanding generalization of neural networks with full-rank weight matrices, and it provides a connection between operator-theoretic analysis and generalization of neural networks.

Activation patching is a popular mechanistic interpretability technique, but has many subtleties regarding how it is applied and how one may interpret the results. We provide a summary of advice and best practices, based on our experience using this technique in practice. We include an overview of the different ways to apply activation patching and a discussion on how to interpret the results. We focus on what evidence patching experiments provide about circuits, and on the choice of metric and associated pitfalls.

We propose Tied-LoRA, a simple paradigm utilizes weight tying and selective training to further increase parameter efficiency of the Low-rank adaptation (LoRA) method. Our investigations include all feasible combinations parameter training/freezing in conjunction with weight tying to identify the optimal balance between performance and the number of trainable parameters. Through experiments covering a variety of tasks and two base language models, we provide analysis revealing trade-offs between efficiency and performance. Our experiments uncovered a particular Tied-LoRA configuration that stands out by demonstrating comparable performance across several tasks while employing only 13~\% percent of parameters utilized by the standard LoRA method.